[{"scheme":"-> PurN","substrates":null,"products":{"p1":{"theSubstance":{"name":"PurN","type":"protein","synonyms":["PurN"],"links":[],"id":"SS0000375"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"purN","type":"gene","synonyms":["b2500","purN"],"links":[],"id":"SS0000398"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"PurR","type":"protein","synonyms":["PurR","PurR transcriptional repressor"],"links":[],"id":"SS0000358"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"Gua","type":"substance","synonyms":["Gua","Guanosine"],"links":[],"id":"SS0000113"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"ks*((1+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR))/(1+((((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k1PurR)+((((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k2PurR)+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Meng et al., 1990].","Mathematical model links":" ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurN = 0, where PurN - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter purMp. ks - protein synthesis generalized constant from the promoter purMp. kd = 0.002 [1/sec],PurN = 0.00504 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Structural model information":" Expression of the purine biosynthetic gene purN is repressed by purines (guanine and hypoxanthine) in wild-type cells of Escherichia coli. This regulation is carried out through a protein PurR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]. ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;"},"mmid":"MM0000235","psid":"PS0000225","gnid":"GN0000226","reversible":false,"information":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Meng et al., 1990].","Mathematical model links":" ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurN = 0, where PurN - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter purMp. ks - protein synthesis generalized constant from the promoter purMp. kd = 0.002 [1/sec],PurN = 0.00504 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Structural model information":" Expression of the purine biosynthetic gene purN is repressed by purines (guanine and hypoxanthine) in wild-type cells of Escherichia coli. This regulation is carried out through a protein PurR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]. ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;"},"parameters":[{"units":"mM","information":"","name":"k1PurR","value":"0.00019"},{"units":"mM","information":"","name":"k2PurR","value":"0.00019"},{"units":"mM","information":"","name":"k3PurR","value":"0.0008"},{"units":"mM","information":"","name":"kdisPurRgua","value":"0.0015"},{"units":"mM","information":"","name":"kdisPurRhyp","value":"0.0093"},{"units":"mM/sec","information":"","name":"ks","value":"0.00001"}]},{"scheme":"dUDP + ATP -> dUTP + ADP + H+","substrates":{"s1":{"theSubstance":{"name":"dUDP","type":"substance","synonyms":["2'-Deoxyuridine 5'-diphosphate","dUDP"],"links":[],"id":"SS0000049"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"dUTP","type":"substance","synonyms":["2'-Deoxyuridine 5'-triphosphate","dUTP"],"links":[],"id":"SS0000048"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Ndk","type":"protein","synonyms":["Ndk","NDP kinase","nucleoside diphosphate kinase"],"links":[],"id":"SS0000154"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"(r1*kcat*(s1/kmdudp)*(s2/kmatp))/((1+(s1/kmdudp))*(1+(s2/kmatp)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"dUDP is phosphorylated to dUTP [Roisin et al., 1978, Ginther et al., 1974, Jong et al., 1991]. We proposed a simple model without competitive substrates such as dCDP,dGDP,dADP... as they are rapidly consumed in their reactions.","Mathematical model links":" ID: Ginther et al., 1974 Nucleoside diphosphokinase of Salmonella typhimurium. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4364654 ; ID: Jong et al., 1991 Saccharomyces cerevisiae nucleoside-diphosphate kinase: purification, characterization, and substrate specificity. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1659321 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Parameter set information":"Parameters kmdudp and kmatp were evaluated basing on [Roisin, 1978] data.","Parameter set links":" ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Structural model information":" Nucleoside diphosphate kinase catalyzes the reaction in which the terminal phosphate of a nucleoside-triphosphate is transferred to a nucleoside-diphosphate. The enzyme exhibits broad substrate specificity. The reaction mechanism is an ordered bi-molecular ping-pong type. The intracellular levels of ATP are considerably higher than other nucleoside triphosphates. In addition, ATP is far more abundant than ADP or AMP, so there is a strong thermodynamic tendency for the potential energy of ATP to be used in the synthesis of other high-energy compounds. Therefore nucleoside diphosphate kinase is unlikely to be involved in the synthesis of ATP. The purified enzyme is tetrameric and was detected in the periplasmic fraction after cold osmotic shock. A periplasmic location for the enzyme appears inconsistent with its function. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=DUDPKIN-RXN ;"},"mmid":"MM0000130","psid":"PS0000160","gnid":"GN0000067","reversible":false,"information":{"Mathematical model information":"dUDP is phosphorylated to dUTP [Roisin et al., 1978, Ginther et al., 1974, Jong et al., 1991]. We proposed a simple model without competitive substrates such as dCDP,dGDP,dADP... as they are rapidly consumed in their reactions.","Mathematical model links":" ID: Ginther et al., 1974 Nucleoside diphosphokinase of Salmonella typhimurium. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4364654 ; ID: Jong et al., 1991 Saccharomyces cerevisiae nucleoside-diphosphate kinase: purification, characterization, and substrate specificity. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1659321 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Parameter set information":"Parameters kmdudp and kmatp were evaluated basing on [Roisin, 1978] data.","Parameter set links":" ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Structural model information":" Nucleoside diphosphate kinase catalyzes the reaction in which the terminal phosphate of a nucleoside-triphosphate is transferred to a nucleoside-diphosphate. The enzyme exhibits broad substrate specificity. The reaction mechanism is an ordered bi-molecular ping-pong type. The intracellular levels of ATP are considerably higher than other nucleoside triphosphates. In addition, ATP is far more abundant than ADP or AMP, so there is a strong thermodynamic tendency for the potential energy of ATP to be used in the synthesis of other high-energy compounds. Therefore nucleoside diphosphate kinase is unlikely to be involved in the synthesis of ATP. The purified enzyme is tetrameric and was detected in the periplasmic fraction after cold osmotic shock. A periplasmic location for the enzyme appears inconsistent with its function. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=DUDPKIN-RXN ;"},"parameters":[{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kmatp","value":"1.43"},{"units":"mM","information":"","name":"kmdudp","value":"0.47"}]},{"scheme":"-> PurD","substrates":null,"products":{"p1":{"theSubstance":{"name":"PurD","type":"protein","synonyms":["PurD"],"links":[],"id":"SS0000373"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"purD","type":"gene","synonyms":["purD"],"links":[],"id":"SS0000397"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"PurR","type":"protein","synonyms":["PurR","PurR transcriptional repressor"],"links":[],"id":"SS0000358"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"Gua","type":"substance","synonyms":["Gua","Guanosine"],"links":[],"id":"SS0000113"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"ks*((1+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR))/(1+((((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k1PurR)+((((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k2PurR)+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Meng et al., 1990].","Mathematical model links":" ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurD = 0, where PurD - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter purH. ks - protein synthesis generalized constant from the promoter purH. kd = 0.002 [1/sec],PurD = 0.001278 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Structural model information":" Expression of the purine biosynthetic gene purD is repressed by purines (guanine and hypoxanthine) in wild-type cells of Escherichia coli. This regulation is carried out through a protein PurR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]. ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;"},"mmid":"MM0000234","psid":"PS0000224","gnid":"GN0000225","reversible":false,"information":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Meng et al., 1990].","Mathematical model links":" ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurD = 0, where PurD - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter purH. ks - protein synthesis generalized constant from the promoter purH. kd = 0.002 [1/sec],PurD = 0.001278 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Structural model information":" Expression of the purine biosynthetic gene purD is repressed by purines (guanine and hypoxanthine) in wild-type cells of Escherichia coli. This regulation is carried out through a protein PurR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]. ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;"},"parameters":[{"units":"mM","information":"","name":"k1PurR","value":"0.00029"},{"units":"mM","information":"","name":"k2PurR","value":"0.00029"},{"units":"mM","information":"","name":"k3PurR","value":"0.0008"},{"units":"mM","information":"","name":"kdisPurRgua","value":"0.0015"},{"units":"mM","information":"","name":"kdisPurRhyp","value":"0.0093"},{"units":"mM/sec","information":"","name":"ks","value":"0.00000256"}]},{"scheme":"-> PurM","substrates":null,"products":{"p1":{"theSubstance":{"name":"PurM","type":"protein","synonyms":["PurM"],"links":[],"id":"SS0000377"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"purM","type":"gene","synonyms":["b2499","purG","purI","purM"],"links":[],"id":"SS0000400"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"PurR","type":"protein","synonyms":["PurR","PurR transcriptional repressor"],"links":[],"id":"SS0000358"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"Gua","type":"substance","synonyms":["Gua","Guanosine"],"links":[],"id":"SS0000113"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"ks*((1+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR))/(1+((((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k1PurR)+((((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k2PurR)+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Meng et al., 1990].","Mathematical model links":" ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurM = 0, where PurM - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter purMp. ks - protein synthesis generalized constant from the promoter purMp. kd = 0.002 [1/sec],PurM = 0.0117192 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Structural model information":" Expression of the purine biosynthetic gene purM is repressed by purines (guanine and hypoxanthine) in wild-type cells of Escherichia coli. This regulation is carried out through a protein PurR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]. ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;"},"mmid":"MM0000237","psid":"PS0000227","gnid":"GN0000228","reversible":false,"information":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Meng et al., 1990].","Mathematical model links":" ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurM = 0, where PurM - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter purMp. ks - protein synthesis generalized constant from the promoter purMp. kd = 0.002 [1/sec],PurM = 0.0117192 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Structural model information":" Expression of the purine biosynthetic gene purM is repressed by purines (guanine and hypoxanthine) in wild-type cells of Escherichia coli. This regulation is carried out through a protein PurR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]. ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;"},"parameters":[{"units":"mM","information":"","name":"k1PurR","value":"0.00019"},{"units":"mM","information":"","name":"k2PurR","value":"0.00019"},{"units":"mM","information":"","name":"k3PurR","value":"0.0008"},{"units":"mM","information":"","name":"kdisPurRgua","value":"0.0015"},{"units":"mM","information":"","name":"kdisPurRhyp","value":"0.0093"},{"units":"mM/sec","information":"","name":"ks","value":"0.0000234"}]},{"scheme":"dCDP + ATP -> dCTP + ADP + H+","substrates":{"s1":{"theSubstance":{"name":"dCDP","type":"substance","synonyms":["2'-Deoxycytidine 5'-diphosphate","2'-Deoxycytidine diphosphate","dCDP"],"links":[],"id":"SS0000044"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"dCTP","type":"substance","synonyms":["2'-Deoxycytidine 5'-triphosphate","dCTP","Deoxycytidine 5'-triphosphate","Deoxycytidine triphosphate"],"links":[],"id":"SS0000043"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Ndk","type":"protein","synonyms":["Ndk","NDP kinase","nucleoside diphosphate kinase"],"links":[],"id":"SS0000154"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"(r1*kcat*(s1/kmdcdp)*(s2/kmatp))/((1+(s1/kmdcdp))*(1+(s2/kmatp)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"  dCDP is phosphorylated to dCTP [Roisin et al., 1978, Ginther et al., 1974, Jong et al., 1991, Bernard et al., 2000]. We proposed a simple model without competitive substrates such as dGDP,dADP,dUDP... as they are rapidly consumed in their reactions.  ","Mathematical model links":" ID: Bernard et al., 2000 Metabolic functions of microbial nucleoside diphosphate kinases. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11768309 ; ID: Ginther et al., 1974 Nucleoside diphosphokinase of Salmonella typhimurium. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4364654 ; ID: Jong et al., 1991 Saccharomyces cerevisiae nucleoside-diphosphate kinase: purification, characterization, and substrate specificity. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1659321 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Parameter set information":"Parameter kcat was evaluated basing on [Bernard et al., 2000] data.\nParameters kmdcdp and kmatp were evaluated basing on [Roisin, 1978] data.","Parameter set links":" ID: Bernard et al., 2000 Metabolic functions of microbial nucleoside diphosphate kinases. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11768309 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Structural model information":" Nucleoside diphosphate kinase catalyzes the reaction in which the terminal phosphate of a nucleoside-triphosphate is transferred to a nucleoside-diphosphate. \nThe enzyme exhibits broad substrate specificity. The reaction mechanism is an ordered bi-molecular ping-pong type. The intracellular levels of ATP are considerably \nhigher than other nucleoside triphosphates. In addition, ATP is far more abundant than ADP or AMP, so there is a strong thermodynamic tendency for the potential energy \nof ATP to be used in the synthesis of other high-energy compounds. Therefore nucleoside diphosphate kinase is \nunlikely to be involved in the synthesis of ATP. The purified enzyme is tetrameric and was detected in the periplasmic fraction after cold osmotic shock. \nA periplasmic location for the enzyme appears inconsistent with its function. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=DCDPKIN-RXN ;"},"mmid":"MM0000129","psid":"PS0000161","gnid":"GN0000093","reversible":false,"information":{"Mathematical model information":"  dCDP is phosphorylated to dCTP [Roisin et al., 1978, Ginther et al., 1974, Jong et al., 1991, Bernard et al., 2000]. We proposed a simple model without competitive substrates such as dGDP,dADP,dUDP... as they are rapidly consumed in their reactions.  ","Mathematical model links":" ID: Bernard et al., 2000 Metabolic functions of microbial nucleoside diphosphate kinases. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11768309 ; ID: Ginther et al., 1974 Nucleoside diphosphokinase of Salmonella typhimurium. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4364654 ; ID: Jong et al., 1991 Saccharomyces cerevisiae nucleoside-diphosphate kinase: purification, characterization, and substrate specificity. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1659321 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Parameter set information":"Parameter kcat was evaluated basing on [Bernard et al., 2000] data.\nParameters kmdcdp and kmatp were evaluated basing on [Roisin, 1978] data.","Parameter set links":" ID: Bernard et al., 2000 Metabolic functions of microbial nucleoside diphosphate kinases. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11768309 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Structural model information":" Nucleoside diphosphate kinase catalyzes the reaction in which the terminal phosphate of a nucleoside-triphosphate is transferred to a nucleoside-diphosphate. \nThe enzyme exhibits broad substrate specificity. The reaction mechanism is an ordered bi-molecular ping-pong type. The intracellular levels of ATP are considerably \nhigher than other nucleoside triphosphates. In addition, ATP is far more abundant than ADP or AMP, so there is a strong thermodynamic tendency for the potential energy \nof ATP to be used in the synthesis of other high-energy compounds. Therefore nucleoside diphosphate kinase is \nunlikely to be involved in the synthesis of ATP. The purified enzyme is tetrameric and was detected in the periplasmic fraction after cold osmotic shock. \nA periplasmic location for the enzyme appears inconsistent with its function. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=DCDPKIN-RXN ;"},"parameters":[{"units":"1/sec","information":"","name":"kcat","value":"4.9"},{"units":"mM","information":"","name":"kmatp","value":"1.43"},{"units":"mM","information":"","name":"kmdcdp","value":"0.47"}]},{"scheme":"-> PurL","substrates":null,"products":{"p1":{"theSubstance":{"name":"PurL","type":"protein","synonyms":["PurL"],"links":[],"id":"SS0000376"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"purL","type":"gene","synonyms":["b2557","purL"],"links":[],"id":"SS0000399"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"PurR","type":"protein","synonyms":["PurR","PurR transcriptional repressor"],"links":[],"id":"SS0000358"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"Gua","type":"substance","synonyms":["Gua","Guanosine"],"links":[],"id":"SS0000113"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"ks*((1+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR))/(1+((((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k1PurR)+((((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k2PurR)+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Meng et al., 1990].","Mathematical model links":" ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurL = 0, where PurL - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter purLp. ks - protein synthesis generalized constant from the promoter purLp. kd = 0.002 [1/sec],PurL = 0.002106 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Structural model information":" Expression of the purine biosynthetic gene purL is repressed by purines (guanine and hypoxanthine) in wild-type cells of Escherichia coli. This regulation is carried out through a protein PurR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]. ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;"},"mmid":"MM0000236","psid":"PS0000226","gnid":"GN0000227","reversible":false,"information":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Meng et al., 1990].","Mathematical model links":" ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurL = 0, where PurL - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter purLp. ks - protein synthesis generalized constant from the promoter purLp. kd = 0.002 [1/sec],PurL = 0.002106 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Structural model information":" Expression of the purine biosynthetic gene purL is repressed by purines (guanine and hypoxanthine) in wild-type cells of Escherichia coli. This regulation is carried out through a protein PurR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]. ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;"},"parameters":[{"units":"mM","information":"","name":"k1PurR","value":"0.00017"},{"units":"mM","information":"","name":"k2PurR","value":"0.00017"},{"units":"mM","information":"","name":"k3PurR","value":"0.0008"},{"units":"mM","information":"","name":"kdisPurRgua","value":"0.0015"},{"units":"mM","information":"","name":"kdisPurRhyp","value":"0.0093"},{"units":"mM/sec","information":"","name":"ks","value":"0.0000042"}]},{"scheme":"dUTP + H2O -> dUMP + ppi + H+","substrates":{"s1":{"theSubstance":{"name":"dUTP","type":"substance","synonyms":["2'-Deoxyuridine 5'-triphosphate","dUTP"],"links":[],"id":"SS0000048"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"dUMP","type":"substance","synonyms":["2'-Deoxyuridine 5'-phosphate","Deoxyuridine 5'-phosphate","Deoxyuridine monophosphate","Deoxyuridylic acid","dUMP"],"links":[],"id":"SS0000050"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ppi","type":"substance","synonyms":["Diphosphate","PP","ppi","pyrophosphate"],"links":[],"id":"SS0000023"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Dut","type":"protein","synonyms":["deoxyuridine triphosphatase","DnaS","Dut","EC:3.6.1.23","Sof"],"links":[],"id":"SS0000163"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"dUDP","type":"substance","synonyms":["2'-Deoxyuridine 5'-diphosphate","dUDP"],"links":[],"id":"SS0000049"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"r1*kcat*s1/(kms1*(1+(r2/kr2))+s1)","theSubMathModel":null,"theInformation":{"Mathematical model information":"  Reaction follows Michaelis Menten kinetics. dUDP is a competitive inhibitor of dUTP relative to the enzyme [Larsson et al., 1996]  ","Mathematical model links":" ID: Larsson et al., 1996 Kinetic characterization of dUTPase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8798636 ;","Parameter set information":"kcat equals to 1 as there are different publications using different values of the rate constant of the enzyme: 58 (1/sec) [Shlomai et al., 1978]. However, the most publications do not indicate the used concentrations of the enzyme. In spite of this fact Vmax=kcat*r1 (where r1 is the enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. Parameters kms1 and kr2 were evaluated basing on [Larsson et al., 1996] experimental data.","Parameter set links":" ID: Larsson et al., 1996 Kinetic characterization of dUTPase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8798636 ; ID: Shlomai J., Kornberg A., 1978 Deoxyuridine triphosphatase of Escherichia coli. Purification, properties, and use as a reagent to reduce uracil incorporation into DNA. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/346589 ;","Structural model information":" Deoxyuridine triphosphatase (dUTPase) catalyzes the hydrolysis of dUTP, maintaining a low intracellular concentration of dUTP so that uracil cannot be incorporated into DNA. dUTPase is specific for dUTP as a substrate, the active site discriminating between nucleotides with respect to the sugar moiety as well as the pyrimidine base. ","Structural model links":" ID: PubMed ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=DUTP-PYROP-RXN ;"},"mmid":"MM0000065","psid":"PS0000172","gnid":"GN0000101","reversible":false,"information":{"Mathematical model information":"  Reaction follows Michaelis Menten kinetics. dUDP is a competitive inhibitor of dUTP relative to the enzyme [Larsson et al., 1996]  ","Mathematical model links":" ID: Larsson et al., 1996 Kinetic characterization of dUTPase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8798636 ;","Parameter set information":"kcat equals to 1 as there are different publications using different values of the rate constant of the enzyme: 58 (1/sec) [Shlomai et al., 1978]. However, the most publications do not indicate the used concentrations of the enzyme. In spite of this fact Vmax=kcat*r1 (where r1 is the enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. Parameters kms1 and kr2 were evaluated basing on [Larsson et al., 1996] experimental data.","Parameter set links":" ID: Larsson et al., 1996 Kinetic characterization of dUTPase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8798636 ; ID: Shlomai J., Kornberg A., 1978 Deoxyuridine triphosphatase of Escherichia coli. Purification, properties, and use as a reagent to reduce uracil incorporation into DNA. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/346589 ;","Structural model information":" Deoxyuridine triphosphatase (dUTPase) catalyzes the hydrolysis of dUTP, maintaining a low intracellular concentration of dUTP so that uracil cannot be incorporated into DNA. dUTPase is specific for dUTP as a substrate, the active site discriminating between nucleotides with respect to the sugar moiety as well as the pyrimidine base. ","Structural model links":" ID: PubMed ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=DUTP-PYROP-RXN ;"},"parameters":[{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kms1","value":"0.000223"},{"units":"mM","information":"","name":"kr2","value":"0.015"}]},{"scheme":"dADP + ATP -> dATP + ADP","substrates":{"s1":{"theSubstance":{"name":"dADP","type":"substance","synonyms":["2'-Deoxyadenosine 5'-diphosphate","dADP"],"links":[],"id":"SS0000078"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"dATP","type":"substance","synonyms":["2'-Deoxyadenosine 5'-triphosphate","dATP","Deoxyadenosine 5'-triphosphate","Deoxyadenosine triphosphate"],"links":[],"id":"SS0000079"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Ndk","type":"protein","synonyms":["Ndk","NDP kinase","nucleoside diphosphate kinase"],"links":[],"id":"SS0000154"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"(r1*kcat*s1*s2)/((kms1+s1)*(kms2+s2))","theSubMathModel":null,"theInformation":{"Mathematical model information":"dADP is phosphorylated to dATP [Roisin et al., 1978, Ginther et al., 1974, Jong et al., 1991, Bernard et al., 2000]. We proposed a simple model without competitive substrates such as dGDP,dCDP,dUDP... as they are rapidly consumed in their reactions.","Mathematical model links":" ID: Bernard et al., 2000 Metabolic functions of microbial nucleoside diphosphate kinases. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11768309 ; ID: Ginther et al., 1974 Nucleoside diphosphokinase of Salmonella typhimurium. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4364654 ; ID: Jong et al., 1991 Saccharomyces cerevisiae nucleoside-diphosphate kinase: purification, characterization, and substrate specificity. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1659321 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Parameter set information":"Parameter kcat was evaluated basing on [Bernard et al., 2000] data.\nParameters kmdadp and kmatp were evaluated basing on [Roisin, 1978] data.","Parameter set links":" ID: Bernard et al., 2000 Metabolic functions of microbial nucleoside diphosphate kinases. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11768309 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Structural model information":" Nucleoside diphosphate kinase catalyzes the reaction in which the terminal phosphate of a nucleoside-triphosphate is transferred to a nucleoside-diphosphate. \nThe enzyme exhibits broad substrate specificity. The reaction mechanism is an ordered bi-molecular ping-pong type. The intracellular levels of ATP are considerably \nhigher than other nucleoside triphosphates. In addition, ATP is far more abundant than ADP or AMP, so there is a strong thermodynamic tendency for the potential energy \nof ATP to be used in the synthesis of other high-energy compounds. Therefore nucleoside diphosphate kinase is \nunlikely to be involved in the synthesis of ATP. The purified enzyme is tetrameric and was detected in the periplasmic fraction after cold osmotic shock. \nA periplasmic location for the enzyme appears inconsistent with its function. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=DADPKIN-RXN ;"},"mmid":"MM0000137","psid":"PS0000164","gnid":"GN0000131","reversible":false,"information":{"Mathematical model information":"dADP is phosphorylated to dATP [Roisin et al., 1978, Ginther et al., 1974, Jong et al., 1991, Bernard et al., 2000]. We proposed a simple model without competitive substrates such as dGDP,dCDP,dUDP... as they are rapidly consumed in their reactions.","Mathematical model links":" ID: Bernard et al., 2000 Metabolic functions of microbial nucleoside diphosphate kinases. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11768309 ; ID: Ginther et al., 1974 Nucleoside diphosphokinase of Salmonella typhimurium. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4364654 ; ID: Jong et al., 1991 Saccharomyces cerevisiae nucleoside-diphosphate kinase: purification, characterization, and substrate specificity. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1659321 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Parameter set information":"Parameter kcat was evaluated basing on [Bernard et al., 2000] data.\nParameters kmdadp and kmatp were evaluated basing on [Roisin, 1978] data.","Parameter set links":" ID: Bernard et al., 2000 Metabolic functions of microbial nucleoside diphosphate kinases. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11768309 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Structural model information":" Nucleoside diphosphate kinase catalyzes the reaction in which the terminal phosphate of a nucleoside-triphosphate is transferred to a nucleoside-diphosphate. \nThe enzyme exhibits broad substrate specificity. The reaction mechanism is an ordered bi-molecular ping-pong type. The intracellular levels of ATP are considerably \nhigher than other nucleoside triphosphates. In addition, ATP is far more abundant than ADP or AMP, so there is a strong thermodynamic tendency for the potential energy \nof ATP to be used in the synthesis of other high-energy compounds. Therefore nucleoside diphosphate kinase is \nunlikely to be involved in the synthesis of ATP. The purified enzyme is tetrameric and was detected in the periplasmic fraction after cold osmotic shock. \nA periplasmic location for the enzyme appears inconsistent with its function. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=DADPKIN-RXN ;"},"parameters":[{"units":"1/sec","information":"","name":"kcat","value":"6.5"},{"units":"mM","information":"","name":"kms1","value":"0.47"},{"units":"mM","information":"","name":"kms2","value":"1.43"}]},{"scheme":"CTP + a reduced flavodoxin <=> dCTP + an oxidized flavodoxin + H2O","substrates":{"s1":{"theSubstance":{"name":"CTP","type":"substance","synonyms":["CTP","Cytidine 5'-triphosphate","Cytidine triphosphate"],"links":[],"id":"SS0000027"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"Reduced flavodoxin","type":"substance","synonyms":["Reduced flavodoxin"],"links":[],"id":"SS0000159"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"dCTP","type":"substance","synonyms":["2'-Deoxycytidine 5'-triphosphate","dCTP","Deoxycytidine 5'-triphosphate","Deoxycytidine triphosphate"],"links":[],"id":"SS0000043"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"Oxidized flavodoxin","type":"substance","synonyms":["an oxidized flavodoxin","Oxidized flavodoxin"],"links":[],"id":"SS0000160"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"NrdD","type":"protein","synonyms":["EC:1.17.4.2","NrdD","ribonucleoside-triphosphate reductase","RNTRase"],"links":[],"id":"SS0000161"},"theState":null,"compartment":"","theInfluence":"activator"},"r2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"TTP","type":"substance","synonyms":["Deoxythymidine 5'-triphosphate","Deoxythymidine triphosphate","dTTP","TTP"],"links":[],"id":"SS0000052"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"dATP","type":"substance","synonyms":["2'-Deoxyadenosine 5'-triphosphate","dATP","Deoxyadenosine 5'-triphosphate","Deoxyadenosine triphosphate"],"links":[],"id":"SS0000079"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"dGTP","type":"substance","synonyms":["2'-Deoxyguanosine 5'-triphosphate","Deoxyguanosine 5'-triphosphate","Deoxyguanosine triphosphate","dGTP"],"links":[],"id":"SS0000121"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"(r1*kcat*s1/((kmctp/(1+(r2/katp)))+s1))*(1/(1+(r4/kdatp)+(r5/kdgtp)+(r3/kttp)))","theSubMathModel":null,"theInformation":{"Mathematical model information":" Reaction follows Michaelis-Menten kinetics. As dATP, dGTP and TTP are known to be noncompetetive inhibitors[Eliasson et al., 1994] of this reaction the equasion can be written as a sum of inhibitors influenses. As ATP and CTP are known to be competitive activators [Eliasson et al., 1994] of this reaction the equasion can be written as a \nratio Michaelis constant with respect to activator (ATP). ","Parameter set information":" kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax = kcat*r1 (where r1 is enzyme concentration) \ncan be calculated from the whole model basing on the flow rate magnitude.\nParametrs kmctp, katp, kdatp, kdgtp and kttp were evaluated basing on [Eliasson et al.,1994] experimental data.    ","Parameter set links":" ID: Eliasson et al., 1994 Allosteric control of the substrate specificity of the anaerobic ribonucleotide reductase from Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7929317 ;","Structural model information":" \nThe NrdD reductase is activated by the NrdG activase under anaerobic conditions and is inactivated by oxygen. The protein is highly sensitive to O2.\nAn nrdD null mutant does not grow under entirely anaerobic conditions, but grows under aerobic or microaerophilic conditions due to the activity of NrdA \nand/or NrdB. Ribonucleotide reductase catalyzes the rate-limiting step in DNA biosynthesis. Its central role in DNA replication and repair makes its regulation \nimportant to ensure appropriate pools of deoxyribonucleotides for these processes. Three major classes I, II and III have been designated that share similar catalytic \nmechanisms. Enterobacteria, including Escherichia coli and Salmonella enterica serovar \nTyphimurium contain class Ia (encoded by nrdA and nrdB ), class Ib (encoded by nrdE and nrdF ) and class III (encoded by nrdD ) enzymes. This enzyme is a \nclass III ribonucleotide reductase that is essential for anaerobic growth.\n ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=RXN0-723 ;"},"mmid":"MM0000113","psid":"PS0000107","gnid":"GN0000068","reversible":true,"information":{"Mathematical model information":" Reaction follows Michaelis-Menten kinetics. As dATP, dGTP and TTP are known to be noncompetetive inhibitors[Eliasson et al., 1994] of this reaction the equasion can be written as a sum of inhibitors influenses. As ATP and CTP are known to be competitive activators [Eliasson et al., 1994] of this reaction the equasion can be written as a \nratio Michaelis constant with respect to activator (ATP). ","Parameter set information":" kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax = kcat*r1 (where r1 is enzyme concentration) \ncan be calculated from the whole model basing on the flow rate magnitude.\nParametrs kmctp, katp, kdatp, kdgtp and kttp were evaluated basing on [Eliasson et al.,1994] experimental data.    ","Parameter set links":" ID: Eliasson et al., 1994 Allosteric control of the substrate specificity of the anaerobic ribonucleotide reductase from Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7929317 ;","Structural model information":" \nThe NrdD reductase is activated by the NrdG activase under anaerobic conditions and is inactivated by oxygen. The protein is highly sensitive to O2.\nAn nrdD null mutant does not grow under entirely anaerobic conditions, but grows under aerobic or microaerophilic conditions due to the activity of NrdA \nand/or NrdB. Ribonucleotide reductase catalyzes the rate-limiting step in DNA biosynthesis. Its central role in DNA replication and repair makes its regulation \nimportant to ensure appropriate pools of deoxyribonucleotides for these processes. Three major classes I, II and III have been designated that share similar catalytic \nmechanisms. Enterobacteria, including Escherichia coli and Salmonella enterica serovar \nTyphimurium contain class Ia (encoded by nrdA and nrdB ), class Ib (encoded by nrdE and nrdF ) and class III (encoded by nrdD ) enzymes. This enzyme is a \nclass III ribonucleotide reductase that is essential for anaerobic growth.\n ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=RXN0-723 ;"},"parameters":[{"units":"mM","information":"","name":"katp","value":"0.0127"},{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kdatp","value":"0.17"},{"units":"mM","information":"","name":"kdgtp","value":"0.12"},{"units":"mM","information":"","name":"kmctp","value":"4"},{"units":"mM","information":"","name":"kttp","value":"0.22"}]},{"scheme":"NADP+ + NADH + HEXT <=> NADPH + NAD+","substrates":{"s1":{"theSubstance":{"name":"NADP+","type":"substance","synonyms":["beta-Nicotinamide adenine dinucleotide phosphate","NADP","NADP+","Nicotinamide adenine dinucleotide phosphate","TPN","Triphosphopyridine nucleotide"],"links":[],"id":"SS0000067"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"NADH","type":"substance","synonyms":["DPNH","NADH","Nicotinamide adenine dinucleotide"],"links":[],"id":"SS0000064"},"theState":null,"compartment":""},"s3":{"theSubstance":{"name":"HEXT","type":"substance","synonyms":["external H+","external hydrogen ion","HEXT","H+ external","hydrogen ion external"],"links":[],"id":"SS0000279"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"NADPH","type":"substance","synonyms":["NADPH","Reduced nicotinamide adenine dinucleotide phosphate","TPNH"],"links":[],"id":"SS0000066"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"NAD+","type":"substance","synonyms":["NAD+"],"links":[],"id":"SS0000188"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PntAB","type":"protein","synonyms":["ec:1.6.1.2","NADPH:NAD+ oxidoreductase (AB-specific)","NAD(P)(+) transhydrogenase (AB-specific)","nicotinamide nucleotide transhydrogenase","PntAB","Pyridine nucleotide transhydrogenase","transhydrogenase","Transporter: pyridine nucleotide transhydrogenase"],"links":[],"id":"SS0000340"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"2'-AMP","type":"substance","synonyms":["2'-Adenylic acid","2'-AMP","Adenosine-2'-monophosphate","Adenosine 2'-phosphate","AMP 2'-phosphate"],"links":[],"id":"SS0000342"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"AMP","type":"substance","synonyms":["5'-Adenosine monophosphate","5'-Adenylic acid","5'-AMP","Adenosine 5'-monophosphate","Adenosine 5'-phosphate","Adenylate","Adenylic acid","AMP"],"links":[],"id":"SS0000073"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"(r1*kf*(s1/kia)^na*(s2/kmb)^nb - kr*p1*p2/(kmp*kiq* (1 + r2/ki1) *(1 + r3/ki2)* (1 + s1/kis1)*(1 + s2/kis2)))/ (1 + (s1/kia)^na + (s2/kib)^nb + p1/(kip*(1 + r2/ki1)* (1 + s1/kis1)) + p2/(kiq* (1 + r3/ki2)* (1 + s2/kis2)) + (s1/kia)^na*(s2/kmb)^nb + p1*p2/(kmp*kiq* (1 + r2/ki1) *(1 + r3/ki2)* (1 + s1/kis1)*(1 + s2/kis2)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Substrates NADP and NADH are both substrate inhibitors. NADPH and NAD have complex inhibitory function: as competitive product inhibitors, and as additional complex inhibitors [Sweetman AJ, Griffiths DE, 1971; Hanson RL, 1979]. \r\nThe main feature of the model is a composite Michaelis constant for NADPH-NAD complex, inhibiting the forward reaction (which depends on 2’-AMP and AMP inhibitors). \r\nThe model is written in terms of generalized Hill functions. ","Mathematical model links":" ID: Hanson RL (1979) The kinetic mechanism of pyridine nucleotide transhydrogenase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/368063 ; ID: Sweetman AJ, Griffiths DE (1971) Studies on energy-linked reactions. Energy-linked transhydrogenase reaction in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4398957 ;","Parameter set information":"All parameters were verified using literature data (Sweetman, Griffiths 1971; Hanson 1979; Zhang J et al 1997).","Parameter set links":" ID: Hanson RL (1979) The kinetic mechanism of pyridine nucleotide transhydrogenase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/368063 ; ID: Sweetman AJ, Griffiths DE (1971)  Studies on energy-linked reactions. Energy-linked transhydrogenase reaction in Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4398957 ; ID: Zhang J et al (1997) Effects of metal ions on the substrate-specificity and activity of proton-pumping nicotinamide nucleotide transhydrogenase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9131054 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=PYRNUTRANSHYDROGEN-CPLX ; ID: Sweetman AJ, Griffiths DE (1971) Studies on energy-linked reactions. Energy-linked transhydrogenase reaction in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4398957 ;"},"mmid":"MM0000156","psid":"PS0000148","gnid":"GN0000170","reversible":true,"information":{"Mathematical model information":"Substrates NADP and NADH are both substrate inhibitors. NADPH and NAD have complex inhibitory function: as competitive product inhibitors, and as additional complex inhibitors [Sweetman AJ, Griffiths DE, 1971; Hanson RL, 1979]. \r\nThe main feature of the model is a composite Michaelis constant for NADPH-NAD complex, inhibiting the forward reaction (which depends on 2’-AMP and AMP inhibitors). \r\nThe model is written in terms of generalized Hill functions. ","Mathematical model links":" ID: Hanson RL (1979) The kinetic mechanism of pyridine nucleotide transhydrogenase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/368063 ; ID: Sweetman AJ, Griffiths DE (1971) Studies on energy-linked reactions. Energy-linked transhydrogenase reaction in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4398957 ;","Parameter set information":"All parameters were verified using literature data (Sweetman, Griffiths 1971; Hanson 1979; Zhang J et al 1997).","Parameter set links":" ID: Hanson RL (1979) The kinetic mechanism of pyridine nucleotide transhydrogenase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/368063 ; ID: Sweetman AJ, Griffiths DE (1971)  Studies on energy-linked reactions. Energy-linked transhydrogenase reaction in Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4398957 ; ID: Zhang J et al (1997) Effects of metal ions on the substrate-specificity and activity of proton-pumping nicotinamide nucleotide transhydrogenase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9131054 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=PYRNUTRANSHYDROGEN-CPLX ; ID: Sweetman AJ, Griffiths DE (1971) Studies on energy-linked reactions. Energy-linked transhydrogenase reaction in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4398957 ;"},"parameters":[{"units":"1/s","information":"","name":"kf","value":"0.0525"},{"units":"mcM","information":"","name":"ki1","value":"1650"},{"units":"mcM","information":"","name":"ki2","value":"2000"},{"units":"mcM","information":"","name":"kia","value":"1400"},{"units":"mcM","information":"","name":"kib","value":"67"},{"units":"mcM","information":"","name":"kip","value":"3.5"},{"units":"mcM","information":"","name":"kiq","value":"7"},{"units":"mcM","information":"","name":"kis1","value":"100"},{"units":"mcM","information":"","name":"kis2","value":"80"},{"units":"mcM","information":"","name":"kmb","value":"1.1"},{"units":"mcM","information":"","name":"kmp","value":"15"},{"units":"1/s","information":"","name":"kr","value":"0.075"},{"units":"","information":"","name":"na","value":"0.78"},{"units":"","information":"","name":"nb","value":"0.61"}]},{"scheme":"dTDP + ATP -> TTP + ADP + H+","substrates":{"s1":{"theSubstance":{"name":"dTDP","type":"substance","synonyms":["Deoxythymidine 5'-diphosphate","dTDP"],"links":[],"id":"SS0000053"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"TTP","type":"substance","synonyms":["Deoxythymidine 5'-triphosphate","Deoxythymidine triphosphate","dTTP","TTP"],"links":[],"id":"SS0000052"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Ndk","type":"protein","synonyms":["Ndk","NDP kinase","nucleoside diphosphate kinase"],"links":[],"id":"SS0000154"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"(r1*kcat*(s1/kmdtdp)*(s2/kmatp))/((1+(s1/kmdtdp))*(1+(s2/kmatp)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"dTDP is phosphorylated to TTP [Roisin et al., 1978, Ginther et al., 1974, Jong et al., 1991]. We proposed a simple model without competitive substrates such as dCDP,dGDP,dADP... as they are rapidly consumed in their reactions.","Mathematical model links":" ID: Ginther et al., 1974 Nucleoside diphosphokinase of Salmonella typhimurium. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4364654 ; ID: Jong et al., 1991 Saccharomyces cerevisiae nucleoside-diphosphate kinase: purification, characterization, and substrate specificity. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1659321 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Parameter set information":"Parameter kcat was evaluated basing on [Bernard et al., 2000] data.\nParameters kmdtdp and kmatp were evaluated basing on [Roisin, 1978] data.","Parameter set links":" ID: Bernard et al., 2000 Metabolic functions of microbial nucleoside diphosphate kinases. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11768309 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Structural model information":" Nucleoside diphosphate kinase catalyzes the reaction in which the terminal phosphate of a nucleoside-triphosphate is transferred to a nucleoside-diphosphate. \nThe enzyme exhibits broad substrate specificity. The reaction mechanism is an ordered bi-molecular ping-pong type. The intracellular levels of ATP are considerably \nhigher than other nucleoside triphosphates. In addition, ATP is far more abundant than ADP or AMP, so there is a strong thermodynamic tendency for the potential energy \nof ATP to be used in the synthesis of other high-energy compounds. Therefore nucleoside diphosphate kinase is \nunlikely to be involved in the synthesis of ATP. The purified enzyme is tetrameric and was detected in the periplasmic fraction after cold osmotic shock. \nA periplasmic location for the enzyme appears inconsistent with its function. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=DTDPKIN-RXN ;"},"mmid":"MM0000132","psid":"PS0000162","gnid":"GN0000079","reversible":false,"information":{"Mathematical model information":"dTDP is phosphorylated to TTP [Roisin et al., 1978, Ginther et al., 1974, Jong et al., 1991]. We proposed a simple model without competitive substrates such as dCDP,dGDP,dADP... as they are rapidly consumed in their reactions.","Mathematical model links":" ID: Ginther et al., 1974 Nucleoside diphosphokinase of Salmonella typhimurium. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4364654 ; ID: Jong et al., 1991 Saccharomyces cerevisiae nucleoside-diphosphate kinase: purification, characterization, and substrate specificity. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1659321 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Parameter set information":"Parameter kcat was evaluated basing on [Bernard et al., 2000] data.\nParameters kmdtdp and kmatp were evaluated basing on [Roisin, 1978] data.","Parameter set links":" ID: Bernard et al., 2000 Metabolic functions of microbial nucleoside diphosphate kinases. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11768309 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Structural model information":" Nucleoside diphosphate kinase catalyzes the reaction in which the terminal phosphate of a nucleoside-triphosphate is transferred to a nucleoside-diphosphate. \nThe enzyme exhibits broad substrate specificity. The reaction mechanism is an ordered bi-molecular ping-pong type. The intracellular levels of ATP are considerably \nhigher than other nucleoside triphosphates. In addition, ATP is far more abundant than ADP or AMP, so there is a strong thermodynamic tendency for the potential energy \nof ATP to be used in the synthesis of other high-energy compounds. Therefore nucleoside diphosphate kinase is \nunlikely to be involved in the synthesis of ATP. The purified enzyme is tetrameric and was detected in the periplasmic fraction after cold osmotic shock. \nA periplasmic location for the enzyme appears inconsistent with its function. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=DTDPKIN-RXN ;"},"parameters":[{"units":"1/sec","information":"","name":"kcat","value":"3.9"},{"units":"mM","information":"","name":"kmatp","value":"1.43"},{"units":"mM","information":"","name":"kmdtdp","value":"0.47"}]},{"scheme":"dTMP + ATP -> dTDP + ADP","substrates":{"s1":{"theSubstance":{"name":"dTMP","type":"substance","synonyms":["Deoxythymidine 5'-phosphate","Deoxythymidylic acid","dTMP","Thymidine 5'-phosphate","Thymidine monophosphate","Thymidylate","Thymidylic acid"],"links":[],"id":"SS0000054"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"dTDP","type":"substance","synonyms":["Deoxythymidine 5'-diphosphate","dTDP"],"links":[],"id":"SS0000053"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Tmk","type":"protein","synonyms":["dTMP kinase","EC:2.7.4.9","Tmk","YcfG"],"links":[],"id":"SS0000166"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"dUMP","type":"substance","synonyms":["2'-Deoxyuridine 5'-phosphate","Deoxyuridine 5'-phosphate","Deoxyuridine monophosphate","Deoxyuridylic acid","dUMP"],"links":[],"id":"SS0000050"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"(kcat*r1*s1*s2)/((KmdTMP*(1+(r2/kdUMP))+s1)*(KmATP+s2))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis Menten kinetics. dUMP is a noncompetitive inhibitor [Nelson et al., 1969]","Mathematical model links":" ID: Nelson D.J., Carter C.E., 1969 Purification and characterization of Thymidine 5-monophosphate kinase from Escherichia coli B. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4899016 ;","Parameter set information":"Parameters was evaluated basing on [Nelson et al., 1969] experimental data.In spite of this fact Vmax=kcat*r1 (where r1 is the enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. ","Parameter set links":" ID: Nelson D.J., Carter C.E., 1969 Purification and characterization of Thymidine 5-monophosphate kinase from Escherichia coli B. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4899016 ;","Structural model information":" The enzyme is responsible for specifically catalyzing the conversion of dTMP to dTDP. dTMP kinase is the last unique enzyme in the pathway leading to TTP. Thymidylate kinase is essential for growth. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=DTMPKI-RXN ;"},"mmid":"MM0000177","psid":"PS0000173","gnid":"GN0000153","reversible":false,"information":{"Mathematical model information":"Reaction follows Michaelis Menten kinetics. dUMP is a noncompetitive inhibitor [Nelson et al., 1969]","Mathematical model links":" ID: Nelson D.J., Carter C.E., 1969 Purification and characterization of Thymidine 5-monophosphate kinase from Escherichia coli B. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4899016 ;","Parameter set information":"Parameters was evaluated basing on [Nelson et al., 1969] experimental data.In spite of this fact Vmax=kcat*r1 (where r1 is the enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. ","Parameter set links":" ID: Nelson D.J., Carter C.E., 1969 Purification and characterization of Thymidine 5-monophosphate kinase from Escherichia coli B. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4899016 ;","Structural model information":" The enzyme is responsible for specifically catalyzing the conversion of dTMP to dTDP. dTMP kinase is the last unique enzyme in the pathway leading to TTP. Thymidylate kinase is essential for growth. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=DTMPKI-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmATP","value":"1.2"},{"units":"mM","information":"","name":"KmdTMP","value":"0.05"},{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kdUMP","value":"0.9"}]},{"scheme":"GTP + a reduced flavodoxin -> dGTP + H2O + an oxidized flavodoxin","substrates":{"s1":{"theSubstance":{"name":"GTP","type":"substance","synonyms":["GTP","Guanosine 5'-triphosphate"],"links":[],"id":"SS0000140"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"Reduced flavodoxin","type":"substance","synonyms":["Reduced flavodoxin"],"links":[],"id":"SS0000159"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"dGTP","type":"substance","synonyms":["2'-Deoxyguanosine 5'-triphosphate","Deoxyguanosine 5'-triphosphate","Deoxyguanosine triphosphate","dGTP"],"links":[],"id":"SS0000121"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"Oxidized flavodoxin","type":"substance","synonyms":["an oxidized flavodoxin","Oxidized flavodoxin"],"links":[],"id":"SS0000160"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"NrdD","type":"protein","synonyms":["EC:1.17.4.2","NrdD","ribonucleoside-triphosphate reductase","RNTRase"],"links":[],"id":"SS0000161"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"TTP","type":"substance","synonyms":["Deoxythymidine 5'-triphosphate","Deoxythymidine triphosphate","dTTP","TTP"],"links":[],"id":"SS0000052"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"dGTP","type":"substance","synonyms":["2'-Deoxyguanosine 5'-triphosphate","Deoxyguanosine 5'-triphosphate","Deoxyguanosine triphosphate","dGTP"],"links":[],"id":"SS0000121"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"dATP","type":"substance","synonyms":["2'-Deoxyadenosine 5'-triphosphate","dATP","Deoxyadenosine 5'-triphosphate","Deoxyadenosine triphosphate"],"links":[],"id":"SS0000079"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"(r1*kcat*s1/(kmgtp+s1))*((1+(r2/kttp1)+(r5/katp1))/(1+(r2/kttp2)+(r5/katp2)+(r3/kdgtp)+(r4/kdatp)))","theSubMathModel":null,"theInformation":{"Mathematical model information":" Reaction follows Michaelis-Menten kinetics. As dGTP, dATP and TTP, ATP are known to be noncompetetive inhibitors and activators [Eliasson et al., 1994] of this reaction the equasion can be written as a sum of inhibitors and activators influenses.  ","Mathematical model links":" ID: Eliasson et al., 1994 Allosteric control of the substrate specificity of the anaerobic ribonucleotide reductase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7929317 ;","Parameter set information":" Parametr(s) kttp1, kttp2 katp1, katp2, kdgtp and kdatp were evaluated basing on [Eliasson et al., 1994] experimental data.  \n\n\nParametr kmgtp was taken from [Eliasson et al., 1994] article.\n\nkcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) \ncan be calculated from the whole model basing on the flow rate magnitude.\n ","Parameter set links":" ID: Eliasson et al., 1994 Allosteric control of the substrate specificity of the anaerobic ribonucleotide reductase from Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7929317 ;","Structural model information":"Reaction follows Michaelis-Menten kinetic.\n\nAs dGTP, dATP and TTP, ATP are known to be noncompetetive inhibitors and activators [Eliasson et al., 1994] of this reaction the equasion can be written as a sum of inhibitors and activators influenses.\n","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=RXN0-746 ;"},"mmid":"MM0000116","psid":"PS0000110","gnid":"GN0000147","reversible":false,"information":{"Mathematical model information":" Reaction follows Michaelis-Menten kinetics. As dGTP, dATP and TTP, ATP are known to be noncompetetive inhibitors and activators [Eliasson et al., 1994] of this reaction the equasion can be written as a sum of inhibitors and activators influenses.  ","Mathematical model links":" ID: Eliasson et al., 1994 Allosteric control of the substrate specificity of the anaerobic ribonucleotide reductase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7929317 ;","Parameter set information":" Parametr(s) kttp1, kttp2 katp1, katp2, kdgtp and kdatp were evaluated basing on [Eliasson et al., 1994] experimental data.  \n\n\nParametr kmgtp was taken from [Eliasson et al., 1994] article.\n\nkcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) \ncan be calculated from the whole model basing on the flow rate magnitude.\n ","Parameter set links":" ID: Eliasson et al., 1994 Allosteric control of the substrate specificity of the anaerobic ribonucleotide reductase from Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7929317 ;","Structural model information":"Reaction follows Michaelis-Menten kinetic.\n\nAs dGTP, dATP and TTP, ATP are known to be noncompetetive inhibitors and activators [Eliasson et al., 1994] of this reaction the equasion can be written as a sum of inhibitors and activators influenses.\n","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=RXN0-746 ;"},"parameters":[{"units":"mM","information":"","name":"katp1","value":"0.035"},{"units":"mM","information":"","name":"katp2","value":"0.09"},{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kdatp","value":"0.004"},{"units":"mM","information":"","name":"kdgtp","value":"0.26"},{"units":"mM","information":"","name":"kmgtp","value":"0.4"},{"units":"mM","information":"","name":"kttp1","value":"0.0022"},{"units":"mM","information":"","name":"kttp2","value":"0.03"}]},{"scheme":"NO3 -> NO2","substrates":{"s1":{"theSubstance":{"name":"NO3","type":"substance","synonyms":["nitrate","NO3","NO3-"],"links":[],"id":"SS0000016"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"NO2","type":"substance","synonyms":["nitrite","NO2","NO2-"],"links":[],"id":"SS0000017"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"NRA","type":"protein","synonyms":["EC:1.7.5.1","nitrate reductase A","NRA"],"links":[],"id":"SS0000018"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"r1*(((k1*((k2/k3)^k4))/(1+k5/k6+(k2/k3)^k4))*(s1/(k7+s1))+((k8*(k5/k9)^k4)/(1+k2/k10+((k5/k9)^k4))*(s1/(k11+s1))))","theSubMathModel":null,"theInformation":{"Mathematical model information":"s1 is the internal concentration of nitrate","Parameter set information":" Giordani et al., obtained parameter values by fitting the equation to experimental data set  ","Parameter set links":" ID: Giordani et al., 1997. Kinetics of membrane-bound nitrate reductase A from Escherichia coli with analogues of physiological electron donors--different reaction sites for menadiol and duroquinol. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9428711 ;","Structural model information":" The whole reaction catalyzed by NRA enzyme is as follows:\nUQH2 + MKH2 + NO3 + 2H+ (cytosol) -&gt; UQ + MK + NO2 + H2O + 2H+ (periplasmic space) ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=RXN0-3501 ;"},"mmid":"MM0000002","psid":"PS0000002","gnid":"GN0000003","reversible":false,"information":{"Mathematical model information":"s1 is the internal concentration of nitrate","Parameter set information":" Giordani et al., obtained parameter values by fitting the equation to experimental data set  ","Parameter set links":" ID: Giordani et al., 1997. Kinetics of membrane-bound nitrate reductase A from Escherichia coli with analogues of physiological electron donors--different reaction sites for menadiol and duroquinol. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9428711 ;","Structural model information":" The whole reaction catalyzed by NRA enzyme is as follows:\nUQH2 + MKH2 + NO3 + 2H+ (cytosol) -&gt; UQ + MK + NO2 + H2O + 2H+ (periplasmic space) ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=RXN0-3501 ;"},"parameters":[{"units":"s^(-1)","information":"","name":"k1","value":"31.9"},{"units":"mM","information":"","name":"k10","value":"0.028"},{"units":"mM","information":"","name":"k11","value":"0.746"},{"units":"mM","information":"","name":"k2","value":"0.126"},{"units":"mM","information":"","name":"k3","value":"0.319"},{"units":"","information":"","name":"k4","value":"2"},{"units":"mM","information":"","name":"k5","value":"0.126"},{"units":"mM","information":"","name":"k6","value":"0.037"},{"units":"mM","information":"","name":"k7","value":"0.9"},{"units":"s^(-1)","information":"","name":"k8","value":"12.25"},{"units":"mM","information":"","name":"k9","value":"0.359"}]},{"scheme":"UTP + a reduced flavodoxin <=> dUTP + H2O + an oxidized flavodoxin","substrates":{"s1":{"theSubstance":{"name":"UTP","type":"substance","synonyms":["Uridine 5'-triphosphate","Uridine triphosphate","UTP"],"links":[],"id":"SS0000026"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"Reduced flavodoxin","type":"substance","synonyms":["Reduced flavodoxin"],"links":[],"id":"SS0000159"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"dUTP","type":"substance","synonyms":["2'-Deoxyuridine 5'-triphosphate","dUTP"],"links":[],"id":"SS0000048"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"Oxidized flavodoxin","type":"substance","synonyms":["an oxidized flavodoxin","Oxidized flavodoxin"],"links":[],"id":"SS0000160"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"NrdD","type":"protein","synonyms":["EC:1.17.4.2","NrdD","ribonucleoside-triphosphate reductase","RNTRase"],"links":[],"id":"SS0000161"},"theState":null,"compartment":"","theInfluence":"activator"},"r2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"TTP","type":"substance","synonyms":["Deoxythymidine 5'-triphosphate","Deoxythymidine triphosphate","dTTP","TTP"],"links":[],"id":"SS0000052"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"dGTP","type":"substance","synonyms":["2'-Deoxyguanosine 5'-triphosphate","Deoxyguanosine 5'-triphosphate","Deoxyguanosine triphosphate","dGTP"],"links":[],"id":"SS0000121"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"dATP","type":"substance","synonyms":["2'-Deoxyadenosine 5'-triphosphate","dATP","Deoxyadenosine 5'-triphosphate","Deoxyadenosine triphosphate"],"links":[],"id":"SS0000079"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"(r1*kcat*s1/(kmutp+s1))*((1+(r2/katp1))/(1+(r2/katp2)+(r5/kdatp)+(r4/kdgtp)+(r3/kttp)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"  Reaction follows Michaelis-Menten kinetics. As dATP, dGTP and TTP are known to be noncompetetive inhibitors and activator - ATP [Eliasson et al., 1994] of this reaction the equation can be written as a sum of inhibitors and activator - ATP influences.  ","Mathematical model links":" ID: Eliasson et al., 1994. Allosteric control of the substrate specificity of the anaerobic ribonucleotide reductase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7929317 ;","Parameter set information":" Parameters kmutp, katp1, katp2, kdatp, kdgtp and kttp were evaluated basing on experimental data [Eliasson et al., 1994]. Parameter kmutp was taken from article [Eliasson et al., 1994]. kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. ","Parameter set links":" ID: Eliasson et al., 1994 Allosteric control of the substrate specificity of the anaerobic ribonucleotide reductase from Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7929317 ;","Structural model information":" The NrdD reductase is activated by the NrdG activase under anaerobic conditions and is inactivated by oxygen. The protein is highly sensitive to O2.\n\nAn nrdD null mutant does not grow under entirely anaerobic conditions, but grows under aerobic or microaerophilic conditions due to the activity of NrdA and/or NrdB. Ribonucleotide reductase catalyzes the rate-limiting step in DNA biosynthesis. Its central role in DNA replication and repair makes its regulation important to ensure appropriate pools of deoxyribonucleotides for these processes. Three major classes I, II and III have been designated that share similar catalytic mechanisms. Enterobacteria, including Escherichia coli and Salmonella enterica serovar Typhimurium contain class Ia (encoded by nrdA and nrdB ), class Ib (encoded by nrdE and nrdF ) and class III (encoded by nrdD ) enzymes. This enzyme is a class III ribonucleotide reductase that is essential for anaerobic growth. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=RXN0-724 ;"},"mmid":"MM0000114","psid":"PS0000108","gnid":"GN0000030","reversible":true,"information":{"Mathematical model information":"  Reaction follows Michaelis-Menten kinetics. As dATP, dGTP and TTP are known to be noncompetetive inhibitors and activator - ATP [Eliasson et al., 1994] of this reaction the equation can be written as a sum of inhibitors and activator - ATP influences.  ","Mathematical model links":" ID: Eliasson et al., 1994. Allosteric control of the substrate specificity of the anaerobic ribonucleotide reductase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7929317 ;","Parameter set information":" Parameters kmutp, katp1, katp2, kdatp, kdgtp and kttp were evaluated basing on experimental data [Eliasson et al., 1994]. Parameter kmutp was taken from article [Eliasson et al., 1994]. kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. ","Parameter set links":" ID: Eliasson et al., 1994 Allosteric control of the substrate specificity of the anaerobic ribonucleotide reductase from Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7929317 ;","Structural model information":" The NrdD reductase is activated by the NrdG activase under anaerobic conditions and is inactivated by oxygen. The protein is highly sensitive to O2.\n\nAn nrdD null mutant does not grow under entirely anaerobic conditions, but grows under aerobic or microaerophilic conditions due to the activity of NrdA and/or NrdB. Ribonucleotide reductase catalyzes the rate-limiting step in DNA biosynthesis. Its central role in DNA replication and repair makes its regulation important to ensure appropriate pools of deoxyribonucleotides for these processes. Three major classes I, II and III have been designated that share similar catalytic mechanisms. Enterobacteria, including Escherichia coli and Salmonella enterica serovar Typhimurium contain class Ia (encoded by nrdA and nrdB ), class Ib (encoded by nrdE and nrdF ) and class III (encoded by nrdD ) enzymes. This enzyme is a class III ribonucleotide reductase that is essential for anaerobic growth. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=RXN0-724 ;"},"parameters":[{"units":"mM","information":"","name":"katp1","value":"0.003"},{"units":"mM","information":"","name":"katp2","value":"0.04"},{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kdatp","value":"0.004"},{"units":"mM","information":"","name":"kdgtp","value":"0.004"},{"units":"mM","information":"","name":"kmutp","value":"1"},{"units":"mM","information":"","name":"kttp","value":"0.17"}]},{"scheme":"ATP + a reduced flavodoxin -> dATP + H2O + an oxidized flavodoxin","substrates":{"s1":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"Reduced flavodoxin","type":"substance","synonyms":["Reduced flavodoxin"],"links":[],"id":"SS0000159"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"dATP","type":"substance","synonyms":["2'-Deoxyadenosine 5'-triphosphate","dATP","Deoxyadenosine 5'-triphosphate","Deoxyadenosine triphosphate"],"links":[],"id":"SS0000079"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"Oxidized flavodoxin","type":"substance","synonyms":["an oxidized flavodoxin","Oxidized flavodoxin"],"links":[],"id":"SS0000160"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"NrdD","type":"protein","synonyms":["EC:1.17.4.2","NrdD","ribonucleoside-triphosphate reductase","RNTRase"],"links":[],"id":"SS0000161"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"dATP","type":"substance","synonyms":["2'-Deoxyadenosine 5'-triphosphate","dATP","Deoxyadenosine 5'-triphosphate","Deoxyadenosine triphosphate"],"links":[],"id":"SS0000079"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"TTP","type":"substance","synonyms":["Deoxythymidine 5'-triphosphate","Deoxythymidine triphosphate","dTTP","TTP"],"links":[],"id":"SS0000052"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"dGTP","type":"substance","synonyms":["2'-Deoxyguanosine 5'-triphosphate","Deoxyguanosine 5'-triphosphate","Deoxyguanosine triphosphate","dGTP"],"links":[],"id":"SS0000121"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"(r1*kcat*s1/(kmatp+s1))*((0.05+(r4/kdgtp1))/(1+(r4/kdgtp2)+(r3/kttp)+(r2/kdatp)))","theSubMathModel":null,"theInformation":{"Mathematical model information":" Reaction follows Michaelis-Menten kinetics. As TTP, dATP and dGTP are known to be noncompetetive inhibitors and activator [Eliasson et al., 1994] of this reaction the equasion can be written as a sum of inhibitors and activator influenses.  ","Mathematical model links":" ID: Eliasson et al., 1994 Allosteric control of the substrate specificity of the anaerobic ribonucleotide reductase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7929317 ;","Parameter set information":" Parametrs kdgtp1, kdgtp2, kttp and kdatp were evaluated basing on [Eliasson et al., 1994] experimental data.   \n\nParametr kmatp was taken from [Eliasson et al., 1994] article.\nkcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) \ncan be calculated from the whole model basing on the flow rate magnitude. ","Parameter set links":" ID: Eliasson et al., 1994 Allosteric control of the substrate specificity of the anaerobic ribonucleotide reductase from Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7929317 ;","Structural model information":"The reaction product is auto-inhibitor dATP","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=RXN0-745 ;"},"mmid":"MM0000115","psid":"PS0000109","gnid":"GN0000146","reversible":false,"information":{"Mathematical model information":" Reaction follows Michaelis-Menten kinetics. As TTP, dATP and dGTP are known to be noncompetetive inhibitors and activator [Eliasson et al., 1994] of this reaction the equasion can be written as a sum of inhibitors and activator influenses.  ","Mathematical model links":" ID: Eliasson et al., 1994 Allosteric control of the substrate specificity of the anaerobic ribonucleotide reductase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7929317 ;","Parameter set information":" Parametrs kdgtp1, kdgtp2, kttp and kdatp were evaluated basing on [Eliasson et al., 1994] experimental data.   \n\nParametr kmatp was taken from [Eliasson et al., 1994] article.\nkcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) \ncan be calculated from the whole model basing on the flow rate magnitude. ","Parameter set links":" ID: Eliasson et al., 1994 Allosteric control of the substrate specificity of the anaerobic ribonucleotide reductase from Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7929317 ;","Structural model information":"The reaction product is auto-inhibitor dATP","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=RXN0-745 ;"},"parameters":[{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kdatp","value":"0.03"},{"units":"mM","information":"","name":"kdgtp1","value":"1.7"},{"units":"mM","information":"","name":"kdgtp2","value":"1.7"},{"units":"mM","information":"","name":"kmatp","value":"4"},{"units":"mM","information":"","name":"kttp","value":"0.06"}]},{"scheme":"deoxyadenosine + H2O <=> NH3 + deoxyinosine","substrates":{"s1":{"theSubstance":{"name":"2-deoxy-adenosine","type":"substance","synonyms":["2-deoxy-adenosine","2'-deoxyadenosine","deoxyadenosine"],"links":[],"id":"SS0000240"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"NH3","type":"substance","synonyms":["Ammonia","NH3"],"links":[],"id":"SS0000060"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"deoxyinosine","type":"substance","synonyms":["2-deoxyinosine","deoxyinosine"],"links":[],"id":"SS0000241"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Add","type":"protein","synonyms":["Add","deoxyadenosine deaminase / adenosine deaminase","ec:3.5.4.4"],"links":[],"id":"SS0000242"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"kcat*r1*s1/(s1+km)","theSubMathModel":null,"theInformation":{"Mathematical model information":" Reaction follows Michaelis-Menten kinetics. ","Parameter set information":" kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax = kcat*r1 (where r1 is enzyme concentration) \ncan be calculated from the whole model basing on the flow rate magnitude.\n ","Parameter set links":" ID: Nygaard et al., 1978 Adenosine deaminase from Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/357905 ;","Structural model information":" Deoxyadenosine deaminase / adenosine deaminase is part of a pathway which converts adenine, adenosine and deoxyadenosine to guanine nucleotides. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=ADDALT-RXN ;"},"mmid":"MM0000117","psid":"PS0000111","gnid":"GN0000148","reversible":true,"information":{"Mathematical model information":" Reaction follows Michaelis-Menten kinetics. ","Parameter set information":" kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax = kcat*r1 (where r1 is enzyme concentration) \ncan be calculated from the whole model basing on the flow rate magnitude.\n ","Parameter set links":" ID: Nygaard et al., 1978 Adenosine deaminase from Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/357905 ;","Structural model information":" Deoxyadenosine deaminase / adenosine deaminase is part of a pathway which converts adenine, adenosine and deoxyadenosine to guanine nucleotides. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=ADDALT-RXN ;"},"parameters":[{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"km","value":"0.04"}]},{"scheme":"adenosine + H2O <=> NH3 + inosine","substrates":{"s1":{"theSubstance":{"name":"adenosine","type":"substance","synonyms":["adenine-D-ribose","adenosine"],"links":[],"id":"SS0000243"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"NH3","type":"substance","synonyms":["Ammonia","NH3"],"links":[],"id":"SS0000060"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"inosine","type":"substance","synonyms":["hypoxanthine-ribose","inosine","iso-prinosine","riboxine"],"links":[],"id":"SS0000244"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Add","type":"protein","synonyms":["Add","deoxyadenosine deaminase / adenosine deaminase","ec:3.5.4.4"],"links":[],"id":"SS0000242"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"kcat*r1*s1/(s1+km)","theSubMathModel":null,"theInformation":{"Mathematical model information":" Reaction follows Michaelis-Menten kinetics.\n ","Parameter set information":" kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax = kcat*r1 (where r1 is enzyme concentration) \ncan be calculated from the whole model basing on the flow rate magnitude. ","Parameter set links":" ID: KOCH et al, 1959 The properties of adenosine deaminase and adenosine nucleoside phosphorylase in extracts of Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/13654350 ;","Structural model information":" Deoxyadenosine deaminase / adenosine deaminase is part of a pathway which converts adenine, adenosine and deoxyadenosine to guanine nucleotides. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=ADENODEAMIN-RXN ;"},"mmid":"MM0000118","psid":"PS0000112","gnid":"GN0000149","reversible":true,"information":{"Mathematical model information":" Reaction follows Michaelis-Menten kinetics.\n ","Parameter set information":" kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax = kcat*r1 (where r1 is enzyme concentration) \ncan be calculated from the whole model basing on the flow rate magnitude. ","Parameter set links":" ID: KOCH et al, 1959 The properties of adenosine deaminase and adenosine nucleoside phosphorylase in extracts of Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/13654350 ;","Structural model information":" Deoxyadenosine deaminase / adenosine deaminase is part of a pathway which converts adenine, adenosine and deoxyadenosine to guanine nucleotides. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=ADENODEAMIN-RXN ;"},"parameters":[{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"km","value":"0.13"}]},{"scheme":"NO2 -> NH3","substrates":{"s1":{"theSubstance":{"name":"NO2","type":"substance","synonyms":["nitrite","NO2","NO2-"],"links":[],"id":"SS0000017"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"NH3","type":"substance","synonyms":["Ammonia","NH3"],"links":[],"id":"SS0000060"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"NirB","type":"protein","synonyms":["EC:1.7.1.4","NADH:nitrite oxidoreductase","NirB","nitrite reductase NADH"],"links":[],"id":"SS0000151"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"(k1*k2*s1)/(k3*(1 + (k4/k5)^k6/(1 + (k4/k7)^k6))*k8*  (1 + k2/(k3*(1 + (k4/k5)^k6/(1 + (k4/k7)^k6))) + s1/k8))","theSubMathModel":null,"theInformation":{"Parameter set information":"k1 equals to 1 as there is no experimental data for this subsystem.Steady-state concentrations of NAD and NADH were listed in Bennett work.Parameters describing NAD influence on nitrite Michaelis constant fit experimental data from Coleman work.","Parameter set links":" ID: Bennett et al., 2009. Absolute metabolite concentrations and implied enzyme active site occupancy in ; Value:http://www.ncbi.nlm.nih.gov/pubmed/19561621 ; ID: Coleman et al., 1978. Activation of nitrite reductase from ; Value:http://www.ncbi.nlm.nih.gov/pubmed/217343 ;","Structural model information":"NO2 is intracellular concentration of nitrite. The whole reaction is as follows: 3NADH+NO2+5H+ -> 3NAD+ NH3 +2H2O.","Structural model links":" ID: Wang et al., 2000. The nrfA and nirB nitrite reductase operons in Escherichia coli are expressed differently in response to nitrate than to nitrite. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11004182 ;"},"mmid":"MM0000120","psid":"PS0000114","gnid":"GN0000141","reversible":false,"information":{"Parameter set information":"k1 equals to 1 as there is no experimental data for this subsystem.Steady-state concentrations of NAD and NADH were listed in Bennett work.Parameters describing NAD influence on nitrite Michaelis constant fit experimental data from Coleman work.","Parameter set links":" ID: Bennett et al., 2009. Absolute metabolite concentrations and implied enzyme active site occupancy in ; Value:http://www.ncbi.nlm.nih.gov/pubmed/19561621 ; ID: Coleman et al., 1978. Activation of nitrite reductase from ; Value:http://www.ncbi.nlm.nih.gov/pubmed/217343 ;","Structural model information":"NO2 is intracellular concentration of nitrite. The whole reaction is as follows: 3NADH+NO2+5H+ -> 3NAD+ NH3 +2H2O.","Structural model links":" ID: Wang et al., 2000. The nrfA and nirB nitrite reductase operons in Escherichia coli are expressed differently in response to nitrate than to nitrite. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11004182 ;"},"parameters":[{"units":"s^(-1)","information":"","name":"k1","value":"1"},{"units":"mM","information":"","name":"k2","value":"0.83"},{"units":"mM","information":"","name":"k3","value":"0.008"},{"units":"mM","information":"","name":"k4","value":"1.5"},{"units":"mM","information":"","name":"k5","value":"0.53"},{"units":"","information":"","name":"k6","value":"1.2"},{"units":"mM","information":"","name":"k7","value":"1.2"},{"units":"mM","information":"","name":"k8","value":"0.0053"}]},{"scheme":"GDP + ATP -> GTP + ADP","substrates":{"s1":{"theSubstance":{"name":"GDP","type":"substance","synonyms":["GDP","Guanosine 5'-diphosphate","Guanosine diphosphate"],"links":[],"id":"SS0000087"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"GTP","type":"substance","synonyms":["GTP","Guanosine 5'-triphosphate"],"links":[],"id":"SS0000140"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Ndk","type":"protein","synonyms":["Ndk","NDP kinase","nucleoside diphosphate kinase"],"links":[],"id":"SS0000154"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"(r1*kcat*(s1/kmgdp18)*(s2/kmatp18))/((1+(s1/kmgdp18))*(1+(s2/kmatp18)))","theSubMathModel":null,"theInformation":{"Mathematical model information":" Reaction follows Michaelis-Menten kinetics. ","Parameter set information":"Parameters kmgdp18 and kmatp18 were evaluated basing on [Roisin, 1978] data.","Parameter set links":" ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Structural model information":" Nucleoside diphosphate kinase catalyzes the reaction in which the terminal phosphate of a nucleoside-triphosphate is transferred to a nucleoside-diphosphate. \nThe enzyme exhibits broad substrate specificity. The reaction mechanism is an ordered bi-molecular ping-pong type. The intracellular levels of ATP are considerably \nhigher than other nucleoside triphosphates. In addition, ATP is far more abundant than ADP or AMP, so there is a strong thermodynamic tendency for the potential energy \nof ATP to be used in the synthesis of other high-energy compounds. Therefore nucleoside diphosphate kinase is \nunlikely to be involved in the synthesis of ATP. The purified enzyme is tetrameric and was detected in the periplasmic fraction after cold osmotic shock. \nA periplasmic location for the enzyme appears inconsistent with its function. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=GDPKIN-RXN ;"},"mmid":"MM0000093","psid":"PS0000163","gnid":"GN0000127","reversible":false,"information":{"Mathematical model information":" Reaction follows Michaelis-Menten kinetics. ","Parameter set information":"Parameters kmgdp18 and kmatp18 were evaluated basing on [Roisin, 1978] data.","Parameter set links":" ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Structural model information":" Nucleoside diphosphate kinase catalyzes the reaction in which the terminal phosphate of a nucleoside-triphosphate is transferred to a nucleoside-diphosphate. \nThe enzyme exhibits broad substrate specificity. The reaction mechanism is an ordered bi-molecular ping-pong type. The intracellular levels of ATP are considerably \nhigher than other nucleoside triphosphates. In addition, ATP is far more abundant than ADP or AMP, so there is a strong thermodynamic tendency for the potential energy \nof ATP to be used in the synthesis of other high-energy compounds. Therefore nucleoside diphosphate kinase is \nunlikely to be involved in the synthesis of ATP. The purified enzyme is tetrameric and was detected in the periplasmic fraction after cold osmotic shock. \nA periplasmic location for the enzyme appears inconsistent with its function. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=GDPKIN-RXN ;"},"parameters":[{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kmatp18","value":"1.43"},{"units":"mM","information":"","name":"kmgdp18","value":"0.47"}]},{"scheme":"dGDP + ATP -> dGTP + ADP","substrates":{"s1":{"theSubstance":{"name":"dGDP","type":"substance","synonyms":["2'-Deoxyguanosine 5'-diphosphate","dGDP"],"links":[],"id":"SS0000120"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"dGTP","type":"substance","synonyms":["2'-Deoxyguanosine 5'-triphosphate","Deoxyguanosine 5'-triphosphate","Deoxyguanosine triphosphate","dGTP"],"links":[],"id":"SS0000121"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Ndk","type":"protein","synonyms":["Ndk","NDP kinase","nucleoside diphosphate kinase"],"links":[],"id":"SS0000154"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"(r1*kcat*s1*s2)/((kms1+s1)*(kms2+s2))","theSubMathModel":null,"theInformation":{"Mathematical model information":"dGDP is phosphorylated to dGTP [Roisin et al., 1978, Ginther et al., 1974, Jong et al., 1991, Bernard et al., 2000]. We proposed a simple model without competitive substrates such as dCDP,dADP,dUDP... as they are rapidly consumed in their reactions.","Mathematical model links":" ID: Bernard et al., 2000 Metabolic functions of microbial nucleoside diphosphate kinases. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11768309 ; ID: Ginther et al., 1974 Nucleoside diphosphokinase of Salmonella typhimurium. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4364654 ; ID: Jong et al., 1991 Saccharomyces cerevisiae nucleoside-diphosphate kinase: purification, characterization, and substrate specificity. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1659321 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Parameter set information":"Parameter kcat was evaluated basing on [Bernard et al., 2000] data.\nParameters kmdgdp and kmatp were evaluated basing on [Roisin, 1978] data.","Parameter set links":" ID: Bernard et al., 2000 Metabolic functions of microbial nucleoside diphosphate kinases. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11768309 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4364654 ;","Structural model information":" Nucleoside diphosphate kinase catalyzes the reaction in which the terminal phosphate of a nucleoside-triphosphate is transferred to a nucleoside-diphosphate. \nThe enzyme exhibits broad substrate specificity. The reaction mechanism is an ordered bi-molecular ping-pong type. The intracellular levels of ATP are considerably \nhigher than other nucleoside triphosphates. In addition, ATP is far more abundant than ADP or AMP, so there is a strong thermodynamic tendency for the potential energy \nof ATP to be used in the synthesis of other high-energy compounds. Therefore nucleoside diphosphate kinase is \nunlikely to be involved in the synthesis of ATP. The purified enzyme is tetrameric and was detected in the periplasmic fraction after cold osmotic shock. \nA periplasmic location for the enzyme appears inconsistent with its function. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=DGDPKIN-RXN ;"},"mmid":"MM0000135","psid":"PS0000165","gnid":"GN0000132","reversible":false,"information":{"Mathematical model information":"dGDP is phosphorylated to dGTP [Roisin et al., 1978, Ginther et al., 1974, Jong et al., 1991, Bernard et al., 2000]. We proposed a simple model without competitive substrates such as dCDP,dADP,dUDP... as they are rapidly consumed in their reactions.","Mathematical model links":" ID: Bernard et al., 2000 Metabolic functions of microbial nucleoside diphosphate kinases. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11768309 ; ID: Ginther et al., 1974 Nucleoside diphosphokinase of Salmonella typhimurium. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4364654 ; ID: Jong et al., 1991 Saccharomyces cerevisiae nucleoside-diphosphate kinase: purification, characterization, and substrate specificity. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1659321 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Parameter set information":"Parameter kcat was evaluated basing on [Bernard et al., 2000] data.\nParameters kmdgdp and kmatp were evaluated basing on [Roisin, 1978] data.","Parameter set links":" ID: Bernard et al., 2000 Metabolic functions of microbial nucleoside diphosphate kinases. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11768309 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4364654 ;","Structural model information":" Nucleoside diphosphate kinase catalyzes the reaction in which the terminal phosphate of a nucleoside-triphosphate is transferred to a nucleoside-diphosphate. \nThe enzyme exhibits broad substrate specificity. The reaction mechanism is an ordered bi-molecular ping-pong type. The intracellular levels of ATP are considerably \nhigher than other nucleoside triphosphates. In addition, ATP is far more abundant than ADP or AMP, so there is a strong thermodynamic tendency for the potential energy \nof ATP to be used in the synthesis of other high-energy compounds. Therefore nucleoside diphosphate kinase is \nunlikely to be involved in the synthesis of ATP. The purified enzyme is tetrameric and was detected in the periplasmic fraction after cold osmotic shock. \nA periplasmic location for the enzyme appears inconsistent with its function. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=DGDPKIN-RXN ;"},"parameters":[{"units":"1/sec","information":"","name":"kcat","value":"4.1"},{"units":"mM","information":"","name":"kms1","value":"0.47"},{"units":"mM","information":"","name":"kms2","value":"1.43"}]},{"scheme":"NO2 -> NH3","substrates":{"s1":{"theSubstance":{"name":"NO2","type":"substance","synonyms":["nitrite","NO2","NO2-"],"links":[],"id":"SS0000017"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"NH3","type":"substance","synonyms":["Ammonia","NH3"],"links":[],"id":"SS0000060"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"NrfA","type":"protein","synonyms":["aeg-93","EC:1.7.2.2","NrfA","periplasmic cytochrome c nitrite reductase"],"links":[],"id":"SS0000150"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"k1*r1*s1/(k2+s1)","theSubMathModel":null,"theInformation":{"Mathematical model information":" This reaction follows Michaelis-Menten kinetics. ","Mathematical model links":" ID: Kemp et al., 2010. Kinetic and thermodynamic resolution of the interactions between sulfite and the pentahaem cytochrome NrfA from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/20629638 ;","Parameter set links":" ID: Kemp et al., 2010. Kinetic and thermodynamic resolution of the interactions between sulfite and the pentahaem cytochrome NrfA from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/20629638 ;","Structural model information":"Periplasmic enzyme converts extracellular nitrite to ammonia. The whole reaction is \nNO2 + 7H+ -> NH3 + 2H2O","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=CYTOCHROMEC552-MONOMER ;"},"mmid":"MM0000069","psid":"PS0000067","gnid":"GN0000102","reversible":false,"information":{"Mathematical model information":" This reaction follows Michaelis-Menten kinetics. ","Mathematical model links":" ID: Kemp et al., 2010. Kinetic and thermodynamic resolution of the interactions between sulfite and the pentahaem cytochrome NrfA from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/20629638 ;","Parameter set links":" ID: Kemp et al., 2010. Kinetic and thermodynamic resolution of the interactions between sulfite and the pentahaem cytochrome NrfA from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/20629638 ;","Structural model information":"Periplasmic enzyme converts extracellular nitrite to ammonia. The whole reaction is \nNO2 + 7H+ -> NH3 + 2H2O","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=CYTOCHROMEC552-MONOMER ;"},"parameters":[{"units":"1/sec","information":"","name":"k1","value":"770"},{"units":"mM","information":"","name":"k2","value":"0.03"}]},{"scheme":"-> GuaA","substrates":null,"products":{"p1":{"theSubstance":{"name":"GuaA","type":"protein","synonyms":["GuaA"],"links":[],"id":"SS0000385"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"guaA","type":"gene","synonyms":["b2507","guaA"],"links":[],"id":"SS0000407"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"PurR","type":"protein","synonyms":["PurR","PurR transcriptional repressor"],"links":[],"id":"SS0000358"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"Gua","type":"substance","synonyms":["Gua","Guanosine"],"links":[],"id":"SS0000113"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"CRP","type":"protein","synonyms":["CRP"],"links":[],"id":"SS0000393"},"theState":null,"compartment":"","theInfluence":"activator"},"r6":{"theSubstance":{"name":"cAMP","type":"substance","synonyms":["3',5'-Cyclic AMP","Adenosine 3',5'-cyclic phosphate","Adenosine 3',5'-phosphate","cAMP","Cyclic adenylic acid","Cyclic AMP"],"links":[],"id":"SS0000074"},"theState":null,"compartment":"","theInfluence":"activator"},"r7":{"theSubstance":{"name":"DnaA","type":"protein","synonyms":["DnaA"],"links":[],"id":"SS0000390"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r8":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r9":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"ks*((1+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR))/(1+((((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k1PurR)+((((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k2PurR)+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR)))*((1+(k1CRP*(((((r5*(r6^2))/(kdisCRPcAMP^2))/(1+((2*r5*r6+(r6^2))/(kdisCRPcAMP^2))))/k2CRP)^hCRP)))/(1+((((r5*(r6^2))/(kdisCRPcAMP^2))/(1+((2*r5*r6+(r6^2))/(kdisCRPcAMP^2))))/k2CRP)))*(1/(1+((((k0*(((r7*r8)/kdisDnaAATP)/(1+((r7*r8)/kdisDnaAATP)+((r7*r9)/kdisDnaAADP))))^3)/((kdisDnaA^2)+3*((k0*(((r7*r8)/kdisDnaAATP)/(1+((r7*r8)/kdisDnaAATP)+((r7*r9)/kdisDnaAADP))))^2)))/kDnaA)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the articles [Meng et al., 1990; Tesfa-Selase and Drabble W.T., 1992; Hutchings and Drabble, 2000].","Mathematical model links":" ID: Hutchings M.I., Drabble W.T., 2000 Regulation of the divergent guaBA and xseA promoters of Escherichia coli by the cyclic AMP receptor protein. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10856643 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ; ID: Tesfa-Selase F., Drabble W.T., 1992 Regulation of the gua operon of Escherichia coli by the DnaA protein. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1736096 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*GuaA = 0, where GuaA - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter guaBp. ks - protein synthesis generalized constant from the promoter guaBp. kd = 0.002 [1/sec],GuaA = 0.00454 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data. Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data. Parameters k1CRP, k2CRP and hCRP were evaluated basing on [Hutchings M.I., Drabble W.T., 2000] experimental data. Parameter kdisCRPcAMP is taken from article [Malecki et al., 2000]. Parameters kdisDnaAATP, and kdisDnaAADP are taken from article [Kaguni, 2006]. Parameter kdisDnaA was evaluated basing on [Olliver et al., 2010] experimental data.","Parameter set links":" ID: Hutchings M.I., Drabble W.T., 2000 Regulation of the divergent guaBA and xseA promoters of Escherichia coli by the cyclic AMP receptor protein. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10856643 ; ID: Kaguni J.M., 2006 DnaA: controlling the initiation of bacterial DNA replication and more. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16753031 ; ID: Malecki J. et al., 2000 Kinetic studies of cAMP-induced allosteric changes in cyclic AMP receptor protein from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10722684 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ; ID: Olliver A. et al., 2010 DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/20487274 ;","Structural model information":"  Genes guaA and guaB encodes the structure of the subunits of enzymes GMP synthetase(GMPSase, EC 6.3.5.2) and IMP dehydrogenase(IMPDase, EC 1.1.1.205), respectively, and are part of an operon guaAB. Regulation of expression of the operon guaBA positively controlled by transcription factor CRP [Hutchings and Drabble, 2000] and negatively PurR and DnaA [Meng et al., 1990; Tesfa-Selase et al., 1992]. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]. The concentration of DnaA (monomer) = 0.0017 mM [Ali Azam et al., 1999]. The concentration of CRP (dimer) = 0.0013445 mM [calculation from the work of Lu, 2007].   The concentration of cAMP = 0.01 mM [Notley - McRobb et al., 1997].    ","Structural model links":" ID: Ali Azam et al., 1999 Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10515926 ; ID: Hutchings M.I., Drabble W.T. 2000 Regulation of the divergent guaBA and xseA promoters of Escherichia coli by the cyclic AMP receptor protein. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10856643 ; ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ; ID: Notley - McRobb et al., 1997 The relationship between external glucose concentration and cAMP levels inside Escherichia coli: implications for models of phosphotransferase-mediated regulation of adenylate cyclase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9202467 ; ID: Tesfa-Selase F., Drabble W.T., 1992 Regulation of the gua operon of Escherichia coli by the DnaA protein. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1736096 ;"},"mmid":"MM0000246","psid":"PS0000236","gnid":"GN0000236","reversible":false,"information":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the articles [Meng et al., 1990; Tesfa-Selase and Drabble W.T., 1992; Hutchings and Drabble, 2000].","Mathematical model links":" ID: Hutchings M.I., Drabble W.T., 2000 Regulation of the divergent guaBA and xseA promoters of Escherichia coli by the cyclic AMP receptor protein. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10856643 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ; ID: Tesfa-Selase F., Drabble W.T., 1992 Regulation of the gua operon of Escherichia coli by the DnaA protein. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1736096 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*GuaA = 0, where GuaA - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter guaBp. ks - protein synthesis generalized constant from the promoter guaBp. kd = 0.002 [1/sec],GuaA = 0.00454 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data. Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data. Parameters k1CRP, k2CRP and hCRP were evaluated basing on [Hutchings M.I., Drabble W.T., 2000] experimental data. Parameter kdisCRPcAMP is taken from article [Malecki et al., 2000]. Parameters kdisDnaAATP, and kdisDnaAADP are taken from article [Kaguni, 2006]. Parameter kdisDnaA was evaluated basing on [Olliver et al., 2010] experimental data.","Parameter set links":" ID: Hutchings M.I., Drabble W.T., 2000 Regulation of the divergent guaBA and xseA promoters of Escherichia coli by the cyclic AMP receptor protein. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10856643 ; ID: Kaguni J.M., 2006 DnaA: controlling the initiation of bacterial DNA replication and more. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16753031 ; ID: Malecki J. et al., 2000 Kinetic studies of cAMP-induced allosteric changes in cyclic AMP receptor protein from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10722684 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ; ID: Olliver A. et al., 2010 DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/20487274 ;","Structural model information":"  Genes guaA and guaB encodes the structure of the subunits of enzymes GMP synthetase(GMPSase, EC 6.3.5.2) and IMP dehydrogenase(IMPDase, EC 1.1.1.205), respectively, and are part of an operon guaAB. Regulation of expression of the operon guaBA positively controlled by transcription factor CRP [Hutchings and Drabble, 2000] and negatively PurR and DnaA [Meng et al., 1990; Tesfa-Selase et al., 1992]. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]. The concentration of DnaA (monomer) = 0.0017 mM [Ali Azam et al., 1999]. The concentration of CRP (dimer) = 0.0013445 mM [calculation from the work of Lu, 2007].   The concentration of cAMP = 0.01 mM [Notley - McRobb et al., 1997].    ","Structural model links":" ID: Ali Azam et al., 1999 Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10515926 ; ID: Hutchings M.I., Drabble W.T. 2000 Regulation of the divergent guaBA and xseA promoters of Escherichia coli by the cyclic AMP receptor protein. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10856643 ; ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ; ID: Notley - McRobb et al., 1997 The relationship between external glucose concentration and cAMP levels inside Escherichia coli: implications for models of phosphotransferase-mediated regulation of adenylate cyclase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9202467 ; ID: Tesfa-Selase F., Drabble W.T., 1992 Regulation of the gua operon of Escherichia coli by the DnaA protein. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1736096 ;"},"parameters":[{"units":"","information":"","name":"hCRP","value":"5"},{"units":"","information":"","name":"k0","value":"0.12"},{"units":"","information":"","name":"k1CRP","value":"3.471"},{"units":"mM","information":"","name":"k1PurR","value":"0.0006"},{"units":"mM","information":"","name":"k2CRP","value":"0.0006"},{"units":"mM","information":"","name":"k2PurR","value":"0.0006"},{"units":"mM","information":"","name":"k3PurR","value":"0.0008"},{"units":"mM","information":"","name":"kDnaA","value":"0.01"},{"units":"mM","information":"","name":"kdisCRPcAMP","value":"0.0275"},{"units":"mM","information":"","name":"kdisDnaA","value":"0.00134"},{"units":"mM","information":"","name":"kdisDnaAADP","value":"0.0001"},{"units":"mM","information":"","name":"kdisDnaAATP","value":"0.00003"},{"units":"mM","information":"","name":"kdisPurRgua","value":"0.0015"},{"units":"mM","information":"","name":"kdisPurRhyp","value":"0.0093"},{"units":"mM/sec","information":"","name":"ks","value":"0.0000113"}]},{"scheme":"Ura + prpp -> UMP + ppi","substrates":{"s1":{"theSubstance":{"name":"Ura","type":"substance","synonyms":["Ura","Uracil"],"links":[],"id":"SS0000040"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"prpp","type":"substance","synonyms":["5-Phospho-alpha-D-ribose 1-diphosphate","5-Phosphoribosyl 1-pyrophosphate","5-Phosphoribosyl diphosphate","prpp"],"links":[],"id":"SS0000021"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"UMP","type":"substance","synonyms":["5'Uridylic acid","UMP","Uridine 5'-monophosphate","Uridine monophosphate","Uridylic acid"],"links":[],"id":"SS0000024"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ppi","type":"substance","synonyms":["Diphosphate","PP","ppi","pyrophosphate"],"links":[],"id":"SS0000023"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Upp","type":"protein","synonyms":["ec:2.4.2.9","Upp","uracil phosphoribosyltransferase","UraP"],"links":[],"id":"SS0000274"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"GTP","type":"substance","synonyms":["GTP","Guanosine 5'-triphosphate"],"links":[],"id":"SS0000140"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":" ((kcat*r1*s1*s2)/((KmUra+s1)*(KmPRPP*(1/(1+(r2/k1GTP)))+s2)))*((1+k2GTP*((r2/k3GTP)^hGTP))/(1+((r2/k3GTP)^hGTP)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the articles [Rasmussen et al., 1986].","Mathematical model links":" ID: Rasmussen et al., 1986 Purification and some properties of uracil phosphoribosyltransferase from Escherichia coli K12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3513846 ;","Parameter set information":"Parameters k1GTP, k2GTP, k3GTP and hGTP were evaluated basing on [Rasmussen et al., 1986] experimental data.Parameters KmUra and KmPRPP are taken from article [Rasmussen et al., 1986]. Parameter kcat is taken from article [Lundegaard and Jensen, 1999].","Parameter set links":" ID: Lundegaard and Jensen, 1999 Kinetic mechanism of uracil phosphoribosyltransferase from Escherichia coli and catalytic importance of the conserved proline in the PRPP binding site. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10079076 ; ID: Rasmussen et al., 1986 Purification and some properties of uracil phosphoribosyltransferase from Escherichia coli K12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3513846 ;","Structural model information":"Uracil phosphoribosyltransferase (EC 2.4.2.9) catalyzes the conversion of uracil and phosphoribosylpyrophosphate (PRPP) to UMP and PPi- UMP is the precursor for all pyrimidine nucleoside triphosphates, and in the cell it is synthesized via the de novo pathway and the salvage pathway. The role of uracil phosphoribosyltransferase in the salvage of endogenously formed uracil and in the utilization of exogenous uracil and cytosine has been demonstrated in several microorganisms including E. coli.","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=URACIL-PRIBOSYLTRANS-RXN ;"},"mmid":"MM0000247","psid":"PS0000237","gnid":"GN0000237","reversible":false,"information":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the articles [Rasmussen et al., 1986].","Mathematical model links":" ID: Rasmussen et al., 1986 Purification and some properties of uracil phosphoribosyltransferase from Escherichia coli K12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3513846 ;","Parameter set information":"Parameters k1GTP, k2GTP, k3GTP and hGTP were evaluated basing on [Rasmussen et al., 1986] experimental data.Parameters KmUra and KmPRPP are taken from article [Rasmussen et al., 1986]. Parameter kcat is taken from article [Lundegaard and Jensen, 1999].","Parameter set links":" ID: Lundegaard and Jensen, 1999 Kinetic mechanism of uracil phosphoribosyltransferase from Escherichia coli and catalytic importance of the conserved proline in the PRPP binding site. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10079076 ; ID: Rasmussen et al., 1986 Purification and some properties of uracil phosphoribosyltransferase from Escherichia coli K12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3513846 ;","Structural model information":"Uracil phosphoribosyltransferase (EC 2.4.2.9) catalyzes the conversion of uracil and phosphoribosylpyrophosphate (PRPP) to UMP and PPi- UMP is the precursor for all pyrimidine nucleoside triphosphates, and in the cell it is synthesized via the de novo pathway and the salvage pathway. The role of uracil phosphoribosyltransferase in the salvage of endogenously formed uracil and in the utilization of exogenous uracil and cytosine has been demonstrated in several microorganisms including E. coli.","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=URACIL-PRIBOSYLTRANS-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmPRPP","value":"0.3"},{"units":"mM","information":"","name":"KmUra","value":"0.007"},{"units":"","information":"","name":"hGTP","value":"3"},{"units":"mM","information":"","name":"k1GTP","value":"0.43"},{"units":"","information":"","name":"k2GTP","value":"1.2"},{"units":"mM","information":"","name":"k3GTP","value":"0.1"},{"units":"1/sec","information":"","name":"kcat","value":"2.7"}]},{"scheme":"A + H2O -> Hypoxanthine + NH3","substrates":{"s1":{"theSubstance":{"name":"A","type":"substance","synonyms":["6-Aminopurine","A","Adenine"],"links":[],"id":"SS0000080"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"NH3","type":"substance","synonyms":["Ammonia","NH3"],"links":[],"id":"SS0000060"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"AdeD","type":"protein","synonyms":["Ade","AdeD","Adu","cryptic adenine deaminase","ec:1.11.1.6","ec:3.5.4.2","YicP"],"links":[],"id":"SS0000276"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"(kcat*r1*s1)/(KmAde+s1)","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Kamat et al., 2011 Catalytic Mechanism and Three-Dimensional Structure of Adenine Deaminase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/21247091 ;","Parameter set information":"Parameters kcat and KmAde are taken from article [Kamat et al., 2011].","Parameter set links":" ID: Kamat et al., 2011 Catalytic Mechanism and Three-Dimensional Structure of Adenine Deaminase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/21247091 ;","Structural model information":"Adenine deaminase catalyzes the conversion of adenine to hypoxanthine and ammonia.","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=ADENINE-DEAMINASE-RXN ;"},"mmid":"MM0000248","psid":"PS0000238","gnid":"GN0000238","reversible":false,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Kamat et al., 2011 Catalytic Mechanism and Three-Dimensional Structure of Adenine Deaminase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/21247091 ;","Parameter set information":"Parameters kcat and KmAde are taken from article [Kamat et al., 2011].","Parameter set links":" ID: Kamat et al., 2011 Catalytic Mechanism and Three-Dimensional Structure of Adenine Deaminase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/21247091 ;","Structural model information":"Adenine deaminase catalyzes the conversion of adenine to hypoxanthine and ammonia.","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=ADENINE-DEAMINASE-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmAde","value":"0.33"},{"units":"1/sec","information":"","name":"kcat","value":"196"}]},{"scheme":"-> PurK","substrates":null,"products":{"p1":{"theSubstance":{"name":"PurK","type":"protein","synonyms":["PurK"],"links":[],"id":"SS0000378"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"purK","type":"gene","synonyms":["b0522","purK"],"links":[],"id":"SS0000401"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"PurR","type":"protein","synonyms":["PurR","PurR transcriptional repressor"],"links":[],"id":"SS0000358"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"Gua","type":"substance","synonyms":["Gua","Guanosine"],"links":[],"id":"SS0000113"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"ks*((1+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR))/(1+((((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k1PurR)+((((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k2PurR)+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Meng et al., 1990].","Mathematical model links":" ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurK = 0, where PurK - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter purEp. ks - protein synthesis generalized constant from the promoter purEp. kd = 0.002 [1/sec],PurK = 0.003447 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Structural model information":" Expression of the purine biosynthetic gene purK is repressed by purines (guanine and hypoxanthine) in wild-type cells of Escherichia coli. This regulation is carried out through a protein PurR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]. ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;"},"mmid":"MM0000238","psid":"PS0000228","gnid":"GN0000229","reversible":false,"information":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Meng et al., 1990].","Mathematical model links":" ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurK = 0, where PurK - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter purEp. ks - protein synthesis generalized constant from the promoter purEp. kd = 0.002 [1/sec],PurK = 0.003447 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Structural model information":" Expression of the purine biosynthetic gene purK is repressed by purines (guanine and hypoxanthine) in wild-type cells of Escherichia coli. This regulation is carried out through a protein PurR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]. ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;"},"parameters":[{"units":"mM","information":"","name":"k1PurR","value":"0.00017"},{"units":"mM","information":"","name":"k2PurR","value":"0.00017"},{"units":"mM","information":"","name":"k3PurR","value":"0.0008"},{"units":"mM","information":"","name":"kdisPurRgua","value":"0.0015"},{"units":"mM","information":"","name":"kdisPurRhyp","value":"0.0093"},{"units":"mM/sec","information":"","name":"ks","value":"0.00000689"}]},{"scheme":"-> PurE","substrates":null,"products":{"p1":{"theSubstance":{"name":"PurE","type":"protein","synonyms":["PurE"],"links":[],"id":"SS0000379"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"purE","type":"gene","synonyms":["purE"],"links":[],"id":"SS0000402"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"PurR","type":"protein","synonyms":["PurR","PurR transcriptional repressor"],"links":[],"id":"SS0000358"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"Gua","type":"substance","synonyms":["Gua","Guanosine"],"links":[],"id":"SS0000113"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"ks*((1+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR))/(1+((((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k1PurR)+((((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k2PurR)+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Meng et al., 1990].","Mathematical model links":" ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurE = 0, where PurE - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter purEp. ks - protein synthesis generalized constant from the promoter purEp. kd = 0.002 [1/sec],PurE = 0.00645 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Structural model information":" Expression of the purine biosynthetic gene purE is repressed by purines (guanine and hypoxanthine) in wild-type cells of Escherichia coli. This regulation is carried out through a protein PurR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]. ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;"},"mmid":"MM0000239","psid":"PS0000229","gnid":"GN0000230","reversible":false,"information":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Meng et al., 1990].","Mathematical model links":" ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurE = 0, where PurE - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter purEp. ks - protein synthesis generalized constant from the promoter purEp. kd = 0.002 [1/sec],PurE = 0.00645 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Structural model information":" Expression of the purine biosynthetic gene purE is repressed by purines (guanine and hypoxanthine) in wild-type cells of Escherichia coli. This regulation is carried out through a protein PurR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]. ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;"},"parameters":[{"units":"mM","information":"","name":"k1PurR","value":"0.00017"},{"units":"mM","information":"","name":"k2PurR","value":"0.00017"},{"units":"mM","information":"","name":"k3PurR","value":"0.0008"},{"units":"mM","information":"","name":"kdisPurRgua","value":"0.0015"},{"units":"mM","information":"","name":"kdisPurRhyp","value":"0.0093"},{"units":"mM/sec","information":"","name":"ks","value":"0.0000129"}]},{"scheme":"-> PurC","substrates":null,"products":{"p1":{"theSubstance":{"name":"PurC","type":"protein","synonyms":["PurC"],"links":[],"id":"SS0000380"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"purC","type":"gene","synonyms":["ade","b2476","purC"],"links":[],"id":"SS0000403"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"PurR","type":"protein","synonyms":["PurR","PurR transcriptional repressor"],"links":[],"id":"SS0000358"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"Gua","type":"substance","synonyms":["Gua","Guanosine"],"links":[],"id":"SS0000113"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"ks*((1+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR))/(1+((((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k1PurR)+((((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k2PurR)+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Meng et al., 1990].","Mathematical model links":" ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurC = 0, where PurC - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter purCp. ks - protein synthesis generalized constant from the promoter purCp. kd = 0.002 [1/sec],PurC = 0.01795 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Structural model information":"   Expression of the purine biosynthetic gene purC is repressed by purines (guanine and hypoxanthine) in wild-type cells of Escherichia coli. This regulation is carried out through a protein PurR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007].  ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;"},"mmid":"MM0000240","psid":"PS0000230","gnid":"GN0000231","reversible":false,"information":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Meng et al., 1990].","Mathematical model links":" ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurC = 0, where PurC - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter purCp. ks - protein synthesis generalized constant from the promoter purCp. kd = 0.002 [1/sec],PurC = 0.01795 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Structural model information":"   Expression of the purine biosynthetic gene purC is repressed by purines (guanine and hypoxanthine) in wild-type cells of Escherichia coli. This regulation is carried out through a protein PurR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007].  ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;"},"parameters":[{"units":"mM","information":"","name":"k1PurR","value":"0.00015"},{"units":"mM","information":"","name":"k2PurR","value":"0.00015"},{"units":"mM","information":"","name":"k3PurR","value":"0.0008"},{"units":"mM","information":"","name":"kdisPurRgua","value":"0.0015"},{"units":"mM","information":"","name":"kdisPurRhyp","value":"0.0093"},{"units":"mM/sec","information":"","name":"ks","value":"0.0000359"}]},{"scheme":"NO3 -> NO2","substrates":{"s1":{"theSubstance":{"name":"NO3","type":"substance","synonyms":["nitrate","NO3","NO3-"],"links":[],"id":"SS0000016"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"NO2","type":"substance","synonyms":["nitrite","NO2","NO2-"],"links":[],"id":"SS0000017"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Nap","type":"protein","synonyms":["EC:1.7.99.4","Nap","NapABC","periplasmic nitrate reductase"],"links":[],"id":"SS0000203"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"k1*k2*s1/(k3*s1+k4*k2+k2*s1)","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Theorell-Chance mechanism.\n","Mathematical model links":" ID: Morpeth et al., 1985. Kinetic analysis of respiratory nitrate reductase from Escherichia coli K12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3888257 ;","Parameter set information":"UQH2 concentration were calculated based on Giordani experimental work.\nParameters k1, k3, k4 were taken from Morpeth work.","Parameter set links":" ID: Giordani et al., 1997. Kinetics of membrane-bound nitrate reductase A from Escherichia coli with analogues of physiological electron donors--different reaction sites for menadiol and duroquinol. ; Value:http://www.ncbi.nlm.nih.gov/pubmed?term=giordani%20567-77&cmd=correctspelling ; ID: Morpeth et al., 1985. Kinetic analysis of respiratory nitrate reductase from Escherichia coli K12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3888257 ;","Structural model information":"The whole reaction catalized by Nap enzyme is \nNO3+UQH2 ->NO2+UQ+H2O. This reaction takes place in periplasmic space.","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=NAP-CPLX ;"},"mmid":"MM0000083","psid":"PS0000080","gnid":"GN0000117","reversible":false,"information":{"Mathematical model information":"Reaction follows Theorell-Chance mechanism.\n","Mathematical model links":" ID: Morpeth et al., 1985. Kinetic analysis of respiratory nitrate reductase from Escherichia coli K12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3888257 ;","Parameter set information":"UQH2 concentration were calculated based on Giordani experimental work.\nParameters k1, k3, k4 were taken from Morpeth work.","Parameter set links":" ID: Giordani et al., 1997. Kinetics of membrane-bound nitrate reductase A from Escherichia coli with analogues of physiological electron donors--different reaction sites for menadiol and duroquinol. ; Value:http://www.ncbi.nlm.nih.gov/pubmed?term=giordani%20567-77&cmd=correctspelling ; ID: Morpeth et al., 1985. Kinetic analysis of respiratory nitrate reductase from Escherichia coli K12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3888257 ;","Structural model information":"The whole reaction catalized by Nap enzyme is \nNO3+UQH2 ->NO2+UQ+H2O. This reaction takes place in periplasmic space.","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=NAP-CPLX ;"},"parameters":[{"units":"s^(-1)","information":"","name":"k1","value":"7.194"},{"units":"mM","information":"","name":"k2","value":"0.126"},{"units":"mM","information":"","name":"k3","value":"0.0777"},{"units":"mM","information":"","name":"k4","value":"0.0019"}]},{"scheme":"AMP + ATP <=> ADP","substrates":{"s1":{"theSubstance":{"name":"AMP","type":"substance","synonyms":["5'-Adenosine monophosphate","5'-Adenylic acid","5'-AMP","Adenosine 5'-monophosphate","Adenosine 5'-phosphate","Adenylate","Adenylic acid","AMP"],"links":[],"id":"SS0000073"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Adk","type":"protein","synonyms":["adenylate kinase","Adk","DnaW","EC:2.7.4.3","PlsA"],"links":[],"id":"SS0000187"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"(r1*kcat*(s1/kmamp)*(s2/kmatp14))/((1+(s1/kmamp))*(1+(s2/kmatp14)))","theSubMathModel":null,"theInformation":{"Mathematical model information":" Reaction follows Michaelis-Menten kinetics. ","Parameter set information":"  Parametr kmamp was taken from Reinstein et al., 1990 article and Sinev et al., 1996.\n\nParametr kmatp14 was taken from Reinstein et al., 1990 article.\n\nkcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) \ncan be calculated from the whole model basing on the flow rate magnitude.  ","Parameter set links":" ID: Reinstein et al., 1990 Fluorescence and NMR investigations on the ligand binding properties of adenylate kinases ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2223775 ; ID: Sinev et al., 1996 Towards a mechanism of AMP-substrate inhibition in adenylate kinase from Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8955362 ;","Structural model information":" Adenylate kinase is an essential enzyme required for the biosynthesis of purine ribonucleotides and has a key role in controlling the rate of cell growth. There are estimated to be approximately 10,000 molecules of adenylate kinase present in the cell. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=ADENYL-KIN-RXN ;"},"mmid":"MM0000089","psid":"PS0000086","gnid":"GN0000123","reversible":true,"information":{"Mathematical model information":" Reaction follows Michaelis-Menten kinetics. ","Parameter set information":"  Parametr kmamp was taken from Reinstein et al., 1990 article and Sinev et al., 1996.\n\nParametr kmatp14 was taken from Reinstein et al., 1990 article.\n\nkcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) \ncan be calculated from the whole model basing on the flow rate magnitude.  ","Parameter set links":" ID: Reinstein et al., 1990 Fluorescence and NMR investigations on the ligand binding properties of adenylate kinases ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2223775 ; ID: Sinev et al., 1996 Towards a mechanism of AMP-substrate inhibition in adenylate kinase from Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8955362 ;","Structural model information":" Adenylate kinase is an essential enzyme required for the biosynthesis of purine ribonucleotides and has a key role in controlling the rate of cell growth. There are estimated to be approximately 10,000 molecules of adenylate kinase present in the cell. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=ADENYL-KIN-RXN ;"},"parameters":[{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kmamp","value":"0.026"},{"units":"mM","information":"","name":"kmatp14","value":"0.071"}]},{"scheme":"omp + H+ -> UMP + CO2","substrates":{"s1":{"theSubstance":{"name":"omp","type":"substance","synonyms":["omp","Orotidine 5'-phosphate","Orotidylic acid"],"links":[],"id":"SS0000022"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"UMP","type":"substance","synonyms":["5'Uridylic acid","UMP","Uridine 5'-monophosphate","Uridine monophosphate","Uridylic acid"],"links":[],"id":"SS0000024"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"CO2","type":"substance","synonyms":["Carbon dioxide","CO2"],"links":[],"id":"SS0000071"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PyrF","type":"protein","synonyms":["orotidine-5'-phosphate decarboxylase","pyrF","PyrF"],"links":[],"id":"SS0000214"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"(kcat*r1*(s1/kmomp))/(1+(s1/kmomp))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Donovan et al., 1983 Purification and characterization of orotidine-5-phosphate decarboxylase from Escherichia coli K-12 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6355062 ;","Parameter set information":"Parameters kcat, Kmomp were extracted from Donovan et al., 1983 data. The model was simulated upon steady state concentration of PyrF enzyme, which equals 0.0037 mM (Lu et al., 2007).","Parameter set links":" ID: Donovan et al., 1983 Purification and characterization of orotidine-5-phosphate decarboxylase from Escherichia coli K-12 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6355062 ; ID: Lu P et al. 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol. 2007 Jan;25(1):117-124. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=17187058 ;","Structural model information":"Orotidine-5&apos;-phosphate-decarboxylase (PyrF) catalyzes the last essential step in the de novo biosynthesis of pyrimidines, the synthesis of UMP by decarboxylation of omp. The enzyme has a homodimer structural organization (Donovan et al, 1983)","Structural model links":" ID: Donovan et al, 1983 Purification and characterization of orotidine-5&apos;-phosphate decarboxylase from Escherichia coli K-12. J Bacteriol. 1983 Nov;156(2):620-4. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=6355062 ; ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=OROTPDECARB-RXN ;"},"mmid":"MM0000167","psid":"PS0000156","gnid":"GN0000143","reversible":false,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Donovan et al., 1983 Purification and characterization of orotidine-5-phosphate decarboxylase from Escherichia coli K-12 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6355062 ;","Parameter set information":"Parameters kcat, Kmomp were extracted from Donovan et al., 1983 data. The model was simulated upon steady state concentration of PyrF enzyme, which equals 0.0037 mM (Lu et al., 2007).","Parameter set links":" ID: Donovan et al., 1983 Purification and characterization of orotidine-5-phosphate decarboxylase from Escherichia coli K-12 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6355062 ; ID: Lu P et al. 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol. 2007 Jan;25(1):117-124. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=17187058 ;","Structural model information":"Orotidine-5&apos;-phosphate-decarboxylase (PyrF) catalyzes the last essential step in the de novo biosynthesis of pyrimidines, the synthesis of UMP by decarboxylation of omp. The enzyme has a homodimer structural organization (Donovan et al, 1983)","Structural model links":" ID: Donovan et al, 1983 Purification and characterization of orotidine-5&apos;-phosphate decarboxylase from Escherichia coli K-12. J Bacteriol. 1983 Nov;156(2):620-4. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=6355062 ; ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=OROTPDECARB-RXN ;"},"parameters":[{"units":"1/sec","information":"","name":"kcat","value":"193"},{"units":"mM","information":"","name":"kmomp","value":"0.006"}]},{"scheme":"-> PurB","substrates":null,"products":{"p1":{"theSubstance":{"name":"PurB","type":"protein","synonyms":["PurB"],"links":[],"id":"SS0000381"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"purB","type":"gene","synonyms":["b1131","purB"],"links":[],"id":"SS0000404"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"PurR","type":"protein","synonyms":["PurR","PurR transcriptional repressor"],"links":[],"id":"SS0000358"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"Gua","type":"substance","synonyms":["Gua","Guanosine"],"links":[],"id":"SS0000113"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"ks*((1+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR))/(1+((((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k1PurR)+((((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k2PurR)+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Meng et al., 1990].","Mathematical model links":" ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurB = 0, where PurB - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter hflDp. ks - protein synthesis generalized constant from the promoter hflDp. kd = 0.002 [1/sec],PurB = 0.005483 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Structural model information":"  Expression of the purine biosynthetic gene purB is repressed by purines (guanine and hypoxanthine) in wild-type cells of Escherichia coli. This regulation is carried out through a protein PurR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007].   ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;"},"mmid":"MM0000241","psid":"PS0000231","gnid":"GN0000232","reversible":false,"information":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Meng et al., 1990].","Mathematical model links":" ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurB = 0, where PurB - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter hflDp. ks - protein synthesis generalized constant from the promoter hflDp. kd = 0.002 [1/sec],PurB = 0.005483 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Structural model information":"  Expression of the purine biosynthetic gene purB is repressed by purines (guanine and hypoxanthine) in wild-type cells of Escherichia coli. This regulation is carried out through a protein PurR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007].   ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;"},"parameters":[{"units":"mM","information":"","name":"k1PurR","value":"0.00064"},{"units":"mM","information":"","name":"k2PurR","value":"0.00064"},{"units":"mM","information":"","name":"k3PurR","value":"0.0008"},{"units":"mM","information":"","name":"kdisPurRgua","value":"0.0015"},{"units":"mM","information":"","name":"kdisPurRhyp","value":"0.0093"},{"units":"mM/sec","information":"","name":"ks","value":"0.00001096"}]},{"scheme":"-> PurH","substrates":null,"products":{"p1":{"theSubstance":{"name":"PurH","type":"protein","synonyms":["PurH"],"links":[],"id":"SS0000382"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"purH","type":"gene","synonyms":["b4006","purH"],"links":[],"id":"SS0000405"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"PurR","type":"protein","synonyms":["PurR","PurR transcriptional repressor"],"links":[],"id":"SS0000358"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"Gua","type":"substance","synonyms":["Gua","Guanosine"],"links":[],"id":"SS0000113"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"ks*((1+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR))/(1+((((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k1PurR)+((((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k2PurR)+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Meng et al., 1990].","Mathematical model links":" ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurH = 0, where PurH - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter purH. ks - protein synthesis generalized constant from the promoter purH. kd = 0.002 [1/sec],PurH = 0.00591287 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Structural model information":" Expression of the purine biosynthetic gene purH is repressed by purines (guanine and hypoxanthine) in wild-type cells of Escherichia coli. This regulation is carried out through a protein PurR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007].   ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;"},"mmid":"MM0000242","psid":"PS0000232","gnid":"GN0000233","reversible":false,"information":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Meng et al., 1990].","Mathematical model links":" ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurH = 0, where PurH - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter purH. ks - protein synthesis generalized constant from the promoter purH. kd = 0.002 [1/sec],PurH = 0.00591287 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Structural model information":" Expression of the purine biosynthetic gene purH is repressed by purines (guanine and hypoxanthine) in wild-type cells of Escherichia coli. This regulation is carried out through a protein PurR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007].   ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;"},"parameters":[{"units":"mM","information":"","name":"k1PurR","value":"0.00029"},{"units":"mM","information":"","name":"k2PurR","value":"0.00029"},{"units":"mM","information":"","name":"k3PurR","value":"0.0008"},{"units":"mM","information":"","name":"kdisPurRgua","value":"0.0015"},{"units":"mM","information":"","name":"kdisPurRhyp","value":"0.0093"},{"units":"mM/sec","information":"","name":"ks","value":"0.0000118"}]},{"scheme":"ADS -> fumarate + AMP","substrates":{"s1":{"theSubstance":{"name":"ADS","type":"substance","synonyms":["Adenylosuccinate","Adenylosuccinic acid","ADS","N6-(1,2-Dicarboxyethyl)AMP","N6-(1,2-Dicarboxyethyl)-AMP"],"links":[],"id":"SS0000083"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"fumarate","type":"substance","synonyms":["fum","fumarate","fumaric acid"],"links":[],"id":"SS0000180"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"AMP","type":"substance","synonyms":["5'-Adenosine monophosphate","5'-Adenylic acid","5'-AMP","Adenosine 5'-monophosphate","Adenosine 5'-phosphate","Adenylate","Adenylic acid","AMP"],"links":[],"id":"SS0000073"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PurB","type":"protein","synonyms":["5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole lyase [multifunctional]","Ade","Ade(h)","adenylosuccinate lyase","EC:4.3.2.2","PurB"],"links":[],"id":"SS0000181"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"(r1*kcat*(s1/kmads))/(1+(s1/kmads))","theSubMathModel":null,"theInformation":{"Mathematical model information":" Reaction follows Michaelis-Menten kinetics.\n ","Parameter set information":"  kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) \ncan be calculated from the whole model basing on the flow rate magnitude.  ","Parameter set links":" ID: Green et al., 1996 The purB gene of Escherichia coli K-12 is located in an operon ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8969519 ;","Structural model information":" Adenylosuccinate lyase (ASL), the product of the gene purB in E. coli, catalyzes two reactions in de novo purine nucleotide biosynthesis. In addition to the removal of fumarate from 5&apos;-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole, the enzyme also converts adenylosuccinate to AMP. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=AMPSYN-RXN ;"},"mmid":"MM0000088","psid":"PS0000085","gnid":"GN0000122","reversible":false,"information":{"Mathematical model information":" Reaction follows Michaelis-Menten kinetics.\n ","Parameter set information":"  kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) \ncan be calculated from the whole model basing on the flow rate magnitude.  ","Parameter set links":" ID: Green et al., 1996 The purB gene of Escherichia coli K-12 is located in an operon ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8969519 ;","Structural model information":" Adenylosuccinate lyase (ASL), the product of the gene purB in E. coli, catalyzes two reactions in de novo purine nucleotide biosynthesis. In addition to the removal of fumarate from 5&apos;-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole, the enzyme also converts adenylosuccinate to AMP. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=AMPSYN-RXN ;"},"parameters":[{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kmads","value":"0.0037"}]},{"scheme":"-> Nap","substrates":null,"products":{"p1":{"theSubstance":{"name":"Nap","type":"protein","synonyms":["EC:1.7.99.4","Nap","NapABC","periplasmic nitrate reductase"],"links":[],"id":"SS0000203"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"napA","type":"gene","synonyms":["b2202","b2203","b2204","b2205","b2206","napA","napB","napC","napG","napH"],"links":[],"id":"SS0000204"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"NO3","type":"substance","synonyms":["nitrate","NO3","NO3-"],"links":[],"id":"SS0000016"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"NO2","type":"substance","synonyms":["nitrite","NO2","NO2-"],"links":[],"id":"SS0000017"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"ks*((k0+ w11*(r2/k11)^h11 + w21*(r2/k21)^h21 + w31*(r3/k31)^h31*(1 + w4*(r2/k4)^h4))/(1 + (r2/k11)^h11 + (r2/k21)^h21 + (r3/k31)^h31*(1 + (r2/k4)^h4)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Only two promoters are essential for nitrate and nitrite induction of the napF operon. Nitrate causes repression of the napFp2 promoter in a NarL- or a NarP-protein-dependent way, whereas repression of the same promoter by nitrite is only dependent on the NarP protein. Only slight change in nap expression cam be observed so this promoter activity is not taken into account in the model. When nitrate is present in the medium nitrite do not cause activation of nap expression as it does when only nitrite is added, so term describing inhibition by nitrate is incorporated in the model [Stewart et al., 2003].","Mathematical model links":" ID: Stewart et al., 2003 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12644479 ;","Parameter set information":"There is no experimental data for k1. Other parameters were adaptated for nap expression data when nitrate and/or nitrite are added in the environment [Wang et al., 1999].","Parameter set links":" ID: Wang et al., 1999 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10464201 ;","Structural model information":"The napF operon apparently encodes a \"low-substrate-induced\" reductase that is maximally expressed only at low levels of extracellular nitrate and nitrite.","Structural model links":" ID: Wang et al., 1999. The napF and narG nitrate reductase operons in Escherichia coli are differentially expressed in response to submicromolar concentrations of nitrate but not nitrite. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10464201 ;"},"mmid":"MM0000261","psid":"PS0000250","gnid":"GN0000116","reversible":false,"information":{"Mathematical model information":"Only two promoters are essential for nitrate and nitrite induction of the napF operon. Nitrate causes repression of the napFp2 promoter in a NarL- or a NarP-protein-dependent way, whereas repression of the same promoter by nitrite is only dependent on the NarP protein. Only slight change in nap expression cam be observed so this promoter activity is not taken into account in the model. When nitrate is present in the medium nitrite do not cause activation of nap expression as it does when only nitrite is added, so term describing inhibition by nitrate is incorporated in the model [Stewart et al., 2003].","Mathematical model links":" ID: Stewart et al., 2003 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12644479 ;","Parameter set information":"There is no experimental data for k1. Other parameters were adaptated for nap expression data when nitrate and/or nitrite are added in the environment [Wang et al., 1999].","Parameter set links":" ID: Wang et al., 1999 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10464201 ;","Structural model information":"The napF operon apparently encodes a \"low-substrate-induced\" reductase that is maximally expressed only at low levels of extracellular nitrate and nitrite.","Structural model links":" ID: Wang et al., 1999. The napF and narG nitrate reductase operons in Escherichia coli are differentially expressed in response to submicromolar concentrations of nitrate but not nitrite. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10464201 ;"},"parameters":[{"units":"","information":"","name":"h11","value":"2.5"},{"units":"","information":"","name":"h21","value":"5.5"},{"units":"","information":"","name":"h31","value":"2.3"},{"units":"","information":"","name":"h4","value":"1"},{"units":"","information":"","name":"k0","value":"0.028"},{"units":"mM","information":"","name":"k11","value":"0.45"},{"units":"mM","information":"","name":"k21","value":"1"},{"units":"mM","information":"","name":"k31","value":"1.5"},{"units":"mM","information":"","name":"k4","value":"0.1"},{"units":"mM/s","information":"","name":"ks","value":"1"},{"units":"","information":"","name":"w11","value":"1.27"},{"units":"","information":"","name":"w21","value":"0.02"},{"units":"","information":"","name":"w31","value":"0.275"},{"units":"","information":"","name":"w4","value":"2.2"}]},{"scheme":"-> NRA","substrates":null,"products":{"p1":{"theSubstance":{"name":"NRA","type":"protein","synonyms":["EC:1.7.5.1","nitrate reductase A","NRA"],"links":[],"id":"SS0000018"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"narG","type":"gene","synonyms":["b1224","b1225","b1227","chlC","chlI","narC","narG","narH","narI"],"links":[],"id":"SS0000019"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"NO3","type":"substance","synonyms":["nitrate","NO3","NO3-"],"links":[],"id":"SS0000016"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"NO2","type":"substance","synonyms":["nitrite","NO2","NO2-"],"links":[],"id":"SS0000017"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"ks*((k0+ wno2*(r3/kno2)^hno2 + w1no3*(r2/k1no3)^h1no3 + w2no3*(r2/k2no3)^h2no3)/(1 + (r3/kno2)^hno2 + (r2/k1no3)^h1no3 + (r2/k2no3)^h2no3))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Expression of nar operon increases in response to nitrate and/or nitrite presence in the medium due to binding of activated NarL with eight nonintersecting sites. In the model for nitrite all sites were described as generalized one. Opposite, when nitrate is present dependence of expression on substrate concentration represent a sigmoid curve [Wang et al., 1999] that may be caused mutual influence of NarL sites, that was described in the model as action of two sites of NarL with different characteristics.","Parameter set information":"There is no experimental data for k1. Other parameters were adaptated for nar operon  expression data when nitrate or nitrite are added in the environment [Wang et al., 1999].","Parameter set links":" ID: Wang et al., 1999 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10464201 ;","Structural model information":" Expression of narGHI operon is activated in anaerobic conditions by nitrate and more slightly by nitrite present in the medium. ","Structural model links":" ID: Wang et al., 1999. The napF and narG nitrate reductase operons in Escherichia coli are differentially expressed in response to submicromolar concentrations of nitrate but not nitrite. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10464201 ;"},"mmid":"MM0000259","psid":"PS0000249","gnid":"GN0000014","reversible":false,"information":{"Mathematical model information":"Expression of nar operon increases in response to nitrate and/or nitrite presence in the medium due to binding of activated NarL with eight nonintersecting sites. In the model for nitrite all sites were described as generalized one. Opposite, when nitrate is present dependence of expression on substrate concentration represent a sigmoid curve [Wang et al., 1999] that may be caused mutual influence of NarL sites, that was described in the model as action of two sites of NarL with different characteristics.","Parameter set information":"There is no experimental data for k1. Other parameters were adaptated for nar operon  expression data when nitrate or nitrite are added in the environment [Wang et al., 1999].","Parameter set links":" ID: Wang et al., 1999 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10464201 ;","Structural model information":" Expression of narGHI operon is activated in anaerobic conditions by nitrate and more slightly by nitrite present in the medium. ","Structural model links":" ID: Wang et al., 1999. The napF and narG nitrate reductase operons in Escherichia coli are differentially expressed in response to submicromolar concentrations of nitrate but not nitrite. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10464201 ;"},"parameters":[{"units":"","information":"","name":"h1no3","value":"2"},{"units":"","information":"","name":"h2no3","value":"17"},{"units":"","information":"","name":"hno2","value":"2.8"},{"units":"","information":"","name":"k0","value":"0.01"},{"units":"mM","information":"","name":"k1no3","value":"3.5"},{"units":"mM","information":"","name":"k2no3","value":"4.8"},{"units":"mM","information":"","name":"kno2","value":"3.5"},{"units":"mM/s","information":"","name":"ks","value":"1"},{"units":"","information":"","name":"w1no3","value":"0.6"},{"units":"","information":"","name":"w2no3","value":"1"},{"units":"","information":"","name":"wno2","value":"0.228"}]},{"scheme":"-> PurF","substrates":null,"products":{"p1":{"theSubstance":{"name":"PurF","type":"protein","synonyms":["PurF"],"links":[],"id":"SS0000372"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"purF","type":"gene","synonyms":["b2312","purF"],"links":[],"id":"SS0000396"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"PurR","type":"protein","synonyms":["PurR","PurR transcriptional repressor"],"links":[],"id":"SS0000358"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"Gua","type":"substance","synonyms":["Gua","Guanosine"],"links":[],"id":"SS0000113"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"ks*((1+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR))/(1+((((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k1PurR)+((((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k2PurR)+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Meng et al., 1990].","Mathematical model links":" ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Parameter set information":" Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurF = 0, where PurF - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter cvpAp1. ks - protein synthesis generalized constant from the promoter cvpAp1. kd = 0.002 [1/sec],PurF = 0.006047 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data. ","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Structural model information":" Expression of the purine biosynthetic gene purF is  repressed  by  purines (guanine and hypoxanthine) in  wild-type cells of Escherichia coli. This regulation is carried out through a protein PurR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]. ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;"},"mmid":"MM0000233","psid":"PS0000223","gnid":"GN0000224","reversible":false,"information":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Meng et al., 1990].","Mathematical model links":" ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Parameter set information":" Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurF = 0, where PurF - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter cvpAp1. ks - protein synthesis generalized constant from the promoter cvpAp1. kd = 0.002 [1/sec],PurF = 0.006047 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data. ","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;","Structural model information":" Expression of the purine biosynthetic gene purF is  repressed  by  purines (guanine and hypoxanthine) in  wild-type cells of Escherichia coli. This regulation is carried out through a protein PurR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]. ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ;"},"parameters":[{"units":"mM","information":"","name":"k1PurR","value":"0.00034"},{"units":"mM","information":"","name":"k2PurR","value":"0.00034"},{"units":"mM","information":"","name":"k3PurR","value":"0.0008"},{"units":"mM","information":"","name":"kdisPurRgua","value":"0.0015"},{"units":"mM","information":"","name":"kdisPurRhyp","value":"0.0093"},{"units":"mM/sec","information":"","name":"ks","value":"0.000012"}]},{"scheme":"melTHF + dUMP -> dTMP + dihydrofolate + H+","substrates":{"s1":{"theSubstance":{"name":"melTHF","type":"substance","synonyms":["5,10-methylenetetrahydrofolate","5,10-methylene-THF","melTHF","N5,N10-methylenetetrahydrofolate"],"links":[],"id":"SS0000164"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"dUMP","type":"substance","synonyms":["2'-Deoxyuridine 5'-phosphate","Deoxyuridine 5'-phosphate","Deoxyuridine monophosphate","Deoxyuridylic acid","dUMP"],"links":[],"id":"SS0000050"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"dTMP","type":"substance","synonyms":["Deoxythymidine 5'-phosphate","Deoxythymidylic acid","dTMP","Thymidine 5'-phosphate","Thymidine monophosphate","Thymidylate","Thymidylic acid"],"links":[],"id":"SS0000054"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"DHF","type":"substance","synonyms":["7,8-dihydrofolate","7,8-dihydropteroylglutamate","DHF","dihydrofolate","FH2","H2PteGlu","H2PteGlu1"],"links":[],"id":"SS0000165"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"ThyA","type":"protein","synonyms":["EC:2.1.1.45","ThyA","thymidylate synthase"],"links":[],"id":"SS0000192"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"(r1*kcat*s1*s2)/(k019*kms1+kms2*s1+kms1*s2+s1*s2)","theSubMathModel":null,"theInformation":{"Mathematical model information":" The equation is written in the article [Spenser et al., 1997] ","Mathematical model links":" ID: Spencer et al., 1997 Kinetic scheme for thymidylate synthase from Escherichia coli: determination from measurements of ligand binding, primary and secondary isotope effects, and pre-steady-state catalysis. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9100016 ;","Parameter set information":"  Values of the parameters were determined by fitting steady-state initial velocity data to the equation for an ordered bi-reactant mechanism [Spenser et al., 2007]. kcat equals to 1 as there are different publications using different values of the rate constant of the enzyme: 1.9 (1/sec) [Spenser et al., 1997]. However, the most publications do not indicate the used concentrations of the enzyme. In spite of this fact Vmax=kcat*r1 (where r1 is the enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. ","Parameter set links":" ID: Spencer et al., 1997 Kinetic scheme for thymidylate synthase from Escherichia coli: determination from measurements of ligand binding, primary and secondary isotope effects, and pre-steady-state catalysis ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9100016 ;","Structural model information":" Thymidylate synthase plays a key role in DNA synthesis. The conversion of dUMP to dTMP is the main pathway of de novo dTMP synthesis in the cell. The enzyme undergoes conformational changes during the initial binding of dUMP, with even larger changes during the binding of the cofactor. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=THYMIDYLATESYN-RXN ;"},"mmid":"MM0000066","psid":"PS0000060","gnid":"GN0000071","reversible":false,"information":{"Mathematical model information":" The equation is written in the article [Spenser et al., 1997] ","Mathematical model links":" ID: Spencer et al., 1997 Kinetic scheme for thymidylate synthase from Escherichia coli: determination from measurements of ligand binding, primary and secondary isotope effects, and pre-steady-state catalysis. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9100016 ;","Parameter set information":"  Values of the parameters were determined by fitting steady-state initial velocity data to the equation for an ordered bi-reactant mechanism [Spenser et al., 2007]. kcat equals to 1 as there are different publications using different values of the rate constant of the enzyme: 1.9 (1/sec) [Spenser et al., 1997]. However, the most publications do not indicate the used concentrations of the enzyme. In spite of this fact Vmax=kcat*r1 (where r1 is the enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. ","Parameter set links":" ID: Spencer et al., 1997 Kinetic scheme for thymidylate synthase from Escherichia coli: determination from measurements of ligand binding, primary and secondary isotope effects, and pre-steady-state catalysis ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9100016 ;","Structural model information":" Thymidylate synthase plays a key role in DNA synthesis. The conversion of dUMP to dTMP is the main pathway of de novo dTMP synthesis in the cell. The enzyme undergoes conformational changes during the initial binding of dUMP, with even larger changes during the binding of the cofactor. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=THYMIDYLATESYN-RXN ;"},"parameters":[{"units":"mM","information":"","name":"k019","value":"0.0042"},{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kms1","value":"0.011"},{"units":"mM","information":"","name":"kms2","value":"0.0012"}]},{"scheme":"-> PurA","substrates":null,"products":{"p1":{"theSubstance":{"name":"PurA","type":"protein","synonyms":["PurA"],"links":[],"id":"SS0000383"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"purA","type":"gene","synonyms":["b4177","purA"],"links":[],"id":"SS0000406"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"PurR","type":"protein","synonyms":["PurR","PurR transcriptional repressor"],"links":[],"id":"SS0000358"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"Gua","type":"substance","synonyms":["Gua","Guanosine"],"links":[],"id":"SS0000113"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"MarA","type":"protein","synonyms":["MarA"],"links":[],"id":"SS0000409"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"ks*((1+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR))/(1+((((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k1PurR)+((((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k2PurR)+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR)))*(1/(1+(r5/kMarA)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the articles [He and Zalkin, 1994, Schneiders et al., 2004].","Mathematical model links":" ID: He B., Zalkin H., 1994 Regulation of Escherichia coli purA by purine repressor, one component of a dual control mechanism. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8106311 ; ID: Schneiders T. et al., 2004 The Escherichia coli transcriptional regulator MarA directly represses transcription of purA and hdeA. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/14701822 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurA = 0, where PurA - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter purAp. ks - protein synthesis generalized constant from the promoter purAp. kd = 0.002 [1/sec],PurA = 0.0135836 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [He B. and Zalkin H. 1994] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data. Parameter kMarA was evaluated basing on [Schneiders T. et al., 2004] experimental data.","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: He B., Zalkin H., 1994 Regulation of Escherichia coli purA by purine repressor, one component of a dual control mechanism. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8106311 ; ID: Schneiders T. et al., 2004 The Escherichia coli transcriptional regulator MarA directly represses transcription of purA and hdeA. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/14701822 ;","Structural model information":" The gene purA encodes the structure of the enzyme adenylosuccinate synthetase (ASSase, EC 6.3.4.4). The enzyme is a homodimer and is involved in the synthesis of inosine monophosphate (IMP). Transcription factors PurR and MarA negatively affect on purA gene expression  [He and Zalkin, 1994, Schneiders et al., 2004]. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]. The concentration of MarA (monomer) = 0.00145 mM [calculation from the work of Lu, 2007].  \n ","Structural model links":" ID: He B., Zalkin H., 1994 Regulation of Escherichia coli purA by purine repressor, one component of a dual control mechanism. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8106311 ; ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Schneiders T. et al., 2004 The Escherichia coli transcriptional regulator MarA directly represses transcription of purA and hdeA. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/14701822 ;"},"mmid":"MM0000244","psid":"PS0000234","gnid":"GN0000234","reversible":false,"information":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the articles [He and Zalkin, 1994, Schneiders et al., 2004].","Mathematical model links":" ID: He B., Zalkin H., 1994 Regulation of Escherichia coli purA by purine repressor, one component of a dual control mechanism. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8106311 ; ID: Schneiders T. et al., 2004 The Escherichia coli transcriptional regulator MarA directly represses transcription of purA and hdeA. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/14701822 ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PurA = 0, where PurA - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter purAp. ks - protein synthesis generalized constant from the promoter purAp. kd = 0.002 [1/sec],PurA = 0.0135836 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [He B. and Zalkin H. 1994] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data. Parameter kMarA was evaluated basing on [Schneiders T. et al., 2004] experimental data.","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: He B., Zalkin H., 1994 Regulation of Escherichia coli purA by purine repressor, one component of a dual control mechanism. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8106311 ; ID: Schneiders T. et al., 2004 The Escherichia coli transcriptional regulator MarA directly represses transcription of purA and hdeA. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/14701822 ;","Structural model information":" The gene purA encodes the structure of the enzyme adenylosuccinate synthetase (ASSase, EC 6.3.4.4). The enzyme is a homodimer and is involved in the synthesis of inosine monophosphate (IMP). Transcription factors PurR and MarA negatively affect on purA gene expression  [He and Zalkin, 1994, Schneiders et al., 2004]. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]. The concentration of MarA (monomer) = 0.00145 mM [calculation from the work of Lu, 2007].  \n ","Structural model links":" ID: He B., Zalkin H., 1994 Regulation of Escherichia coli purA by purine repressor, one component of a dual control mechanism. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8106311 ; ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Schneiders T. et al., 2004 The Escherichia coli transcriptional regulator MarA directly represses transcription of purA and hdeA. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/14701822 ;"},"parameters":[{"units":"mM","information":"","name":"k1PurR","value":"0.00069"},{"units":"mM","information":"","name":"k2PurR","value":"0.00069"},{"units":"mM","information":"","name":"k3PurR","value":"0.0008"},{"units":"mM","information":"","name":"kMarA","value":"0.00016"},{"units":"mM","information":"","name":"kdisPurRgua","value":"0.0015"},{"units":"mM","information":"","name":"kdisPurRhyp","value":"0.0093"},{"units":"mM/sec","information":"","name":"ks","value":"0.00027"}]},{"scheme":"ADP + Pi + H+ <=> ATP + H2O + H+","substrates":{"s1":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"Pi","type":"substance","synonyms":["H3PO4","Orthophosphate","Orthophosphoric acid","Phosphate","Phosphoric acid","Pi"],"links":[],"id":"SS0000070"},"theState":null,"compartment":""},"s3":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"ATP synthase","type":"protein","synonyms":["adenosinetriphosphatase","ATP synthase","ATP synthase F1F0","EC:3.6.3.14","F0 complex","F0F1-ATPase","F-1F-0-type ATPase","FoF1-ATPase"],"links":[],"id":"SS0000202"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"r1*kcat*(s1/kmadp21)/(1+(s1/kmadp21))","theSubMathModel":null,"theInformation":{"Mathematical model information":"  Reaction follows Michaelis-Menten kinetics. We consider a mathematical model without metal ions, assuming that their concentration is constant ","Parameter set information":"   kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) \ncan be calculated from the whole model basing on the flow rate magnitude. Parameter was evaluated basing on [Bald et al., 1998] experimental data.  ","Parameter set links":" ID: Bald et al., 1998 ATP synthesis by F0F1-ATP synthase independent of noncatalytic nucleotide binding sites and insensitive to azide inhibition ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9422743 ;","Structural model information":" ATP synthase catalyzes the synthesis of ATP under aerobic cell growth. The energy derived from oxygen respiration is coupled to ATP synthesis by a process known as electron transport-linked phosphorylation. Under anaerobic growth conditions an electrochemical proton gradient can also be generated using a number of alternative electron acceptors and ATP synthase can also synthesize ATP under these conditions. During fermentation however, ATP is synthesized only by substrate-level phosphorylation reactions. ATP synthase catalyzes the hydrolysis of ATP under these conditions to generate the electrochemical proton gradient needed for other membrane functions. The enzyme is comprised of two subcomplexes known as F-1 and F-O. The F-1 complex contains the catalytic sites and consists of five subunits in a stoichiometry of 3:3:1:1:1. The F-O complex is membrane-embedded and forms the proton channel through the membrane. This complex consists of three subunits in a stoichiometry of 1:2:10-18.\ns3 is outer H+. \np3 is inner H+ .  ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=ATPSYN-RXN ;"},"mmid":"MM0000096","psid":"PS0000092","gnid":"GN0000129","reversible":true,"information":{"Mathematical model information":"  Reaction follows Michaelis-Menten kinetics. We consider a mathematical model without metal ions, assuming that their concentration is constant ","Parameter set information":"   kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) \ncan be calculated from the whole model basing on the flow rate magnitude. Parameter was evaluated basing on [Bald et al., 1998] experimental data.  ","Parameter set links":" ID: Bald et al., 1998 ATP synthesis by F0F1-ATP synthase independent of noncatalytic nucleotide binding sites and insensitive to azide inhibition ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9422743 ;","Structural model information":" ATP synthase catalyzes the synthesis of ATP under aerobic cell growth. The energy derived from oxygen respiration is coupled to ATP synthesis by a process known as electron transport-linked phosphorylation. Under anaerobic growth conditions an electrochemical proton gradient can also be generated using a number of alternative electron acceptors and ATP synthase can also synthesize ATP under these conditions. During fermentation however, ATP is synthesized only by substrate-level phosphorylation reactions. ATP synthase catalyzes the hydrolysis of ATP under these conditions to generate the electrochemical proton gradient needed for other membrane functions. The enzyme is comprised of two subcomplexes known as F-1 and F-O. The F-1 complex contains the catalytic sites and consists of five subunits in a stoichiometry of 3:3:1:1:1. The F-O complex is membrane-embedded and forms the proton channel through the membrane. This complex consists of three subunits in a stoichiometry of 1:2:10-18.\ns3 is outer H+. \np3 is inner H+ .  ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=ATPSYN-RXN ;"},"parameters":[{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kmadp21","value":"0.41"}]},{"scheme":"caasp + H+ <=> doroa + H2O","substrates":{"s1":{"theSubstance":{"name":"caasp","type":"substance","synonyms":["caasp","N-Carbamoyl-L-aspartate"],"links":[],"id":"SS0000030"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"doroa","type":"substance","synonyms":["Dihydro-L-orotic acid","doroa","L-Dihydroorotate","L-Dihydroorotic acid","(S)-4,5-Dihydroorotate","(S)-Dihydroorotate"],"links":[],"id":"SS0000031"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PyrC","type":"protein","synonyms":["dihydroorotase","PyrC"],"links":[],"id":"SS0000366"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"(kcat*r1*(s1/Kmcaasp))/(1+(s1/Kmcaasp))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis Menten kinetics.","Mathematical model links":" ID: Daniel et al., 1996 Assay of Escherichia coli dihydroorotase with enantiomeric substrate: practical preparation of carbamyl L-aspartate and high-performance liquid chromatography analysis of catalysis product. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8811890 ;","Parameter set information":"Parameters kcat and Kmcaasp were taken from Washabaugh and Collins article. The model was simulated upon steady state concentration of PyrC enzyme, which equals 0.0018 mM (Lu et al., 2007).","Parameter set links":" ID: Daniel et al., 1996 Assay of Escherichia coli dihydroorotase with enantiomeric substrate: practical preparation of carbamyl L-aspartate and high-performance liquid chromatography analysis of catalysis product. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8811890 ; ID: Lee M et al., 2005 Dihydroorotase from Escherichia coli: loop movement and cooperativity between subunits. J Mol Biol. 2005 May 6;348(3):523-33. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/15826651 ; ID: Lu P. et al., 2007. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nature Biotechnology, 2007. 25(1), 117-124. PMID: 17187058 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Porter TN et al., 2004 Mechanism of the dihydroorotase reaction. Biochemistry. 2004 Dec 28;43(51):16285-92. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/15610022 ; ID: Washabaugh MW, Collins KD 1984 Dihydroorotase from Escherichia coli. Purification and characterization. J Biol Chem. 1984 Mar 10;259(5):3293-8 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6142052 ;","Structural model information":"Dihydroorotase (PyrC) catalyzes the cyclization of carbamoyl-aspartate to dihydroorotate, the third reaction in the pathway for de novo biosynthesis of pyrimidine nucleotides. Subunit composition of dihydroorotase = [PyrC]2. The enzyme is of particular interest because of its potential as an antimalarial drug target.","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=DIHYDROOROT-RXN ; ID: Lee M et al., 2005 Dihydroorotase from Escherichia coli: loop movement and cooperativity between subunits. J Mol Biol. 2005 May 6;348(3):523-33. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/15826651 ; ID: Porter TN et al., 2004 Mechanism of the dihydroorotase reaction. Biochemistry. 2004 Dec 28;43(51):16285-92. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/15610022 ; ID: Washabaugh MW, Collins KD 1984 Dihydroorotase from Escherichia coli. Purification and characterization. J Biol Chem. 1984 Mar 10;259(5):3293-8 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6142052 ;"},"mmid":"MM0000193","psid":"PS0000187","gnid":"GN0000184","reversible":true,"information":{"Mathematical model information":"Reaction follows Michaelis Menten kinetics.","Mathematical model links":" ID: Daniel et al., 1996 Assay of Escherichia coli dihydroorotase with enantiomeric substrate: practical preparation of carbamyl L-aspartate and high-performance liquid chromatography analysis of catalysis product. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8811890 ;","Parameter set information":"Parameters kcat and Kmcaasp were taken from Washabaugh and Collins article. The model was simulated upon steady state concentration of PyrC enzyme, which equals 0.0018 mM (Lu et al., 2007).","Parameter set links":" ID: Daniel et al., 1996 Assay of Escherichia coli dihydroorotase with enantiomeric substrate: practical preparation of carbamyl L-aspartate and high-performance liquid chromatography analysis of catalysis product. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8811890 ; ID: Lee M et al., 2005 Dihydroorotase from Escherichia coli: loop movement and cooperativity between subunits. J Mol Biol. 2005 May 6;348(3):523-33. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/15826651 ; ID: Lu P. et al., 2007. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nature Biotechnology, 2007. 25(1), 117-124. PMID: 17187058 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Porter TN et al., 2004 Mechanism of the dihydroorotase reaction. Biochemistry. 2004 Dec 28;43(51):16285-92. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/15610022 ; ID: Washabaugh MW, Collins KD 1984 Dihydroorotase from Escherichia coli. Purification and characterization. J Biol Chem. 1984 Mar 10;259(5):3293-8 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6142052 ;","Structural model information":"Dihydroorotase (PyrC) catalyzes the cyclization of carbamoyl-aspartate to dihydroorotate, the third reaction in the pathway for de novo biosynthesis of pyrimidine nucleotides. Subunit composition of dihydroorotase = [PyrC]2. The enzyme is of particular interest because of its potential as an antimalarial drug target.","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=DIHYDROOROT-RXN ; ID: Lee M et al., 2005 Dihydroorotase from Escherichia coli: loop movement and cooperativity between subunits. J Mol Biol. 2005 May 6;348(3):523-33. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/15826651 ; ID: Porter TN et al., 2004 Mechanism of the dihydroorotase reaction. Biochemistry. 2004 Dec 28;43(51):16285-92. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/15610022 ; ID: Washabaugh MW, Collins KD 1984 Dihydroorotase from Escherichia coli. Purification and characterization. J Biol Chem. 1984 Mar 10;259(5):3293-8 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6142052 ;"},"parameters":[{"units":"mM","information":"","name":"Kmcaasp","value":"1.07"},{"units":"1/sec","information":"","name":"kcat","value":"195"}]},{"scheme":"-> GuaB","substrates":null,"products":{"p1":{"theSubstance":{"name":"GuaB","type":"protein","synonyms":["GuaB"],"links":[],"id":"SS0000384"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"guaB","type":"gene","synonyms":["guaB"],"links":[],"id":"SS0000408"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"PurR","type":"protein","synonyms":["PurR","PurR transcriptional repressor"],"links":[],"id":"SS0000358"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"Gua","type":"substance","synonyms":["Gua","Guanosine"],"links":[],"id":"SS0000113"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"CRP","type":"protein","synonyms":["CRP"],"links":[],"id":"SS0000393"},"theState":null,"compartment":"","theInfluence":"activator"},"r6":{"theSubstance":{"name":"cAMP","type":"substance","synonyms":["3',5'-Cyclic AMP","Adenosine 3',5'-cyclic phosphate","Adenosine 3',5'-phosphate","cAMP","Cyclic adenylic acid","Cyclic AMP"],"links":[],"id":"SS0000074"},"theState":null,"compartment":"","theInfluence":"activator"},"r7":{"theSubstance":{"name":"DnaA","type":"protein","synonyms":["DnaA"],"links":[],"id":"SS0000390"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r8":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r9":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"ks*((1+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR))/(1+((((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k1PurR)+((((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))/k2PurR)+((r2-(((r2*(r3^2))/(kdisPurRhyp^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2))))-(((r2*(r4^2))/(kdisPurRgua^2))/(1+((2*r2*r3+r3^2)/(kdisPurRhyp^2))+((2*r2*r4+r4^2)/(kdisPurRgua^2)))))/k3PurR)))*((1+(k1CRP*(((((r5*(r6^2))/(kdisCRPcAMP^2))/(1+((2*r5*r6+(r6^2))/(kdisCRPcAMP^2))))/k2CRP)^hCRP)))/(1+((((r5*(r6^2))/(kdisCRPcAMP^2))/(1+((2*r5*r6+(r6^2))/(kdisCRPcAMP^2))))/k2CRP)))*(1/(1+((((k0*(((r7*r8)/kdisDnaAATP)/(1+((r7*r8)/kdisDnaAATP)+((r7*r9)/kdisDnaAADP))))^3)/((kdisDnaA^2)+3*((k0*(((r7*r8)/kdisDnaAATP)/(1+((r7*r8)/kdisDnaAATP)+((r7*r9)/kdisDnaAADP))))^2)))/kDnaA)))","theSubMathModel":null,"theInformation":{"Mathematical model information":" The structural model is developed on the basis of kinetic data from the articles [Meng et al., 1990; Tesfa-Selase and Drabble W.T., 1992; Hutchings and Drabble, 2000]. ","Mathematical model links":" ID: Hutchings M.I., Drabble W.T., 2000 Regulation of the divergent guaBA and xseA promoters of Escherichia coli by the cyclic AMP receptor protein. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10856643 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ; ID: Tesfa-Selase F., Drabble W.T., 1992 Regulation of the gua operon of Escherichia coli by the DnaA protein. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1736096 ;","Parameter set information":" Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*GuaB = 0, where GuaB - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter guaBp. ks - protein synthesis generalized constant from the promoter guaBp. kd = 0.002 [1/sec],GuaB = 0.0051671 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data. Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data. Parameters k1CRP, k2CRP and hCRP were evaluated basing on [Hutchings M.I., Drabble W.T., 2000] experimental data. Parameter kdisCRPcAMP is taken from article [Malecki et al., 2000]. Parameters kdisDnaAATP, and kdisDnaAADP are taken from article [Kaguni, 2006]. Parameter kdisDnaA was evaluated basing on [Olliver et al., 2010] experimental data. ","Parameter set links":" ID: Hutchings M.I., Drabble W.T., 2000 Regulation of the divergent guaBA and xseA promoters of Escherichia coli by the cyclic AMP receptor protein. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10856643 ; ID: Kaguni J.M., 2006 DnaA: controlling the initiation of bacterial DNA replication and more. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16753031 ; ID: Malecki J. et al., 2000 Kinetic studies of cAMP-induced allosteric changes in cyclic AMP receptor protein from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10722684 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ; ID: Olliver A. et al., 2010 DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/20487274 ;","Structural model information":"   Genes  guaA and guaB encodes the structure of the subunits of enzymes GMP synthetase(GMPSase, EC 6.3.5.2) and IMP dehydrogenase(IMPDase, EC 1.1.1.205), respectively, and are part of an operon guaAB. Regulation of expression of the operon guaBA positively controlled by transcription factor CRP [Hutchings and Drabble, 2000] and negatively PurR and DnaA [Meng et al., 1990; Tesfa-Selase et al., 1992]. Here we consider the process of synthesis protein GuaB with the promoter guaBp. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]. The concentration of DnaA (monomer) = 0.0017 mM [Ali Azam et al., 1999]. The concentration of CRP (dimer) = 0.0013445 mM [calculation from the work of Lu, 2007].   The concentration of cAMP = 0.01 mM [Notley - McRobb et al., 1997].    ","Structural model links":" ID: Ali Azam et al., 1999 Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10515926 ; ID: Hutchings M.I., Drabble W.T. 2000 Regulation of the divergent guaBA and xseA promoters of Escherichia coli by the cyclic AMP receptor protein. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10856643 ; ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ; ID: Notley - McRobb et al., 1997 The relationship between external glucose concentration and cAMP levels inside Escherichia coli: implications for models of phosphotransferase-mediated regulation of adenylate cyclase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9202467 ; ID: Tesfa-Selase F., Drabble W.T., 1992 Regulation of the gua operon of Escherichia coli by the DnaA protein. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1736096 ;"},"mmid":"MM0000245","psid":"PS0000235","gnid":"GN0000235","reversible":false,"information":{"Mathematical model information":" The structural model is developed on the basis of kinetic data from the articles [Meng et al., 1990; Tesfa-Selase and Drabble W.T., 1992; Hutchings and Drabble, 2000]. ","Mathematical model links":" ID: Hutchings M.I., Drabble W.T., 2000 Regulation of the divergent guaBA and xseA promoters of Escherichia coli by the cyclic AMP receptor protein. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10856643 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ; ID: Tesfa-Selase F., Drabble W.T., 1992 Regulation of the gua operon of Escherichia coli by the DnaA protein. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1736096 ;","Parameter set information":" Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*GuaB = 0, where GuaB - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter guaBp. ks - protein synthesis generalized constant from the promoter guaBp. kd = 0.002 [1/sec],GuaB = 0.0051671 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters k1PurR and k2PurR were evaluated basing on [Meng et al., 1990] experimental data. Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data. Parameters k1CRP, k2CRP and hCRP were evaluated basing on [Hutchings M.I., Drabble W.T., 2000] experimental data. Parameter kdisCRPcAMP is taken from article [Malecki et al., 2000]. Parameters kdisDnaAATP, and kdisDnaAADP are taken from article [Kaguni, 2006]. Parameter kdisDnaA was evaluated basing on [Olliver et al., 2010] experimental data. ","Parameter set links":" ID: Hutchings M.I., Drabble W.T., 2000 Regulation of the divergent guaBA and xseA promoters of Escherichia coli by the cyclic AMP receptor protein. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10856643 ; ID: Kaguni J.M., 2006 DnaA: controlling the initiation of bacterial DNA replication and more. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16753031 ; ID: Malecki J. et al., 2000 Kinetic studies of cAMP-induced allosteric changes in cyclic AMP receptor protein from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10722684 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ; ID: Olliver A. et al., 2010 DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/20487274 ;","Structural model information":"   Genes  guaA and guaB encodes the structure of the subunits of enzymes GMP synthetase(GMPSase, EC 6.3.5.2) and IMP dehydrogenase(IMPDase, EC 1.1.1.205), respectively, and are part of an operon guaAB. Regulation of expression of the operon guaBA positively controlled by transcription factor CRP [Hutchings and Drabble, 2000] and negatively PurR and DnaA [Meng et al., 1990; Tesfa-Selase et al., 1992]. Here we consider the process of synthesis protein GuaB with the promoter guaBp. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]. The concentration of DnaA (monomer) = 0.0017 mM [Ali Azam et al., 1999]. The concentration of CRP (dimer) = 0.0013445 mM [calculation from the work of Lu, 2007].   The concentration of cAMP = 0.01 mM [Notley - McRobb et al., 1997].    ","Structural model links":" ID: Ali Azam et al., 1999 Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10515926 ; ID: Hutchings M.I., Drabble W.T. 2000 Regulation of the divergent guaBA and xseA promoters of Escherichia coli by the cyclic AMP receptor protein. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10856643 ; ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Meng et al., 1990 Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2404765 ; ID: Notley - McRobb et al., 1997 The relationship between external glucose concentration and cAMP levels inside Escherichia coli: implications for models of phosphotransferase-mediated regulation of adenylate cyclase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9202467 ; ID: Tesfa-Selase F., Drabble W.T., 1992 Regulation of the gua operon of Escherichia coli by the DnaA protein. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1736096 ;"},"parameters":[{"units":"","information":"","name":"hCRP","value":"5"},{"units":"","information":"","name":"k0","value":"0.12"},{"units":"","information":"","name":"k1CRP","value":"3.471"},{"units":"mM","information":"","name":"k1PurR","value":"0.0006"},{"units":"mM","information":"","name":"k2CRP","value":"0.0006"},{"units":"mM","information":"","name":"k2PurR","value":"0.0006"},{"units":"mM","information":"","name":"k3PurR","value":"0.0008"},{"units":"mM","information":"","name":"kDnaA","value":"0.01"},{"units":"mM","information":"","name":"kdisCRPcAMP","value":"0.0275"},{"units":"mM","information":"","name":"kdisDnaA","value":"0.00134"},{"units":"mM","information":"","name":"kdisDnaAADP","value":"0.0001"},{"units":"mM","information":"","name":"kdisDnaAATP","value":"0.00003"},{"units":"mM","information":"","name":"kdisPurRgua","value":"0.0015"},{"units":"mM","information":"","name":"kdisPurRhyp","value":"0.0093"},{"units":"mM/sec","information":"","name":"ks","value":"0.0000129"}]},{"scheme":"doroa + a quinone <=> oroa + a quinol","substrates":{"s1":{"theSubstance":{"name":"doroa","type":"substance","synonyms":["Dihydro-L-orotic acid","doroa","L-Dihydroorotate","L-Dihydroorotic acid","(S)-4,5-Dihydroorotate","(S)-Dihydroorotate"],"links":[],"id":"SS0000031"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"a quinone","type":"substance","synonyms":["a quinone","Q","quinone"],"links":[],"id":"SS0000146"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"oroa","type":"substance","synonyms":["oroa","Orotate","Orotic acid","Uracil-6-carboxylic acid"],"links":[],"id":"SS0000020"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"a quinol","type":"substance","synonyms":["a hydroquinone","a quinol","a reduced quinone","QH2"],"links":[],"id":"SS0000147"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PyrD","type":"protein","synonyms":["dihydroorotate dehydrogenase","PyrD"],"links":[],"id":"SS0000367"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"r1*(kcatf*(s1/Kmdoroa)*(s2/Kmq)-kcatr*(p1/Kmoroa)*(p2/Kmqh2))/((1+(s2/Kmq)+(p2/Kmqh2))*(1+(s1/Kmdoroa)*(1+(p1/Koroa))+(p1/Kmoroa)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"This reaction is reversible and works by two-site ping-pong mechanism.","Mathematical model links":" ID: Bjornberg et al., 1999 The activity of Escherichia coli dihydroorotate dehydrogenase is dependent on a conserved loop identified by sequence homology, mutagenesis, and limited proteolysis. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10074342 ;","Parameter set information":"Parameters Kcatf, Kmdoroa, Kmq and Koroa were extracted from Bjornberg et al. article. Parameters kcatr, Kmoroa and Kmqh2 were estimated upon model fitting. Moreover, to simulate the enzymatic kinetics you can use steady-state concentrations for Q=0.09 mM (Shestopalov et al., 1997; Bekker et al., 2007). The model was simulated upon steady state concentration of PyrD enzyme, which equals 0.0025 mM (Lu et al., 2007).","Parameter set links":" ID: Bekker M et al. 2007 Changes in the redox state and composition of the quinone pool of Escherichia coli during aerobic batch-culture growth. Microbiology. 2007 Jun;153(Pt 6):1974-80. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=17526854 ; ID: Bjornberg et al., 1999 The activity of Escherichia coli dihydroorotate dehydrogenase is dependent on a conserved loop identified by sequence homology, mutagenesis, and limited proteolysis. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10074342 ; ID: Lu P et al. 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol. 2007 Jan;25(1):117-24. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=17187058 ; ID: Shestopalov AI et al. 1997 Aeration-dependent changes in composition of the quinone pool in Escherichia coli. Evidence of post-transcriptional regulation of the quinone biosynthesis. FEBS Lett. 1997 Mar 10;404(2-3):272-4. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=9119077 ;","Structural model information":"Dihydroorotate dehydrogenase catalyzes the oxidation of dihydroorotate to orotate in the pathway for de novo biosynthesis of pyrimidine nucleotides. The enzyme has a homodimer structural organization and works by a two-site ping-pong mechanism (Bjornberg et al., 1999).","Structural model links":" ID: Bjornberg et al. 1999 The activity of Escherichia coli dihydroorotate dehydrogenase is dependent on a conserved loop identified by sequence homology, mutagenesis, and limited proteolysis. Biochemistry. 1999 Mar 9;38(10):2899-908 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=10074342 ; ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=DIHYDROOROTOX-MONOMER ;"},"mmid":"MM0000194","psid":"PS0000188","gnid":"GN0000185","reversible":true,"information":{"Mathematical model information":"This reaction is reversible and works by two-site ping-pong mechanism.","Mathematical model links":" ID: Bjornberg et al., 1999 The activity of Escherichia coli dihydroorotate dehydrogenase is dependent on a conserved loop identified by sequence homology, mutagenesis, and limited proteolysis. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10074342 ;","Parameter set information":"Parameters Kcatf, Kmdoroa, Kmq and Koroa were extracted from Bjornberg et al. article. Parameters kcatr, Kmoroa and Kmqh2 were estimated upon model fitting. Moreover, to simulate the enzymatic kinetics you can use steady-state concentrations for Q=0.09 mM (Shestopalov et al., 1997; Bekker et al., 2007). The model was simulated upon steady state concentration of PyrD enzyme, which equals 0.0025 mM (Lu et al., 2007).","Parameter set links":" ID: Bekker M et al. 2007 Changes in the redox state and composition of the quinone pool of Escherichia coli during aerobic batch-culture growth. Microbiology. 2007 Jun;153(Pt 6):1974-80. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=17526854 ; ID: Bjornberg et al., 1999 The activity of Escherichia coli dihydroorotate dehydrogenase is dependent on a conserved loop identified by sequence homology, mutagenesis, and limited proteolysis. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10074342 ; ID: Lu P et al. 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol. 2007 Jan;25(1):117-24. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=17187058 ; ID: Shestopalov AI et al. 1997 Aeration-dependent changes in composition of the quinone pool in Escherichia coli. Evidence of post-transcriptional regulation of the quinone biosynthesis. FEBS Lett. 1997 Mar 10;404(2-3):272-4. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=9119077 ;","Structural model information":"Dihydroorotate dehydrogenase catalyzes the oxidation of dihydroorotate to orotate in the pathway for de novo biosynthesis of pyrimidine nucleotides. The enzyme has a homodimer structural organization and works by a two-site ping-pong mechanism (Bjornberg et al., 1999).","Structural model links":" ID: Bjornberg et al. 1999 The activity of Escherichia coli dihydroorotate dehydrogenase is dependent on a conserved loop identified by sequence homology, mutagenesis, and limited proteolysis. Biochemistry. 1999 Mar 9;38(10):2899-908 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=10074342 ; ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=DIHYDROOROTOX-MONOMER ;"},"parameters":[{"units":"mM","information":"","name":"Kmdoroa","value":"0.0288"},{"units":"mM","information":"","name":"Kmoroa","value":"0.01"},{"units":"mM","information":"","name":"Kmq","value":"0.0394"},{"units":"mM","information":"","name":"Kmqh2","value":"0.01"},{"units":"mM","information":"","name":"Koroa","value":"0.0134"},{"units":"1/sec","information":"","name":"kcatf","value":"222"},{"units":"1/sec","information":"","name":"kcatr","value":"10"}]},{"scheme":"UMP + ATP <=> UDP + ADP + H+","substrates":{"s1":{"theSubstance":{"name":"UMP","type":"substance","synonyms":["5'Uridylic acid","UMP","Uridine 5'-monophosphate","Uridine monophosphate","Uridylic acid"],"links":[],"id":"SS0000024"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"UDP","type":"substance","synonyms":["UDP","Uridine 5'-diphosphate"],"links":[],"id":"SS0000025"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PyrH","type":"protein","synonyms":["PyrH","SmbA","Umk","UMP kinase","uridylate kinase"],"links":[],"id":"SS0000153"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"GTP","type":"substance","synonyms":["GTP","Guanosine 5'-triphosphate"],"links":[],"id":"SS0000140"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"UTP","type":"substance","synonyms":["Uridine 5'-triphosphate","Uridine triphosphate","UTP"],"links":[],"id":"SS0000026"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"((r1*kcat*s1*s2)/((kmump*(1+(r3/kutp)^hutp)+s1)*(kmatp+s2)))*((1+(r2/kgtp1)^hgtp)/(1+(r2/kgtp2)^hgtp))","theSubMathModel":null,"theInformation":{"Mathematical model information":"UTP, described as an allosteric inhibitor previously (Serina et al., 1995), was unexpectedly found in the phosphate acceptor site, suggesting that it acts as a competitive inhibitor (Briozzo et al., 2005).","Mathematical model links":" ID: Briozzo et al., 2005 Structure of Escherichia coli UMP kinase differs from that of other nucleoside monophosphate kinases and sheds new light on enzyme regulation ; Value:http://www.ncbi.nlm.nih.gov/pubmed/15857829 ; ID: Serina et al., 1995 Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7711027 ;","Parameter set information":"Parameter kcat was extracted from Serina et al., 1996 data. Parameters kmump, kmatp, kgtp1, kgtp2, hgtp, kutp and hutp were evaluated on basis of the experimental data (Serina et al., 1995). Moreover, to simulate the enzymatic kinetics you can use steady-state concentration for ATP=9.6 mM (Bennett et al., 2009). The model was simulated upon steady state concentration of PyrF enzyme, which equals 0.0007 mM (Lu et al., 2007).","Parameter set links":" ID: Bennett et al. 2009 Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol. 2009 Aug;5(8):593-599. doi: 10.1038/nchembio.186. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=19561621 ; ID: Briozzo et al., 2005 Structure of Escherichia coli UMP kinase differs from that of other nucleoside monophosphate kinases and sheds new light on enzyme regulation ; Value:http://www.ncbi.nlm.nih.gov/pubmed/15857829 ; ID: Lu et al. 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol. 2007 Jan;25(1):117-124. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=17187058 ; ID: Serina et al. 1996 Structural properties of UMP-kinase from Escherichia coli: modulation of protein solubility by pH and UTP. Biochemistry. 1996 Jun 4;35(22):7003-11. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=8679525 ; ID: Serina et al., 1995 Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7711027 ;","Structural model information":"UMP kinase (PyrH) is an essential enzyme in the de novo pyrimidines’ biosynthesis that catalyzes the chemical reaction ATP + UMP (reversible) ADP + UDP.  The enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with a phosphate group as acceptor. The systematic name of this enzyme class is ATP:UMP phosphotransferase. The enzyme is subject to complex regulatory control by GTP and UTP (Serina et al., 1995). Crystal structures of PyrH bound to its substrate, product, competitive inhibitor UTP (Briozzo et al., 2005, that contradicts to earlier data (Serina et al., 1995)) and allosteric regulator GTP (Meyer et al., 2008) have been solved. The GTP and UTP binding sites do not overlap (Meyer et al., 2008, Marco-Marin and Rubio., 2009).","Structural model links":" ID: Briozzo et al. 2005 Structure of Escherichia coli UMP kinase differs from that of other nucleoside monophosphate kinases and sheds new light on enzyme regulation. J Biol Chem. 2005 Jul 8;280(27):25533-25540. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=15857829 ; ID: EcoCyc ; Value:http://biocyc.org/NEW-IMAGE?type=EC-NUMBER&object=EC-2.7.4.22 ; ID: Marco-Marín and Rubio 2009 The site for the allosteric activator GTP of Escherichia coli UMP kinase. FEBS Lett. 2009 Jan 5;583(1):185-9. doi: 10.1016/j.febslet.2008.11.043. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=19071117 ; ID: Meyer et al. 2008 Structural and functional characterization of Escherichia coli UMP kinase in complex with its allosteric regulator GTP. J Biol Chem. 2008 Dec 19;283(51):36011-36018. doi: 10.1074/jbc.M802614200. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=18945668 ; ID: Serina et al. 1995 Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP. Biochemistry. 1995 Apr 18;34(15):5066-5074. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=7711027 ;"},"mmid":"MM0000168","psid":"PS0000158","gnid":"GN0000064","reversible":true,"information":{"Mathematical model information":"UTP, described as an allosteric inhibitor previously (Serina et al., 1995), was unexpectedly found in the phosphate acceptor site, suggesting that it acts as a competitive inhibitor (Briozzo et al., 2005).","Mathematical model links":" ID: Briozzo et al., 2005 Structure of Escherichia coli UMP kinase differs from that of other nucleoside monophosphate kinases and sheds new light on enzyme regulation ; Value:http://www.ncbi.nlm.nih.gov/pubmed/15857829 ; ID: Serina et al., 1995 Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7711027 ;","Parameter set information":"Parameter kcat was extracted from Serina et al., 1996 data. Parameters kmump, kmatp, kgtp1, kgtp2, hgtp, kutp and hutp were evaluated on basis of the experimental data (Serina et al., 1995). Moreover, to simulate the enzymatic kinetics you can use steady-state concentration for ATP=9.6 mM (Bennett et al., 2009). The model was simulated upon steady state concentration of PyrF enzyme, which equals 0.0007 mM (Lu et al., 2007).","Parameter set links":" ID: Bennett et al. 2009 Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol. 2009 Aug;5(8):593-599. doi: 10.1038/nchembio.186. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=19561621 ; ID: Briozzo et al., 2005 Structure of Escherichia coli UMP kinase differs from that of other nucleoside monophosphate kinases and sheds new light on enzyme regulation ; Value:http://www.ncbi.nlm.nih.gov/pubmed/15857829 ; ID: Lu et al. 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol. 2007 Jan;25(1):117-124. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=17187058 ; ID: Serina et al. 1996 Structural properties of UMP-kinase from Escherichia coli: modulation of protein solubility by pH and UTP. Biochemistry. 1996 Jun 4;35(22):7003-11. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=8679525 ; ID: Serina et al., 1995 Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7711027 ;","Structural model information":"UMP kinase (PyrH) is an essential enzyme in the de novo pyrimidines’ biosynthesis that catalyzes the chemical reaction ATP + UMP (reversible) ADP + UDP.  The enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with a phosphate group as acceptor. The systematic name of this enzyme class is ATP:UMP phosphotransferase. The enzyme is subject to complex regulatory control by GTP and UTP (Serina et al., 1995). Crystal structures of PyrH bound to its substrate, product, competitive inhibitor UTP (Briozzo et al., 2005, that contradicts to earlier data (Serina et al., 1995)) and allosteric regulator GTP (Meyer et al., 2008) have been solved. The GTP and UTP binding sites do not overlap (Meyer et al., 2008, Marco-Marin and Rubio., 2009).","Structural model links":" ID: Briozzo et al. 2005 Structure of Escherichia coli UMP kinase differs from that of other nucleoside monophosphate kinases and sheds new light on enzyme regulation. J Biol Chem. 2005 Jul 8;280(27):25533-25540. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=15857829 ; ID: EcoCyc ; Value:http://biocyc.org/NEW-IMAGE?type=EC-NUMBER&object=EC-2.7.4.22 ; ID: Marco-Marín and Rubio 2009 The site for the allosteric activator GTP of Escherichia coli UMP kinase. FEBS Lett. 2009 Jan 5;583(1):185-9. doi: 10.1016/j.febslet.2008.11.043. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=19071117 ; ID: Meyer et al. 2008 Structural and functional characterization of Escherichia coli UMP kinase in complex with its allosteric regulator GTP. J Biol Chem. 2008 Dec 19;283(51):36011-36018. doi: 10.1074/jbc.M802614200. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=18945668 ; ID: Serina et al. 1995 Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP. Biochemistry. 1995 Apr 18;34(15):5066-5074. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=7711027 ;"},"parameters":[{"units":"","information":"","name":"hgtp","value":"1.6"},{"units":"","information":"","name":"hutp","value":"2.4"},{"units":"1/sec","information":"","name":"kcat","value":"332"},{"units":"mM","information":"","name":"kgtp1","value":"0.05"},{"units":"mM","information":"","name":"kgtp2","value":"0.07"},{"units":"mM","information":"","name":"kmatp","value":"0.12"},{"units":"mM","information":"","name":"kmump","value":"0.05"},{"units":"mM","information":"","name":"kutp","value":"0.15"}]},{"scheme":"UDP + ATP -> UTP + ADP + H+","substrates":{"s1":{"theSubstance":{"name":"UDP","type":"substance","synonyms":["UDP","Uridine 5'-diphosphate"],"links":[],"id":"SS0000025"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"UTP","type":"substance","synonyms":["Uridine 5'-triphosphate","Uridine triphosphate","UTP"],"links":[],"id":"SS0000026"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Ndk","type":"protein","synonyms":["Ndk","NDP kinase","nucleoside diphosphate kinase"],"links":[],"id":"SS0000154"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"(r1*kcat*(s1/kmudp)*(s2/kmatp))/((1+(s1/kmudp))*(1+(s2/kmatp)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"UDP is phosphorylated to UTP (Roisin et al., 1978, Ginther et al., 1974, Jong et al., 1991). We proposed a simple model without competitive substrates such as CDP, GDP and ADP, since these metabolites are rapidly consumed in a bunch of reactions.","Mathematical model links":" ID: Ginther et al., 1974 Nucleoside diphosphokinase of Salmonella typhimurium. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4364654 ; ID: Jong et al., 1991 Saccharomyces cerevisiae nucleoside-diphosphate kinase: purification, characterization, and substrate specificity. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1659321 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Parameter set information":"Parameters kcat, kmudp and kmatp were extracted from Roisin and Kepes, 1978 data. Moreover, to simulate the enzymatic kinetics you can use steady-state concentration for ATP=9.6 mM (Bennett et al., 2009). The model was simulated upon steady state concentration of Ndk enzyme, which equals 0.0079 mM (Lu et al., 2007).","Parameter set links":" ID: Bennett et al. 2009 Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol. 2009 Aug;5(8):593-599. doi: 10.1038/nchembio.186. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/19561621 ; ID: Lu et al. 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol. 2007 Jan;25(1):117-124. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=17187058 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Structural model information":"Nucleoside diphosphate kinase catalyzes the reaction in which the terminal phosphate of a nucleoside-triphosphate is transferred to a nucleoside-diphosphate. The enzyme exhibits broad substrate specificity. The reaction mechanism is an ordered bi-molecular ping-pong type (Roisin and Kepes, 1978). The intracellular levels of ATP are considerably higher than other nucleoside triphosphates. In addition, ATP is far more abundant than ADP or AMP, so there is a strong thermodynamic tendency for the potential energy of ATP to be used in the synthesis of other high-energy compounds. The purified enzyme is tetrameric (Ohtsuki et al., 1984) and was detected in the periplasmic fraction after cold osmotic shock (Roisin and Kepes, 1978). A periplasmic location for the enzyme appears inconsistent with its function (Neidhardt et al., 1996).","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=UDPKIN-RXN ; ID: Neidhardt FC. 1996 Escherichia coli and Salmonella, Cellular and Molecular Biology, Second Edition. Neidhardt FC, Curtiss III R, Ingraham JL, Lin ECC, Low Jr KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE. American Society for Microbiology, Washington, D.C., 1996 ; Value:https://books.google.ru/books/about/Escherichia_Coli_and_Salmonella.html?id=FW0eqAAACAAJ ; ID: Ohtsuki K. et al. 1984 Nucleosidediphosphate kinase in Escherichia coli: its polypeptide structure and reaction intermediate. Biochem Int. 1984 May;8(5):715-723. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=6089829 ; ID: Roisin and Kepes 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. Biochim Biophys Acta. 1978 Oct 12;526(2):418-428. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=214126 ;"},"mmid":"MM0000126","psid":"PS0000159","gnid":"GN0000078","reversible":false,"information":{"Mathematical model information":"UDP is phosphorylated to UTP (Roisin et al., 1978, Ginther et al., 1974, Jong et al., 1991). We proposed a simple model without competitive substrates such as CDP, GDP and ADP, since these metabolites are rapidly consumed in a bunch of reactions.","Mathematical model links":" ID: Ginther et al., 1974 Nucleoside diphosphokinase of Salmonella typhimurium. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4364654 ; ID: Jong et al., 1991 Saccharomyces cerevisiae nucleoside-diphosphate kinase: purification, characterization, and substrate specificity. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1659321 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Parameter set information":"Parameters kcat, kmudp and kmatp were extracted from Roisin and Kepes, 1978 data. Moreover, to simulate the enzymatic kinetics you can use steady-state concentration for ATP=9.6 mM (Bennett et al., 2009). The model was simulated upon steady state concentration of Ndk enzyme, which equals 0.0079 mM (Lu et al., 2007).","Parameter set links":" ID: Bennett et al. 2009 Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol. 2009 Aug;5(8):593-599. doi: 10.1038/nchembio.186. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/19561621 ; ID: Lu et al. 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol. 2007 Jan;25(1):117-124. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=17187058 ; ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Structural model information":"Nucleoside diphosphate kinase catalyzes the reaction in which the terminal phosphate of a nucleoside-triphosphate is transferred to a nucleoside-diphosphate. The enzyme exhibits broad substrate specificity. The reaction mechanism is an ordered bi-molecular ping-pong type (Roisin and Kepes, 1978). The intracellular levels of ATP are considerably higher than other nucleoside triphosphates. In addition, ATP is far more abundant than ADP or AMP, so there is a strong thermodynamic tendency for the potential energy of ATP to be used in the synthesis of other high-energy compounds. The purified enzyme is tetrameric (Ohtsuki et al., 1984) and was detected in the periplasmic fraction after cold osmotic shock (Roisin and Kepes, 1978). A periplasmic location for the enzyme appears inconsistent with its function (Neidhardt et al., 1996).","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=UDPKIN-RXN ; ID: Neidhardt FC. 1996 Escherichia coli and Salmonella, Cellular and Molecular Biology, Second Edition. Neidhardt FC, Curtiss III R, Ingraham JL, Lin ECC, Low Jr KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE. American Society for Microbiology, Washington, D.C., 1996 ; Value:https://books.google.ru/books/about/Escherichia_Coli_and_Salmonella.html?id=FW0eqAAACAAJ ; ID: Ohtsuki K. et al. 1984 Nucleosidediphosphate kinase in Escherichia coli: its polypeptide structure and reaction intermediate. Biochem Int. 1984 May;8(5):715-723. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=6089829 ; ID: Roisin and Kepes 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme. Biochim Biophys Acta. 1978 Oct 12;526(2):418-428. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=214126 ;"},"parameters":[{"units":"1/sec","information":"","name":"kcat","value":"16"},{"units":"mM","information":"","name":"kmatp","value":"1.43"},{"units":"mM","information":"","name":"kmudp","value":"0.47"}]},{"scheme":"NADH + a quinone + H+ -> NAD+ + a quinol + HEXT","substrates":{"s1":{"theSubstance":{"name":"NADH","type":"substance","synonyms":["DPNH","NADH","Nicotinamide adenine dinucleotide"],"links":[],"id":"SS0000064"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"a quinone","type":"substance","synonyms":["a quinone","Q","quinone"],"links":[],"id":"SS0000146"},"theState":null,"compartment":""},"s3":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"NAD+","type":"substance","synonyms":["NAD+"],"links":[],"id":"SS0000188"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"a quinol","type":"substance","synonyms":["a hydroquinone","a quinol","a reduced quinone","QH2"],"links":[],"id":"SS0000147"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"HEXT","type":"substance","synonyms":["external H+","external hydrogen ion","HEXT","H+ external","hydrogen ion external"],"links":[],"id":"SS0000279"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"NDH-1","type":"protein","synonyms":["ec:1.6.5.3","NADH dehydrogenase I","NADH dehydrogenase I (nuoABEFGHIJKLMN)","NADH dhI","NADH:ubiquinone oxidoreductase I","ndh","NDH-1"],"links":[],"id":"SS0000280"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"Mg","type":"substance","synonyms":["Magnesium","Magnesium ion","Mg","Mg++","Mg2+"],"links":[],"id":"SS0000277"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"kcat*r1*(s1/kmNADH)/(1 + s1/kmNADH+ p1/kmNAD)*(s2/kmQ/(1 +s2/kmQ+ p2/kmQH2))*((1 + (laMg*r2/kaMg)/(1 +r2/kaMg)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Quinol is competitive product inhibitor for quinone [Bottcher B et al, 2002]. It is included into model in simple Michaelis form. \r\nMagnesium ion is known to be activator of the reaction [Bottcher B et al, 2002]. It is included into model in simple Hill form.","Mathematical model links":" ID: Bottcher B et al (2002). A novel, enzymatically active conformation of the Escherichia coli NADH:ubiquinone oxidoreductase (complex I). ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11880370 ;","Parameter set information":"The model parameters was verified using the experimental data from (Bottcher et al, 2002).\n\nThe only parameter remained unidentified is kcat. However, this parameter was estimated in the paper in alternative units: kcat = 52.8,mol/min/mg.","Parameter set links":" ID: Bottcher B et al (2002), . A novel, enzymatically active conformation of the Escherichia coli NADH:ubiquinone oxidoreductase (complex I) ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11880370 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=NADH-DHI-CPLX ;"},"mmid":"MM0000139","psid":"PS0000130","gnid":"GN0000157","reversible":false,"information":{"Mathematical model information":"Quinol is competitive product inhibitor for quinone [Bottcher B et al, 2002]. It is included into model in simple Michaelis form. \r\nMagnesium ion is known to be activator of the reaction [Bottcher B et al, 2002]. It is included into model in simple Hill form.","Mathematical model links":" ID: Bottcher B et al (2002). A novel, enzymatically active conformation of the Escherichia coli NADH:ubiquinone oxidoreductase (complex I). ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11880370 ;","Parameter set information":"The model parameters was verified using the experimental data from (Bottcher et al, 2002).\n\nThe only parameter remained unidentified is kcat. However, this parameter was estimated in the paper in alternative units: kcat = 52.8,mol/min/mg.","Parameter set links":" ID: Bottcher B et al (2002), . A novel, enzymatically active conformation of the Escherichia coli NADH:ubiquinone oxidoreductase (complex I) ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11880370 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=NADH-DHI-CPLX ;"},"parameters":[{"units":"mM","information":"","name":"kaMg","value":"12"},{"units":"1/s","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kmNAD","value":"0.5"},{"units":"mM","information":"","name":"kmNADH","value":"0.005"},{"units":"mM","information":"","name":"kmQ","value":"0.4"},{"units":"mM","information":"","name":"kmQH2","value":"40"},{"units":"","information":"","name":"laMg","value":"2.3"}]},{"scheme":"formate + a quinone -> CO2 + a quinol + HEXT","substrates":{"s1":{"theSubstance":{"name":"formate","type":"substance","synonyms":["formate","formic acid"],"links":[],"id":"SS0000170"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"a quinone","type":"substance","synonyms":["a quinone","Q","quinone"],"links":[],"id":"SS0000146"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"CO2","type":"substance","synonyms":["Carbon dioxide","CO2"],"links":[],"id":"SS0000071"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"a quinol","type":"substance","synonyms":["a hydroquinone","a quinol","a reduced quinone","QH2"],"links":[],"id":"SS0000147"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"HEXT","type":"substance","synonyms":["external H+","external hydrogen ion","HEXT","H+ external","hydrogen ion external"],"links":[],"id":"SS0000279"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"FDH-N","type":"protein","synonyms":["ec:1.1.5.6","Fdh-N","FDH-N","FdnGHI","formate dehydrogenase","Formate dehydrogenase-N","formate dehydrogenase, nitrate inducible"],"links":[],"id":"SS0000281"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"Mo2+","type":"substance","synonyms":["Mo++","Mo2+","molybdenum","molybdenum ion"],"links":[],"id":"SS0000282"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"NaN3","type":"substance","synonyms":["azide","hydrazoic acid","NaN3"],"links":[],"id":"SS0000283"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"kcat*r1*(s1/kmFOR)/(1 + s1/kmFOR + r3/kiNaN3)*(s2/kmQ/(1 + s2/kmQ + p2/kmQH2))*((r2/kaMo)^naMo/(1 + (r2/kaMo)^naMo))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Quinol is a competitive product inhibitor for quinone, while NaN3 is a competitive inhibitor for formate [Enoch HG, Lester RL, 1975]. They are both included into model in simple Michaelis form. \r\nMo2+ is known to be activator of the reaction [Enoch HG, Lester RL, 1975]. It is included to model in simple Hill form.","Mathematical model links":" ID: Enoch HG, Lester RL. (1975). . The purification and properties of formate dehydrogenase and nitrate reductase from Escherichia coli. J Biol Chem. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1099093 ;","Parameter set information":"Three model parameters (kcat, kmFOR, kmQ) were taken from (Enoch, Lester, 1975). The other parameters remained unverified, while the model was built using structural data. ","Parameter set links":" ID: Enoch HG, Lester RL. (1975). . The purification and properties of formate dehydrogenase and nitrate reductase from Escherichia coli. J Biol Chem ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1099093 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=FORMATEDEHYDROGN-CPLX ;"},"mmid":"MM0000140","psid":"PS0000131","gnid":"GN0000158","reversible":false,"information":{"Mathematical model information":"Quinol is a competitive product inhibitor for quinone, while NaN3 is a competitive inhibitor for formate [Enoch HG, Lester RL, 1975]. They are both included into model in simple Michaelis form. \r\nMo2+ is known to be activator of the reaction [Enoch HG, Lester RL, 1975]. It is included to model in simple Hill form.","Mathematical model links":" ID: Enoch HG, Lester RL. (1975). . The purification and properties of formate dehydrogenase and nitrate reductase from Escherichia coli. J Biol Chem. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1099093 ;","Parameter set information":"Three model parameters (kcat, kmFOR, kmQ) were taken from (Enoch, Lester, 1975). The other parameters remained unverified, while the model was built using structural data. ","Parameter set links":" ID: Enoch HG, Lester RL. (1975). . The purification and properties of formate dehydrogenase and nitrate reductase from Escherichia coli. J Biol Chem ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1099093 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=FORMATEDEHYDROGN-CPLX ;"},"parameters":[{"units":"mM","information":"","name":"kaMo","value":"1"},{"units":"1/s","information":"","name":"kcat","value":"563"},{"units":"mM","information":"","name":"kiNaN3","value":"1"},{"units":"mM","information":"","name":"kmFOR","value":"0.12"},{"units":"mM","information":"","name":"kmQ","value":"0.4"},{"units":"mM","information":"","name":"kmQH2","value":"40"},{"units":"","information":"","name":"naMo","value":"1"}]},{"scheme":"formate + a quinone -> CO2 + a quinol + HEXT","substrates":{"s1":{"theSubstance":{"name":"formate","type":"substance","synonyms":["formate","formic acid"],"links":[],"id":"SS0000170"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"a quinone","type":"substance","synonyms":["a quinone","Q","quinone"],"links":[],"id":"SS0000146"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"CO2","type":"substance","synonyms":["Carbon dioxide","CO2"],"links":[],"id":"SS0000071"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"a quinol","type":"substance","synonyms":["a hydroquinone","a quinol","a reduced quinone","QH2"],"links":[],"id":"SS0000147"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"HEXT","type":"substance","synonyms":["external H+","external hydrogen ion","HEXT","H+ external","hydrogen ion external"],"links":[],"id":"SS0000279"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"FDH-O","type":"protein","synonyms":["ec:1.1.5.6","FDH-O","FDH-Z","FdoGHI","Formate dehydrogenase-O","Transporter: formate dehydrogenase-O"],"links":[],"id":"SS0000284"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"Mo2+","type":"substance","synonyms":["Mo++","Mo2+","molybdenum","molybdenum ion"],"links":[],"id":"SS0000282"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"kcat*r1*(s1/kmFOR)/(1 +s1/kmFOR)*(s2/kmQ/(1 +s2/kmQ +p2/kmQH2))* ((1+(laMo*r2/kaMo)^naMo)/(1 + (r2/kaMo)^naMo))","theSubMathModel":null,"theInformation":{"Mathematical model information":"  By reason of the lack of experimental data, this mathematical model was built primarily basing on the homology with the FDH-N model, as the enzymes FDH-O and FDH-N are supposed to be quite similar.  The model is constructed on the base of FDH-N model (GN0000158, MM0000140) due to homology of enzymes.","Parameter set information":" All parameters of the model are unverified due to the lack of experimental data. Four parameters (kcat, kmFOR, kmmQ, kmQH2) are estimated basing on the verified parameters of FDH-N model (the same parameter values are taken). The rest parameters (laMo, kaMo, naMo) are neither identified nor estimated. ","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=FORMATEDEHYDROGO-CPLX ;"},"mmid":"MM0000141","psid":"PS0000132","gnid":"GN0000159","reversible":false,"information":{"Mathematical model information":"  By reason of the lack of experimental data, this mathematical model was built primarily basing on the homology with the FDH-N model, as the enzymes FDH-O and FDH-N are supposed to be quite similar.  The model is constructed on the base of FDH-N model (GN0000158, MM0000140) due to homology of enzymes.","Parameter set information":" All parameters of the model are unverified due to the lack of experimental data. Four parameters (kcat, kmFOR, kmmQ, kmQH2) are estimated basing on the verified parameters of FDH-N model (the same parameter values are taken). The rest parameters (laMo, kaMo, naMo) are neither identified nor estimated. ","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=FORMATEDEHYDROGO-CPLX ;"},"parameters":[{"units":"mM","information":"","name":"kaMo","value":"1"},{"units":"1/s","information":"","name":"kcat","value":"563"},{"units":"mM","information":"","name":"kmFOR","value":"0.12"},{"units":"mM","information":"","name":"kmQ","value":"0.4"},{"units":"mM","information":"","name":"kmQH2","value":"40"},{"units":"","information":"","name":"laMo","value":"1"},{"units":"","information":"","name":"naMo","value":"1"}]},{"scheme":"formate + a quinone -> CO2 + a quinol + HEXT","substrates":{"s1":{"theSubstance":{"name":"formate","type":"substance","synonyms":["formate","formic acid"],"links":[],"id":"SS0000170"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"a quinone","type":"substance","synonyms":["a quinone","Q","quinone"],"links":[],"id":"SS0000146"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"CO2","type":"substance","synonyms":["Carbon dioxide","CO2"],"links":[],"id":"SS0000071"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"a quinol","type":"substance","synonyms":["a hydroquinone","a quinol","a reduced quinone","QH2"],"links":[],"id":"SS0000147"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"HEXT","type":"substance","synonyms":["external H+","external hydrogen ion","HEXT","H+ external","hydrogen ion external"],"links":[],"id":"SS0000279"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Formate dehydrogenase-H","type":"protein","synonyms":["ChlF","ec:1.1.5.6","ec:1.1.99.33","FdhF","FDH-H","formate dehydrogenase H","Formate dehydrogenase-H"],"links":[],"id":"SS0000287"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"Mo2+","type":"substance","synonyms":["Mo++","Mo2+","molybdenum","molybdenum ion"],"links":[],"id":"SS0000282"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"Se","type":"substance","synonyms":["Se","Se2-","selenide","selenide ion"],"links":[],"id":"SS0000285"},"theState":null,"compartment":"","theInfluence":"activator"},"r4":{"theSubstance":{"name":"Fe2+","type":"substance","synonyms":["Fe++","Fe2+","fe(ii)","ferrous ion","ferrous iron"],"links":[],"id":"SS0000286"},"theState":null,"compartment":"","theInfluence":"activator"},"r5":{"theSubstance":{"name":"NaN3","type":"substance","synonyms":["azide","hydrazoic acid","NaN3"],"links":[],"id":"SS0000283"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r6":{"theSubstance":{"name":"NO3","type":"substance","synonyms":["nitrate","NO3","NO3-"],"links":[],"id":"SS0000016"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"kcat*r1*(s1/kmFOR)/(1 + s1/kmFOR + r6/kiNO3 + r5/kicNaN3)*(s2/kmQ/(1 + s2/kmQ + p2/kmQH2))* (r2/kaMo/(1 + r2/kaMo))*((1 + r5/kinNaN3)/(1 + liNaN3*r5/kinNaN3))","theSubMathModel":null,"theInformation":{"Mathematical model information":"This simplified model doesn't consider the influence of some cofactors (Se, Fe) due to the lack of experimental data.A quinol (QH2) is a competitive inhibitor for a quinone (Q). NO3 and NaN3 are competitive inhibitors for formate [Axley MJ, Grahame DA, 1991]. These inhibitors are included into model in simple Michaelis form. \r\nThe complex inhibitory mechanism for NaN3 is divided in two parts in this model: Michaelis (for competitive) and Hill (for non-competitive). \r\nMo2+ is known to be activator of the reaction [Axley MJ, Grahame DA, 1991]. It is included to model in simple Hill form.","Mathematical model links":" ID: Axley MJ, Grahame DA (1991), Kinetics for formate dehydrogenase of Escherichia coli formate-hydrogenlyase. J Biol Chem. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1906883 ;","Parameter set information":"The model parameters were estimated using the experimental data from (Axley, Grahame, 1991). The only parameter remained unverified is kcat. However, the Vmax parameter was noted in that paper in alternative units (1, mol/min/mg).\nThe complex inhibitory mechanism for NaN3 is divided in two steps in this model: competetive and non-competetive ones.","Parameter set links":" ID: Axley MJ, Grahame DA (1991), Kinetics for formate dehydrogenase of Escherichia coli formate-hydrogenlyase. J Biol Chem. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1906883 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=FORMATEDEHYDROGH-MONOMER&redirect=T ;"},"mmid":"MM0000142","psid":"PS0000133","gnid":"GN0000160","reversible":false,"information":{"Mathematical model information":"This simplified model doesn't consider the influence of some cofactors (Se, Fe) due to the lack of experimental data.A quinol (QH2) is a competitive inhibitor for a quinone (Q). NO3 and NaN3 are competitive inhibitors for formate [Axley MJ, Grahame DA, 1991]. These inhibitors are included into model in simple Michaelis form. \r\nThe complex inhibitory mechanism for NaN3 is divided in two parts in this model: Michaelis (for competitive) and Hill (for non-competitive). \r\nMo2+ is known to be activator of the reaction [Axley MJ, Grahame DA, 1991]. It is included to model in simple Hill form.","Mathematical model links":" ID: Axley MJ, Grahame DA (1991), Kinetics for formate dehydrogenase of Escherichia coli formate-hydrogenlyase. J Biol Chem. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1906883 ;","Parameter set information":"The model parameters were estimated using the experimental data from (Axley, Grahame, 1991). The only parameter remained unverified is kcat. However, the Vmax parameter was noted in that paper in alternative units (1, mol/min/mg).\nThe complex inhibitory mechanism for NaN3 is divided in two steps in this model: competetive and non-competetive ones.","Parameter set links":" ID: Axley MJ, Grahame DA (1991), Kinetics for formate dehydrogenase of Escherichia coli formate-hydrogenlyase. J Biol Chem. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1906883 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=FORMATEDEHYDROGH-MONOMER&redirect=T ;"},"parameters":[{"units":"mM","information":"","name":"kaMo","value":"0.001"},{"units":"1/s","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kiNO3","value":"7.1"},{"units":"mM","information":"","name":"kicNaN3","value":"0.24"},{"units":"","information":"","name":"kinNaN3","value":"1"},{"units":"mM","information":"","name":"kmFOR","value":"26"},{"units":"mM","information":"","name":"kmQ","value":"2.4"},{"units":"mM","information":"","name":"kmQH2","value":"240"},{"units":"","information":"","name":"liNaN3","value":"2"}]},{"scheme":"XMP + ATP + H2O + gln -> GMP + AMP + glu + ppi + H+","substrates":{"s1":{"theSubstance":{"name":"XMP","type":"substance","synonyms":["(9-D-Ribosylxanthine)-5'-phosphate","Xanthosine 5'-phosphate","Xanthylic acid","XMP"],"links":[],"id":"SS0000109"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""},"s3":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""},"s4":{"theSubstance":{"name":"gln","type":"substance","synonyms":["gln","L-2-Aminoglutaramic acid","L-Glutamine"],"links":[],"id":"SS0000028"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"GMP","type":"substance","synonyms":["GMP","Guanosine 5'-monophosphate","Guanosine 5'-phosphate","Guanosine monophosphate","Guanylic acid"],"links":[],"id":"SS0000112"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"AMP","type":"substance","synonyms":["5'-Adenosine monophosphate","5'-Adenylic acid","5'-AMP","Adenosine 5'-monophosphate","Adenosine 5'-phosphate","Adenylate","Adenylic acid","AMP"],"links":[],"id":"SS0000073"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"glu","type":"substance","synonyms":["glu","Glutamate","L-Glutamate","L-Glutamic acid","L-Glutaminic acid"],"links":[],"id":"SS0000061"},"theState":null,"compartment":""},"p4":{"theSubstance":{"name":"ppi","type":"substance","synonyms":["Diphosphate","PP","ppi","pyrophosphate"],"links":[],"id":"SS0000023"},"theState":null,"compartment":""},"p5":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"GuaA","type":"protein","synonyms":["GuaA"],"links":[],"id":"SS0000385"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"(((r1^2)/(kdis+2*r1))*kcat*(s1/KmXMP)*(s2/KmATP))/((1+(s1/KmXMP))*(1+(s2/KmATP)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Sakamoto 1978 GMP synthetase (Escherichia coli). ; Value:http://www.ncbi.nlm.nih.gov/pubmed/211374 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. Parametrs KmXMP and KmATP were taken from [Sakamoto, 1978] article.","Parameter set links":" ID: Sakamoto 1978 GMP synthetase (Escherichia coli). ; Value:http://www.ncbi.nlm.nih.gov/pubmed/211374 ;","Structural model information":"This reaction is involved in GMP biosynthesis. Subunit composition of enzyme of GMP synthetase = [GuaA]2.","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=GMP-SYN-GLUT-RXN ;"},"mmid":"MM0000219","psid":"PS0000211","gnid":"GN0000212","reversible":false,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Sakamoto 1978 GMP synthetase (Escherichia coli). ; Value:http://www.ncbi.nlm.nih.gov/pubmed/211374 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. Parametrs KmXMP and KmATP were taken from [Sakamoto, 1978] article.","Parameter set links":" ID: Sakamoto 1978 GMP synthetase (Escherichia coli). ; Value:http://www.ncbi.nlm.nih.gov/pubmed/211374 ;","Structural model information":"This reaction is involved in GMP biosynthesis. Subunit composition of enzyme of GMP synthetase = [GuaA]2.","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=GMP-SYN-GLUT-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmATP","value":"0.53"},{"units":"mM","information":"","name":"KmXMP","value":"0.029"},{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kdis","value":"0.001"}]},{"scheme":"oroa + prpp <=> omp + ppi","substrates":{"s1":{"theSubstance":{"name":"oroa","type":"substance","synonyms":["oroa","Orotate","Orotic acid","Uracil-6-carboxylic acid"],"links":[],"id":"SS0000020"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"prpp","type":"substance","synonyms":["5-Phospho-alpha-D-ribose 1-diphosphate","5-Phosphoribosyl 1-pyrophosphate","5-Phosphoribosyl diphosphate","prpp"],"links":[],"id":"SS0000021"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"omp","type":"substance","synonyms":["omp","Orotidine 5'-phosphate","Orotidylic acid"],"links":[],"id":"SS0000022"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ppi","type":"substance","synonyms":["Diphosphate","PP","ppi","pyrophosphate"],"links":[],"id":"SS0000023"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PyrE","type":"protein","synonyms":["orotate phosphoribosyltransferase","PyrE"],"links":[],"id":"SS0000368"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"(kcat*r1*(s1/Kmoroa)*(s2/Kmprpp))/(1+(s1/Kmoroa)+(s2/Kmprpp))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis Menten kinetics [Shimosaka et al., 1984].","Mathematical model links":" ID: Shimosaka et al., 1984 Purine-mediated growth inhibition caused by a pyrE mutation in Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6389507 ;","Parameter set information":"Parameter Kcat was calculated based on Shimosaka et al., 1984, but you can use estimation for this parameter (311 sec-1) based on Poulsen et al., 1983. Parameters Kmoroa and Kmprpp were extracted from Sundararaj et al., 2004. Moreover, to simulate the enzymatic kinetics you can use steady-state concentrations for prpp=0.26 mM (Bennett et al., 2009). The model was simulated upon steady state concentration of PyrE enzyme, which equals 0.05 mM (estimation based on Poulsen et al., 1983).","Parameter set links":" ID: Bennett BD et al. 2009 Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol. 2009 Aug;5(8):593-599. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=19561621 ; ID: Poulsen P et al. 1983 Nucleotide sequence of the Escherichia coli pyrE gene and of the DNA in front of the protein-coding region. Eur J Biochem. 1983 Sep 15;135(2):223-9. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=6349999 ; ID: Shimosaka et al., 1984 Purine-mediated growth inhibition caused by a pyrE mutation in Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6389507 ; ID: Sundararaj S et al. 2004 The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D293-5. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=14681416 ;","Structural model information":"Orotate phosphoribosyltransferase catalyzes the transfer of the phosphoribosyl moiety to the pyrimidine ring in the de novo biosynthesis of pyrimidine nucleotides. Subunit composition of orotate phosphoribosyltransferase = [PyrE]2. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=OROPRIBTRANS-RXN ;"},"mmid":"MM0000195","psid":"PS0000189","gnid":"GN0000186","reversible":true,"information":{"Mathematical model information":"Reaction follows Michaelis Menten kinetics [Shimosaka et al., 1984].","Mathematical model links":" ID: Shimosaka et al., 1984 Purine-mediated growth inhibition caused by a pyrE mutation in Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6389507 ;","Parameter set information":"Parameter Kcat was calculated based on Shimosaka et al., 1984, but you can use estimation for this parameter (311 sec-1) based on Poulsen et al., 1983. Parameters Kmoroa and Kmprpp were extracted from Sundararaj et al., 2004. Moreover, to simulate the enzymatic kinetics you can use steady-state concentrations for prpp=0.26 mM (Bennett et al., 2009). The model was simulated upon steady state concentration of PyrE enzyme, which equals 0.05 mM (estimation based on Poulsen et al., 1983).","Parameter set links":" ID: Bennett BD et al. 2009 Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol. 2009 Aug;5(8):593-599. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=19561621 ; ID: Poulsen P et al. 1983 Nucleotide sequence of the Escherichia coli pyrE gene and of the DNA in front of the protein-coding region. Eur J Biochem. 1983 Sep 15;135(2):223-9. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=6349999 ; ID: Shimosaka et al., 1984 Purine-mediated growth inhibition caused by a pyrE mutation in Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6389507 ; ID: Sundararaj S et al. 2004 The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D293-5. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=14681416 ;","Structural model information":"Orotate phosphoribosyltransferase catalyzes the transfer of the phosphoribosyl moiety to the pyrimidine ring in the de novo biosynthesis of pyrimidine nucleotides. Subunit composition of orotate phosphoribosyltransferase = [PyrE]2. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=OROPRIBTRANS-RXN ;"},"parameters":[{"units":"mM","information":"","name":"Kmoroa","value":"0.03"},{"units":"mM","information":"","name":"Kmprpp","value":"0.04"},{"units":"1/sec","information":"","name":"kcat","value":"12"}]},{"scheme":"a quinol + Oxygen -> a quinone + HEXT","substrates":{"s1":{"theSubstance":{"name":"a quinol","type":"substance","synonyms":["a hydroquinone","a quinol","a reduced quinone","QH2"],"links":[],"id":"SS0000147"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"O2","type":"substance","synonyms":["O2","Oxygen"],"links":[],"id":"SS0000068"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"a quinone","type":"substance","synonyms":["a quinone","Q","quinone"],"links":[],"id":"SS0000146"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"HEXT","type":"substance","synonyms":["external H+","external hydrogen ion","HEXT","H+ external","hydrogen ion external"],"links":[],"id":"SS0000279"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"CydABX","type":"protein","synonyms":["CydABX","cytochrome b558-d complex","cytochrome bd complex","cytochrome bd-I terminal oxidase","cytochrome d complex","cytochrome d ubiquinol oxidase complex","ec:1.10.3.14"],"links":[],"id":"SS0000326"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"Zn2+","type":"substance","synonyms":["Zinc","zinc ion","Zn","Zn++","Zn2+","Zn(II)"],"links":[],"id":"SS0000311"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"HQNO","type":"substance","synonyms":["2-heptyl-4-hydroxyquinoline n-oxide","2-Heptyl-4-quinolinol 1-oxide","2-heptylquinolin-4-ol 1-oxide","2-n-heptyl-4-hydroxyquinoline-N-oxide","HOQNO","HQNO"],"links":[],"id":"SS0000322"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"H2O2","type":"substance","synonyms":["H2O2","hydrogen peroxide","hydroperoxide","perhydrol"],"links":[],"id":"SS0000321"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"KCN","type":"substance","synonyms":["kalium cyanid","KCN","potassium cyanide"],"links":[],"id":"SS0000320"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r6":{"theSubstance":{"name":"NH2OH","type":"substance","synonyms":["hydroxylamine","NH2OH"],"links":[],"id":"SS0000323"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r7":{"theSubstance":{"name":"NaN3","type":"substance","synonyms":["azide","hydrazoic acid","NaN3"],"links":[],"id":"SS0000283"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r8":{"theSubstance":{"name":"asolectin","type":"substance","synonyms":["ASO","asolectin"],"links":[],"id":"SS0000324"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"kf*r1*(s1/kmQH2/(1 + s1/kmQH2+ p1/kmQ))*(s2/kmO2/(1 + s2/kmO2))*(1/(1 + r2/kiZn))* ((1 + r3/kiHQNO)/(1 + liHQNO*r3/kiHQNO))*((1 + (r4/kiH2O2)^niH2O2)/(1 + (liH2O2*r4/kiH2O2)^niH2O2))*((1 + r5/kiKCN)/(1 + liKCN*r5/kiKCN))*((1 + r6/kiNH2OH)/(1 + liNH2OH*r6/kiNH2OH))*((1 + (r7/kiNaN3)^niNaN3)/(1 + (liNaN3*r7/kiNaN3)^niNaN3))*((1 + laASO*r8/kaASO)/(1 + r8/kaASO))","theSubMathModel":null,"theInformation":{"Mathematical model information":"This model is a product of four main parts: \r\n1) Michaelis-Mentent part with product competitive inhibition by a quinone (for a quinol). \r\n2) Zn2+ ions inhibition part written in simple Hill form \r\n3) Other substances (NaN3, KCN, H2O2, HQNQ, NH2OH) inhibition part written in simple Hill form. \r\n4) Asolectin activation part written in simple Hill form. ","Mathematical model links":" ID: Kita K et al (1984) Terminal oxidases of Escherichia coli aerobic respiratory chain. I. Purification and properties of cytochrome b562-o complex from cells in the early exponential phase of aerobic growth. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6365921 ; ID: Kita K et al (1986) Purification and properties of two terminal oxidase complexes of Escherichia coli aerobic respiratory chain. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2856144 ;","Parameter set information":"All parameters (except two ones) were verified using experimental data (Kita et al, 1984, 1986). The parameter kf was not verified due to the alternative measurement units (Vmax = 7.5,O2/min/nmol). KmQ was estimated taking into account biochemical sence of the specie.","Parameter set links":" ID: Kita K et al (1984) Terminal oxidases of Escherichia coli aerobic respiratory chain. I. Purification and properties of cytochrome b562-o complex from cells in the early exponential phase of aerobic growth. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6365921 ; ID: Kita K et al (1986) Purification and properties of two terminal oxidase complexes of Escherichia coli aerobic respiratory chain. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2856144 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=CYT-D-UBIOX-CPLX ;"},"mmid":"MM0000152","psid":"PS0000144","gnid":"GN0000166","reversible":false,"information":{"Mathematical model information":"This model is a product of four main parts: \r\n1) Michaelis-Mentent part with product competitive inhibition by a quinone (for a quinol). \r\n2) Zn2+ ions inhibition part written in simple Hill form \r\n3) Other substances (NaN3, KCN, H2O2, HQNQ, NH2OH) inhibition part written in simple Hill form. \r\n4) Asolectin activation part written in simple Hill form. ","Mathematical model links":" ID: Kita K et al (1984) Terminal oxidases of Escherichia coli aerobic respiratory chain. I. Purification and properties of cytochrome b562-o complex from cells in the early exponential phase of aerobic growth. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6365921 ; ID: Kita K et al (1986) Purification and properties of two terminal oxidase complexes of Escherichia coli aerobic respiratory chain. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2856144 ;","Parameter set information":"All parameters (except two ones) were verified using experimental data (Kita et al, 1984, 1986). The parameter kf was not verified due to the alternative measurement units (Vmax = 7.5,O2/min/nmol). KmQ was estimated taking into account biochemical sence of the specie.","Parameter set links":" ID: Kita K et al (1984) Terminal oxidases of Escherichia coli aerobic respiratory chain. I. Purification and properties of cytochrome b562-o complex from cells in the early exponential phase of aerobic growth. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6365921 ; ID: Kita K et al (1986) Purification and properties of two terminal oxidase complexes of Escherichia coli aerobic respiratory chain. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2856144 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=CYT-D-UBIOX-CPLX ;"},"parameters":[{"units":"mcM","information":"","name":"kaASO","value":"972"},{"units":"1/s","information":"","name":"kf","value":"1"},{"units":"mM","information":"","name":"kiH2O2","value":"120"},{"units":"","information":"","name":"kiHQNO","value":"40"},{"units":"mcM","information":"","name":"kiKCN","value":"65"},{"units":"mcM","information":"","name":"kiNH2OH","value":"110"},{"units":"mM","information":"","name":"kiNaN3","value":"85"},{"units":"mcM","information":"","name":"kiZn","value":"60"},{"units":"mcM","information":"","name":"kmO2","value":"0.38"},{"units":"mcM","information":"","name":"kmQ","value":"23000"},{"units":"mcM","information":"","name":"kmQH2","value":"230"},{"units":"","information":"","name":"laASO","value":"267"},{"units":"","information":"","name":"liH2O2","value":"1.6"},{"units":"","information":"","name":"liHQNO","value":"8"},{"units":"","information":"","name":"liKCN","value":"20"},{"units":"","information":"","name":"liNH2OH","value":"12"},{"units":"","information":"","name":"liNaN3","value":"1.13"},{"units":"","information":"","name":"niH2O2","value":"2.4"},{"units":"","information":"","name":"niNaN3","value":"3.6"}]},{"scheme":"succinate + a quinone <=> fumarate + a quinol","substrates":{"s1":{"theSubstance":{"name":"succinate","type":"substance","synonyms":["succinate"],"links":[],"id":"SS0000191"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"a quinone","type":"substance","synonyms":["a quinone","Q","quinone"],"links":[],"id":"SS0000146"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"fumarate","type":"substance","synonyms":["fum","fumarate","fumaric acid"],"links":[],"id":"SS0000180"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"a quinol","type":"substance","synonyms":["a hydroquinone","a quinol","a reduced quinone","QH2"],"links":[],"id":"SS0000147"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"SQR","type":"protein","synonyms":["ec:1.3.5.1","SdhCDAB","SQR","Succinate dehydrogenase","succinate-ubiquinone oxidoreductase"],"links":[],"id":"SS0000327"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"malonate","type":"substance","synonyms":["malonate","malonyl","propanedioic acid"],"links":[],"id":"SS0000328"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"r1*(kcatf*(s1/kmSUC)*(s2/kmQ) - kcatr*(p1/kmFUM)*(p2/kmQH2))/((1 + s1/kmSUC + p1/kmFUM + r2/kiMAL)*(1 + s2/kmQ + p2/kmQH2))","theSubMathModel":null,"theInformation":{"Mathematical model information":"This model uses simple form for reversible reactions. Malonate is considered as a competetive inhibitor for succinate.This model is written in simple form for reversible reactions. Malonate is considered as a competetive inhibitor for succinate [Kim, Bragg, 1971; Maklashina, Cecchini, 1999].","Mathematical model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=SUCC-DEHASE ; ID: Kim IC, Bragg PD (1971) Some properties of the succinate dehydrogenase of Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4334990 ; ID: Maklashina E., Cecchini G (1999) . Comparison of catalytic activity and inhibitors of quinone reactions of succinate dehydrogenase (Succinate-ubiquinone oxidoreductase) and fumarate reductase (Menaquinol-fumarate oxidoreductase) from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10486141 ;","Parameter set information":"The parameters values were taken from papers. The reverse reaction parameters (kcatr, kmFUM, kmQH2) remained unidentified.","Parameter set links":" ID: Kim IC, Bragg PD (1971)  Some properties of the succinate dehydrogenase of Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4334990 ; ID: Maklashina E., Cecchini G (1999) . Comparison of catalytic activity and inhibitors of quinone reactions of succinate dehydrogenase (Succinate-ubiquinone oxidoreductase) and fumarate reductase (Menaquinol-fumarate oxidoreductase) from Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10486141 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=SUCC-DEHASE ;"},"mmid":"MM0000153","psid":"PS0000145","gnid":"GN0000167","reversible":true,"information":{"Mathematical model information":"This model uses simple form for reversible reactions. Malonate is considered as a competetive inhibitor for succinate.This model is written in simple form for reversible reactions. Malonate is considered as a competetive inhibitor for succinate [Kim, Bragg, 1971; Maklashina, Cecchini, 1999].","Mathematical model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=SUCC-DEHASE ; ID: Kim IC, Bragg PD (1971) Some properties of the succinate dehydrogenase of Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4334990 ; ID: Maklashina E., Cecchini G (1999) . Comparison of catalytic activity and inhibitors of quinone reactions of succinate dehydrogenase (Succinate-ubiquinone oxidoreductase) and fumarate reductase (Menaquinol-fumarate oxidoreductase) from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10486141 ;","Parameter set information":"The parameters values were taken from papers. The reverse reaction parameters (kcatr, kmFUM, kmQH2) remained unidentified.","Parameter set links":" ID: Kim IC, Bragg PD (1971)  Some properties of the succinate dehydrogenase of Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4334990 ; ID: Maklashina E., Cecchini G (1999) . Comparison of catalytic activity and inhibitors of quinone reactions of succinate dehydrogenase (Succinate-ubiquinone oxidoreductase) and fumarate reductase (Menaquinol-fumarate oxidoreductase) from Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10486141 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=SUCC-DEHASE ;"},"parameters":[{"units":"1/s","information":"","name":"kcatf","value":"86"},{"units":"1/s","information":"","name":"kcatr","value":"1"},{"units":"mcM","information":"","name":"kiMAL","value":"7.3"},{"units":"mM","information":"","name":"kmFUM","value":"1"},{"units":"mcM","information":"","name":"kmQ","value":"4.17"},{"units":"mM","information":"","name":"kmQH2","value":"1"},{"units":"mM","information":"","name":"kmSUC","value":"2"}]},{"scheme":"Thioredoxin disulfide + NADPH <=> Thioredoxin + NADP+","substrates":{"s1":{"theSubstance":{"name":"Thioredoxin disulfide","type":"substance","synonyms":["Oxidized thioredoxin","Thioredoxin disulfide","Thioredoxin sulfide"],"links":[],"id":"SS0000045"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"NADPH","type":"substance","synonyms":["NADPH","Reduced nicotinamide adenine dinucleotide phosphate","TPNH"],"links":[],"id":"SS0000066"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"Thioredoxin","type":"protein","synonyms":["Reduced thioredoxin","Thioredoxin"],"links":[],"id":"SS0000046"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"NADP+","type":"substance","synonyms":["beta-Nicotinamide adenine dinucleotide phosphate","NADP","NADP+","Nicotinamide adenine dinucleotide phosphate","TPN","Triphosphopyridine nucleotide"],"links":[],"id":"SS0000067"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"TrxB","type":"protein","synonyms":["ec:1.8.1.9","NADPH::oxidized thioredoxin oxidoreductase","Thioredoxin reductase","TrxB","TrxR"],"links":[],"id":"SS0000339"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"kf*r1*((s1/kmOTHIO)/(1 + s1/kmOTHIO+ p1/kmRTHIO))*((s2/kmNADPH)/(1 + s2/kmNADPH+ p2/kmNADP))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Simple model with products inhibition.Thioredoxin is known to be a competitive inhibitor for thioredoxin disulfide, while NADP+ is competitive inhibitor for NADPH [Prongay AJ et al, 1989]. This model is written in simple form for reversible reactions.","Mathematical model links":" ID: Prongay AJ et al (1989) Characterization of two active site mutations of thioredoxin reductase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2644268 ;","Parameter set information":"KmOTHIO and KmNADPH were taken from (Prongay et al, 1989). The other parameters were estimated on account of biochemical sence.","Parameter set links":" ID: Prongay AJ et al (1989) Characterization of two active site mutations of thioredoxin reductase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2644268 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=THIOREDOXIN-REDUCT-NADPH-RXN ;"},"mmid":"MM0000154","psid":"PS0000146","gnid":"GN0000168","reversible":true,"information":{"Mathematical model information":"Simple model with products inhibition.Thioredoxin is known to be a competitive inhibitor for thioredoxin disulfide, while NADP+ is competitive inhibitor for NADPH [Prongay AJ et al, 1989]. This model is written in simple form for reversible reactions.","Mathematical model links":" ID: Prongay AJ et al (1989) Characterization of two active site mutations of thioredoxin reductase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2644268 ;","Parameter set information":"KmOTHIO and KmNADPH were taken from (Prongay et al, 1989). The other parameters were estimated on account of biochemical sence.","Parameter set links":" ID: Prongay AJ et al (1989) Characterization of two active site mutations of thioredoxin reductase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2644268 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=THIOREDOXIN-REDUCT-NADPH-RXN ;"},"parameters":[{"units":"1/s","information":"","name":"kf","value":"1"},{"units":"mcM","information":"","name":"kmNADP","value":"125"},{"units":"mcM","information":"","name":"kmNADPH","value":"1.25"},{"units":"mcM","information":"","name":"kmOTHIO","value":"2.9"},{"units":"mcM","information":"","name":"kmRTHIO","value":"290"}]},{"scheme":"NADPH + NAD+ <=> NADP+ + NADH","substrates":{"s1":{"theSubstance":{"name":"NADPH","type":"substance","synonyms":["NADPH","Reduced nicotinamide adenine dinucleotide phosphate","TPNH"],"links":[],"id":"SS0000066"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"NAD+","type":"substance","synonyms":["NAD+"],"links":[],"id":"SS0000188"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"NADP+","type":"substance","synonyms":["beta-Nicotinamide adenine dinucleotide phosphate","NADP","NADP+","Nicotinamide adenine dinucleotide phosphate","TPN","Triphosphopyridine nucleotide"],"links":[],"id":"SS0000067"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"NADH","type":"substance","synonyms":["DPNH","NADH","Nicotinamide adenine dinucleotide"],"links":[],"id":"SS0000064"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Sth","type":"protein","synonyms":["ec:1.6.1.1","ec:1.6.1.2","ec:1.6.1.3","NAD(P)+ transhydrogenase (B-specific)","Soluble pyridine nucleotide transhydrogenase","Soluble pyridine nucleotide transhydrogenase (sthA)","Sth","STH","UdhA"],"links":[],"id":"SS0000341"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"Mg","type":"substance","synonyms":["Magnesium","Magnesium ion","Mg","Mg++","Mg2+"],"links":[],"id":"SS0000277"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"r1*(kcatf*(s1/kms1)*(s2/kms2) - kcatr*(p1/kmp1)*(p2/kmp2))/((1 + s1/kms1 + p1/kmp1)*(1 + s2/kms2 + p2/kmp2))*((1 + r2/kiMg)/(1 + liMg*r2/kiMg))","theSubMathModel":null,"theInformation":{"Mathematical model information":"This model is a simple reversible reaction equation with additional magnesium regulation. ","Parameter set information":"In this model only kiMg and liMg parameters are verified using experimental data (Sweetman, Griffiths, 1971). The rest parameters remain unidentified.","Parameter set links":" ID: Sweetman AJ, Griffiths DE (1971)  Studies on energy-linked reactions. Energy-linked transhydrogenase reaction in Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4398957 ;","Structural model information":" no data ","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=UDHA-MONOMER ; ID: Sweetman AJ, Griffiths DE (1971) Studies on energy-linked reactions. Energy-linked transhydrogenase reaction in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4398957 ;"},"mmid":"MM0000155","psid":"PS0000147","gnid":"GN0000169","reversible":true,"information":{"Mathematical model information":"This model is a simple reversible reaction equation with additional magnesium regulation. ","Parameter set information":"In this model only kiMg and liMg parameters are verified using experimental data (Sweetman, Griffiths, 1971). The rest parameters remain unidentified.","Parameter set links":" ID: Sweetman AJ, Griffiths DE (1971)  Studies on energy-linked reactions. Energy-linked transhydrogenase reaction in Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4398957 ;","Structural model information":" no data ","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=UDHA-MONOMER ; ID: Sweetman AJ, Griffiths DE (1971) Studies on energy-linked reactions. Energy-linked transhydrogenase reaction in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4398957 ;"},"parameters":[{"units":"1/s","information":"","name":"kcatf","value":"1"},{"units":"1/s","information":"","name":"kcatr","value":"1"},{"units":"mM","information":"","name":"kiMg","value":"5"},{"units":"mM","information":"","name":"kmp1","value":"1"},{"units":"mM","information":"","name":"kmp2","value":"1"},{"units":"mM","information":"","name":"kms1","value":"1"},{"units":"mM","information":"","name":"kms2","value":"1"},{"units":"","information":"","name":"liMg","value":"5"}]},{"scheme":"glycerol-3-P + a quinone -> dihydroxyacetone phosphate + a quinol","substrates":{"s1":{"theSubstance":{"name":"G3P","type":"substance","synonyms":["a-glycerophosphate","a-glycerophosphoric acid","G3P","glycerol-1-phosphate","glycerol-3-P","glycerol-3-phosphate","L-G3P","L-glycerol 3-phosphate","rac-Glycerol 3-phosphate","sn-glycerol-3-phosphate"],"links":[],"id":"SS0000309"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"a quinone","type":"substance","synonyms":["a quinone","Q","quinone"],"links":[],"id":"SS0000146"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"DHAP","type":"substance","synonyms":["DHAP","dihydroxyacetone 3-phosphate","dihydroxyacetone-P","dihydroxy-acetone phosphate","dihydroxy-acetone-phosphate","dihydroxyacetone phosphate","dihydroxyacetone-phosphate","di-OH-acetone-P","glycerone-phosphate"],"links":[],"id":"SS0000310"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"a quinol","type":"substance","synonyms":["a hydroquinone","a quinol","a reduced quinone","QH2"],"links":[],"id":"SS0000147"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"GlpD","type":"protein","synonyms":["ec:1.1.5.3","G3P dehydrogenase","GlpD","glycerol 3-phosphate dehydrogenase, aerobic","sn-glycerol-3-phosphate:(acceptor) 2-oxidoreductase"],"links":[],"id":"SS0000316"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"Zn2+","type":"substance","synonyms":["Zinc","zinc ion","Zn","Zn++","Zn2+","Zn(II)"],"links":[],"id":"SS0000311"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"Cu2+","type":"substance","synonyms":["Cu++","Cu2+","Cu(II)","cupric copper","cupric ion"],"links":[],"id":"SS0000312"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"GlpD","type":"substance","synonyms":["(2R)-2-hydroxy-3-(phosphonooxy)-propanal","3-phosphoglyceraldehyde","D-glyceraldehyde-3-P","D-glyceraldehyde-3-phosphate","GlpD","glyceraldehyde-3-P","glyceraldehyde-3-phosphate","glyceraldehyde-P","glyceraldehyde-phosphate","GlyD","triose phosphate"],"links":[],"id":"SS0000315"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"2-P-glycolate","type":"substance","synonyms":["2-P-glycolate","2-phosphoglycolate","phosphoglycolate","phosphoglycolic acid"],"links":[],"id":"SS0000314"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r6":{"theSubstance":{"name":"PEP","type":"substance","synonyms":["P-enol-pyr","P-enol-pyruvate","PEP","phosphoenolpyruvate"],"links":[],"id":"SS0000313"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r7":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r8":{"theSubstance":{"name":"GTP","type":"substance","synonyms":["GTP","Guanosine 5'-triphosphate"],"links":[],"id":"SS0000140"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"kf*r1*(s1/kmGL3P)/(1 + s1/kmGL3P + p1/kmT3P2)*(s2/kmQ/(1 + s2/kmQ + p2/kmQH2))* ((1 + r7/kiATP)/(1 + liATP*r7/kiATP))*((1 + r8/kiGTP)/(1 + liGTP*r8/kiGTP))","theSubMathModel":null,"theInformation":{"Mathematical model information":"This simplified model contains only basic regulations described in Schryvers A et al (1978): \r\n1) products competitive inhibition written in Michaelis form (dihydroxyacetone phosphate for glycerol-3-P, and a quinol for a quinone). \r\n2) ATP and GTP inhibition written in simple Hill form. ","Mathematical model links":" ID: Schryvers A et al (1978) Chemical and functional properties of the native and reconstituted forms of the membrane-bound, aerobic glycerol-3-phosphate dehydrogenase of Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/340460 ;","Parameter set information":"The parameters were verified using experimental data from (Schryvers et al, 1978). Only two parameters remained unverified: kf and kmQH2. The latter one is estimated on account of biochemical sence.","Parameter set links":" ID: Schryvers A et al (1978) Chemical and functional properties of the native and reconstituted forms of the membrane-bound, aerobic glycerol-3-phosphate dehydrogenase of Escherichia ; Value:http://www.ncbi.nlm.nih.gov/pubmed/340460 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=AERGLYC3PDEHYDROG-CPLX ; ID: Schryvers A et al (1978) Chemical and functional properties of the native and reconstituted forms of the membrane-bound, aerobic glycerol-3-phosphate dehydrogenase of Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/340460 ; ID: Walz AC et al (2002) Aerobic sn-glycerol-3-phosphate dehydrogenase from Escherichia coli binds to the cytoplasmic membrane through an amphipathic alpha-helix. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11955283 ;"},"mmid":"MM0000149","psid":"PS0000141","gnid":"GN0000163","reversible":false,"information":{"Mathematical model information":"This simplified model contains only basic regulations described in Schryvers A et al (1978): \r\n1) products competitive inhibition written in Michaelis form (dihydroxyacetone phosphate for glycerol-3-P, and a quinol for a quinone). \r\n2) ATP and GTP inhibition written in simple Hill form. ","Mathematical model links":" ID: Schryvers A et al (1978) Chemical and functional properties of the native and reconstituted forms of the membrane-bound, aerobic glycerol-3-phosphate dehydrogenase of Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/340460 ;","Parameter set information":"The parameters were verified using experimental data from (Schryvers et al, 1978). Only two parameters remained unverified: kf and kmQH2. The latter one is estimated on account of biochemical sence.","Parameter set links":" ID: Schryvers A et al (1978) Chemical and functional properties of the native and reconstituted forms of the membrane-bound, aerobic glycerol-3-phosphate dehydrogenase of Escherichia ; Value:http://www.ncbi.nlm.nih.gov/pubmed/340460 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=AERGLYC3PDEHYDROG-CPLX ; ID: Schryvers A et al (1978) Chemical and functional properties of the native and reconstituted forms of the membrane-bound, aerobic glycerol-3-phosphate dehydrogenase of Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/340460 ; ID: Walz AC et al (2002) Aerobic sn-glycerol-3-phosphate dehydrogenase from Escherichia coli binds to the cytoplasmic membrane through an amphipathic alpha-helix. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11955283 ;"},"parameters":[{"units":"1/s","information":"","name":"kf","value":"1"},{"units":"mM","information":"","name":"kiATP","value":"8"},{"units":"mM","information":"","name":"kiGTP","value":"6"},{"units":"mM","information":"","name":"kmGL3P","value":"0.8"},{"units":"mM","information":"","name":"kmQ","value":"0.001"},{"units":"mM","information":"","name":"kmQH2","value":"0.1"},{"units":"mM","information":"","name":"kmT3P2","value":"0.5"},{"units":"","information":"","name":"liATP","value":"1.66"},{"units":"","information":"","name":"liGTP","value":"1.66"}]},{"scheme":"glycerol-3-P + a quinone -> dihydroxyacetone phosphate + a quinol","substrates":{"s1":{"theSubstance":{"name":"G3P","type":"substance","synonyms":["a-glycerophosphate","a-glycerophosphoric acid","G3P","glycerol-1-phosphate","glycerol-3-P","glycerol-3-phosphate","L-G3P","L-glycerol 3-phosphate","rac-Glycerol 3-phosphate","sn-glycerol-3-phosphate"],"links":[],"id":"SS0000309"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"a quinone","type":"substance","synonyms":["a quinone","Q","quinone"],"links":[],"id":"SS0000146"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"DHAP","type":"substance","synonyms":["DHAP","dihydroxyacetone 3-phosphate","dihydroxyacetone-P","dihydroxy-acetone phosphate","dihydroxy-acetone-phosphate","dihydroxyacetone phosphate","dihydroxyacetone-phosphate","di-OH-acetone-P","glycerone-phosphate"],"links":[],"id":"SS0000310"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"a quinol","type":"substance","synonyms":["a hydroquinone","a quinol","a reduced quinone","QH2"],"links":[],"id":"SS0000147"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"GlpABC","type":"protein","synonyms":["anaerobic glycerol-3-phosphate dehydrogenase","ec:1.1.5.3","G3P dehydrogenase, anaerobic","GlpABC","glycerol-3-phosphate-dehydrogenase, anaerobic"],"links":[],"id":"SS0000318"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"FAD","type":"substance","synonyms":["FAD","Flavin adenine dinucleotide","flavin adenine dinucleotide oxidized","flavitan"],"links":[],"id":"SS0000072"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"FMN","type":"substance","synonyms":["flavin mononucleotide","FMN"],"links":[],"id":"SS0000317"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"kf*r1*(s1/(kmGL3P*(1 + lkFMN*r3/kkFMN)/(1 + r3/kkFMN)))/(1 + s1/(kmGL3P*(1 + lkFMN*r3/kkFMN)/(1 + r3/kkFMN)))*(s2/kmQ/(1 + s2/kmQ+ p2/kmQH2))* (r2/kmFAD/(1 + kmFAD))* (((1 + laFMN*r3)/kaFMN)/(1 + r3/kaFMN))","theSubMathModel":null,"theInformation":{"Mathematical model information":"In this model, FAD is considered as a cofactor, so its influence is denoted in Michaelis-Menten form.Complex FMN influence on the reaction [Weiner JH, Heppel LA 1972; Schryvers A, Weiner JH 1981] is two-based in this model using simple Hill form: \r\n1) FMN changes Michaelis constant for glycerol-3-P. \r\n2) FMN additionally increases reaction rate. \r\nFAD is considered as a cofactor, so its influence is denoted in Michaelis-Menten form. \r\nA quinol is considered to be product competitive inhibitor for a quinone which is written in Michaelis form.","Mathematical model links":" ID: Schryvers A, Weiner JH (1981) The anaerobic sn-glycerol-3-phosphate dehydrogenase of Escherichia coli. Purification and characterization. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6792201 ; ID: Weiner JH, Heppel LA (1972) Purification of the membrane-bound and pyridine nucleotide-independent L-glycerol 3-phosphate dehydrogenase from Escherichia coli. Biochem Biophys Res Commun. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4557172 ;","Parameter set information":"FMN influence is two-based in this model: 1) FMN changes Michaelis constant for glycerol-3-P; 2) FMN additionally increases reaction rate. Parameters were verified using experimental data from (Weiner JH, Heppel LA 1972; Schryvers A, Weiner JH 1981). Only two parameters remained unverified: kf and kmQH2. The latter one is estimated on account of biochemical sence.","Parameter set links":" ID: Schryvers A, Weiner JH (1981) The anaerobic sn-glycerol-3-phosphate dehydrogenase of Escherichia coli. Purification and characterization. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6792201 ; ID: Weiner JH, Heppel LA (1972) Purification of the membrane-bound and pyridine nucleotide-independent L-glycerol 3-phosphate dehydrogenase from Escherichia coli. Biochem Biophys Res Commun ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4557172 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=ANGLYC3PDEHYDROG-CPLX ;"},"mmid":"MM0000150","psid":"PS0000142","gnid":"GN0000164","reversible":false,"information":{"Mathematical model information":"In this model, FAD is considered as a cofactor, so its influence is denoted in Michaelis-Menten form.Complex FMN influence on the reaction [Weiner JH, Heppel LA 1972; Schryvers A, Weiner JH 1981] is two-based in this model using simple Hill form: \r\n1) FMN changes Michaelis constant for glycerol-3-P. \r\n2) FMN additionally increases reaction rate. \r\nFAD is considered as a cofactor, so its influence is denoted in Michaelis-Menten form. \r\nA quinol is considered to be product competitive inhibitor for a quinone which is written in Michaelis form.","Mathematical model links":" ID: Schryvers A, Weiner JH (1981) The anaerobic sn-glycerol-3-phosphate dehydrogenase of Escherichia coli. Purification and characterization. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6792201 ; ID: Weiner JH, Heppel LA (1972) Purification of the membrane-bound and pyridine nucleotide-independent L-glycerol 3-phosphate dehydrogenase from Escherichia coli. Biochem Biophys Res Commun. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4557172 ;","Parameter set information":"FMN influence is two-based in this model: 1) FMN changes Michaelis constant for glycerol-3-P; 2) FMN additionally increases reaction rate. Parameters were verified using experimental data from (Weiner JH, Heppel LA 1972; Schryvers A, Weiner JH 1981). Only two parameters remained unverified: kf and kmQH2. The latter one is estimated on account of biochemical sence.","Parameter set links":" ID: Schryvers A, Weiner JH (1981) The anaerobic sn-glycerol-3-phosphate dehydrogenase of Escherichia coli. Purification and characterization. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6792201 ; ID: Weiner JH, Heppel LA (1972) Purification of the membrane-bound and pyridine nucleotide-independent L-glycerol 3-phosphate dehydrogenase from Escherichia coli. Biochem Biophys Res Commun ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4557172 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=ANGLYC3PDEHYDROG-CPLX ;"},"parameters":[{"units":"mM","information":"","name":"kaFMN","value":"0.1"},{"units":"1/s","information":"","name":"kf","value":"1"},{"units":"mM","information":"","name":"kkFMN","value":"0.01"},{"units":"mcM","information":"","name":"kmFAD","value":"0.1"},{"units":"mM","information":"","name":"kmGL3P","value":"0.1"},{"units":"mM","information":"","name":"kmQ","value":"0.001"},{"units":"mM","information":"","name":"kmQH2","value":"0.1"},{"units":"","information":"","name":"laFMN","value":"4"},{"units":"","information":"","name":"lkFMN","value":"2.5"}]},{"scheme":"pyruvate + a quinone -> acetate + a quinol + CO2","substrates":{"s1":{"theSubstance":{"name":"pyruvate","type":"substance","synonyms":["2-oxopropanoate","2-oxopropanoic acid","2-oxo-propionic acid","acetylformic acid","alpha-ketopropionic acid","PYR","pyroracemic acid","pyruvate","pyruvic acid"],"links":[],"id":"SS0000288"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"a quinone","type":"substance","synonyms":["a quinone","Q","quinone"],"links":[],"id":"SS0000146"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"acetate","type":"substance","synonyms":["AC","acetate","acetic acid","ethanoic acid"],"links":[],"id":"SS0000289"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"a quinol","type":"substance","synonyms":["a hydroquinone","a quinol","a reduced quinone","QH2"],"links":[],"id":"SS0000147"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"CO2","type":"substance","synonyms":["Carbon dioxide","CO2"],"links":[],"id":"SS0000071"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PoxB","type":"protein","synonyms":["ec:1.2.5.1","PoxB","POXEC","pyruvate:ferricytochrome b1 oxidoreductase","Pyruvate oxidase","pyruvate:oxygen 2-oxidoreductase (phosphorylating)","pyruvic oxidase"],"links":[],"id":"SS0000302"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r10":{"theSubstance":{"name":"lysolecithin","type":"substance","synonyms":["Acyl-sn-glycero-3-phosphocholine","LLe","lysolecithin"],"links":[],"id":"SS0000297"},"theState":null,"compartment":"","theInfluence":"activator"},"r11":{"theSubstance":{"name":"PA","type":"substance","synonyms":["PA","phosphatidate","phosphatidic acid","phosphatidyl acid"],"links":[],"id":"SS0000299"},"theState":null,"compartment":"","theInfluence":"activator"},"r12":{"theSubstance":{"name":"cardiolipin","type":"substance","synonyms":["cardiolipin","diphosphatidylglycerol"],"links":[],"id":"SS0000301"},"theState":null,"compartment":"","theInfluence":"activator"},"r13":{"theSubstance":{"name":"PS","type":"substance","synonyms":["phosphatidyl-L-serine","phosphatidylserine","phosphatidyl serine","PS"],"links":[],"id":"SS0000300"},"theState":null,"compartment":"","theInfluence":"activator"},"r14":{"theSubstance":{"name":"phospholipid","type":"substance","synonyms":["phospholipid","Plip","PLip"],"links":[],"id":"SS0000298"},"theState":null,"compartment":"","theInfluence":"activator"},"r15":{"theSubstance":{"name":"TDP","type":"substance","synonyms":["TDP","ThDP","thiamin diphosphate","thiamine diphosphate","thiamine-PPi","thiamine pyrophosphate","thiamin-PPi","thiamin pyrophosphate","ThPP","TPP"],"links":[],"id":"SS0000291"},"theState":null,"compartment":"","theInfluence":"activator"},"r2":{"theSubstance":{"name":"N-EM","type":"substance","synonyms":["1-ethyl-","1H-pyrrole-2,5-dione","ethylmaleimide","maleic acid N-ethylimide","maleimide","NEM","N-EM","N-ethyl-","N-ethylmaleimide"],"links":[],"id":"SS0000290"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"ppi","type":"substance","synonyms":["Diphosphate","PP","ppi","pyrophosphate"],"links":[],"id":"SS0000023"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"Ni2+","type":"substance","synonyms":["Ni++","Ni2+","nickel","nickel ion"],"links":[],"id":"SS0000292"},"theState":null,"compartment":"","theInfluence":"activator"},"r5":{"theSubstance":{"name":"Co2+","type":"substance","synonyms":["Co++","Co2+","cobalt","cobalt ion","Co(II)"],"links":[],"id":"SS0000296"},"theState":null,"compartment":"","theInfluence":"activator"},"r6":{"theSubstance":{"name":"Ba2+","type":"substance","synonyms":["Ba++","Ba2+","barium","barium (II) ion"],"links":[],"id":"SS0000295"},"theState":null,"compartment":"","theInfluence":"activator"},"r7":{"theSubstance":{"name":"Mg","type":"substance","synonyms":["Magnesium","Magnesium ion","Mg","Mg++","Mg2+"],"links":[],"id":"SS0000277"},"theState":null,"compartment":"","theInfluence":"complex regulator"},"r8":{"theSubstance":{"name":"Mn2+","type":"substance","synonyms":["manganese (II) ion","manganese ion","Mn++","Mn2+","Mn(II)"],"links":[],"id":"SS0000294"},"theState":null,"compartment":"","theInfluence":"complex regulator"},"r9":{"theSubstance":{"name":"PtdGro","type":"substance","synonyms":["3(3-phosphatidyl-)glycerol","3-(3-sn-phosphatidyl)glycerol","phosphatidylglycerol","PtdGro"],"links":[],"id":"SS0000293"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"r1* iVmPLIP*(1 + lVmPLIP*r14/kVmPLIP)/(1 + r14/kVmPLIP)*(s1/( ikmPYRPLIP*(1 + r14/kkmPYRPLIP)/(1 +lkmPYRPLIP*r14/kkmPYRPLIP))/(1 + s1/( ikmPYRPLIP*(1 + r14/kkmPYRPLIP)/(1 +lkmPYRPLIP*r14/kkmPYRPLIP))+ p1/kmAC))*(s2/kmQ/(1+s2/kmQ+p2/kmQH2))*((r15/( ikmTPP*(1 + r14/kkmTPPPLIP)/(1 + lkmTPPPLIP*r14/kkmTPPPLIP)* (1 + (r7/kkmTPPMg1)^nkmTPPMg1*(1 + (r7/kkmTPPMg2)^nkmTPPMg2))/ (1 + (lkmTPPMg1*r7/kkmTPPMg1)^nkmTPPMg1*(1 + (lkmTPPMg2*r7/kkmTPPMg2)^nkmTPPMg2))* ((1 + lkmTPPPtdGro*r9/kkmTPPPtdGro)/(1 + r9/kkmTPPPtdGro))))^( (1 + lnTPPPLIP*r14/knTPPPLIP)/(1 + r14/knTPPPLIP))/(1 + (r15/( ikmTPP*(1 + r14/kkmTPPPLIP)/(1 + lkmTPPPLIP*r14/kkmTPPPLIP)* (1 + (r7/kkmTPPMg1)^nkmTPPMg1*(1 + (r7/kkmTPPMg2)^nkmTPPMg2))/ (1 + (lkmTPPMg1*r7/kkmTPPMg1)^nkmTPPMg1*(1 + (lkmTPPMg2*r7/kkmTPPMg2)^nkmTPPMg2))* ((1 + lkmTPPPtdGro*r9/kkmTPPPtdGro)/(1 + r9/kkmTPPPtdGro))))^( (1 + lnTPPPLIP*r14/knTPPPLIP)/(1 + r14/knTPPPLIP))))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Phospholipid is known to be complex regulator of the reaction. It has the following effects [Cunningham, Hager, 1971]: \r\n1) General activatory effect (included into model in simple Hill form). \r\n2) Changing the Michaelis constant for pyruvate. \r\n3) Changing the efficiency of thiamine diphosphate activatory effect. \r\nAcetate and a quinol are competitive product inhibitors for pyruvate and a quinone, respectively [Cunningham, Hager, 1971; Blake et al, 1982]. They are included into model in simple Michaelis form. \r\nThiamine diphosphate has also complex activatory effect on reaction, which is regulated by phospholipid, phosphatidylglycerol, and magnesium ions concentrations [Blake et al, 1982]. This part is included into model as the superposition of Hill functions. ","Mathematical model links":" ID: Blake et al (1982) Role of the divalent metal cation in the pyruvate oxidase reaction. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6286628 ; ID: Cunningham CC, Hager LP (1971) Crystalline pyruvate oxidase from Escherichia coli.3. Phospholipid as an allosteric effector for the enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4926543 ;","Parameter set information":"All parameters (except kmAC, kmQH2) were verified using experimental data (Cunningham, Hager, 1971; Blake et al, 1982).\nkmAC and kmQH2 were estimated using biochemical sence of these parameters.","Parameter set links":" ID: Blake et al (1982) Role of the divalent metal cation in the pyruvate oxidase reaction ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6286628 ; ID: Cunningham CC, Hager LP (1971) Crystalline pyruvate oxidase from Escherichia coli.3. Phospholipid as an allosteric effector for the enzyme ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4926543 ;","Structural model links":" ID: Blake R et al (1982) . Role of the divalent metal cation in the pyruvate oxidase reaction ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6286628 ; ID: Cunningham CC, Hager LP (1971) Crystalline pyruvate oxidase from Escherichia coli.3. Phospholipid as an allosteric effector for the enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4926543 ; ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=PYRUVOXID-MONOMER ;"},"mmid":"MM0000143","psid":"PS0000139","gnid":"GN0000161","reversible":false,"information":{"Mathematical model information":"Phospholipid is known to be complex regulator of the reaction. It has the following effects [Cunningham, Hager, 1971]: \r\n1) General activatory effect (included into model in simple Hill form). \r\n2) Changing the Michaelis constant for pyruvate. \r\n3) Changing the efficiency of thiamine diphosphate activatory effect. \r\nAcetate and a quinol are competitive product inhibitors for pyruvate and a quinone, respectively [Cunningham, Hager, 1971; Blake et al, 1982]. They are included into model in simple Michaelis form. \r\nThiamine diphosphate has also complex activatory effect on reaction, which is regulated by phospholipid, phosphatidylglycerol, and magnesium ions concentrations [Blake et al, 1982]. This part is included into model as the superposition of Hill functions. ","Mathematical model links":" ID: Blake et al (1982) Role of the divalent metal cation in the pyruvate oxidase reaction. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6286628 ; ID: Cunningham CC, Hager LP (1971) Crystalline pyruvate oxidase from Escherichia coli.3. Phospholipid as an allosteric effector for the enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4926543 ;","Parameter set information":"All parameters (except kmAC, kmQH2) were verified using experimental data (Cunningham, Hager, 1971; Blake et al, 1982).\nkmAC and kmQH2 were estimated using biochemical sence of these parameters.","Parameter set links":" ID: Blake et al (1982) Role of the divalent metal cation in the pyruvate oxidase reaction ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6286628 ; ID: Cunningham CC, Hager LP (1971) Crystalline pyruvate oxidase from Escherichia coli.3. Phospholipid as an allosteric effector for the enzyme ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4926543 ;","Structural model links":" ID: Blake R et al (1982) . Role of the divalent metal cation in the pyruvate oxidase reaction ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6286628 ; ID: Cunningham CC, Hager LP (1971) Crystalline pyruvate oxidase from Escherichia coli.3. Phospholipid as an allosteric effector for the enzyme. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4926543 ; ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=PYRUVOXID-MONOMER ;"},"parameters":[{"units":"","information":"","name":"iVmPLIP","value":"12.5"},{"units":"mcM","information":"","name":"ikmPYRPLIP","value":"170"},{"units":"","information":"","name":"ikmTPP","value":"0.6"},{"units":"mcM","information":"","name":"kVmPLIP","value":"5"},{"units":"mcM","information":"","name":"kkmPYRPLIP","value":"5"},{"units":"mM","information":"","name":"kkmTPPMg1","value":"1.2"},{"units":"mM","information":"","name":"kkmTPPMg2","value":"10.5"},{"units":"mcM","information":"","name":"kkmTPPPLIP","value":"5"},{"units":"mcM","information":"","name":"kkmTPPPtdGro","value":"1"},{"units":"mcM","information":"","name":"kmAC","value":"500"},{"units":"mM","information":"","name":"kmQ","value":"0.1"},{"units":"mcM","information":"","name":"kmQH2","value":"10"},{"units":"mcM","information":"","name":"knTPPPLIP","value":"5"},{"units":"","information":"","name":"lVmPLIP","value":"2.1"},{"units":"","information":"","name":"lkmPYRPLIP","value":"18"},{"units":"","information":"","name":"lkmTPPMg1","value":"2.32"},{"units":"","information":"","name":"lkmTPPMg2","value":"1.2"},{"units":"","information":"","name":"lkmTPPPLIP","value":"2"},{"units":"","information":"","name":"lkmTPPPtdGro","value":"2.5"},{"units":"","information":"","name":"lnTPPPLIP","value":"2.2"},{"units":"","information":"","name":"nkmTPPMg1","value":"2.5"},{"units":"","information":"","name":"nkmTPPMg2","value":"16"}]},{"scheme":"D-lactate + a quinone -> pyruvate + a quinol","substrates":{"s1":{"theSubstance":{"name":"D-lactate","type":"substance","synonyms":["DLAC","D-lactate","(R)-2-hydroxypropanate","(R)-lactate"],"links":[],"id":"SS0000303"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"a quinone","type":"substance","synonyms":["a quinone","Q","quinone"],"links":[],"id":"SS0000146"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"pyruvate","type":"substance","synonyms":["2-oxopropanoate","2-oxopropanoic acid","2-oxo-propionic acid","acetylformic acid","alpha-ketopropionic acid","PYR","pyroracemic acid","pyruvate","pyruvic acid"],"links":[],"id":"SS0000288"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"a quinol","type":"substance","synonyms":["a hydroquinone","a quinol","a reduced quinone","QH2"],"links":[],"id":"SS0000147"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Dld","type":"protein","synonyms":["D-Lactate Dehydrogenase","D-lactate:quinone oxidoreductase","Dld","ec:1.1.1.28","lactic acid dehydrogenase","Ldh"],"links":[],"id":"SS0000304"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"cardiolipin","type":"substance","synonyms":["cardiolipin","diphosphatidylglycerol"],"links":[],"id":"SS0000301"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"phospholipid","type":"substance","synonyms":["phospholipid","Plip","PLip"],"links":[],"id":"SS0000298"},"theState":null,"compartment":"","theInfluence":"activator"},"r4":{"theSubstance":{"name":"PE","type":"substance","synonyms":["PE","phosphatidyl ethanolamine"],"links":[],"id":"SS0000305"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"oxalate","type":"substance","synonyms":["ethanedioic acid","oxalate","oxalic acid"],"links":[],"id":"SS0000307"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r6":{"theSubstance":{"name":"oxamate","type":"substance","synonyms":["oxamate","OXAMATE"],"links":[],"id":"SS0000306"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"r1*kf*((s1/kms1*(1+r3/k22))/(1+s1/kms1*(1+r3/k22)+p1/kmp1))*((s2/kms2)/(1+s2/kms2+p2/kmp2))*(1+r2/k1+r3/k2+r4/k3)/(1+r2/k11+r3/k21+r4/k31)","theSubMathModel":null,"theInformation":{"Mathematical model information":"There are three regulators (cardiolipin, phospholipid,phosphatidyl ethanolamine) considered in this model. Product inhibition is constructed basing on the structure logic of the reaction.There are three regulators (cardiolipin, phospholipid,phosphatidyl ethanolamine) considered in this model in simple Hill form. \r\nProduct inhibition is constructed basing on the structure logic of the reaction and written in Michaelis form. \r\nPhospholipid is known to affect Michaelis constant for D-lactate [Futai, 1973; Tanaka et al., 1976] and considered in simple Hill form. ","Mathematical model links":" ID: Futai M (1973) Membrane D-lactate dehydrogenase from Escherichia coli. Purification and properties. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4575624 ; ID: Tanaka Y. et.al. (1976) Escherichia coli membrane D-lactate dehydrogenase. Isolation of the enzyme in aggregated from and its activation by Triton X-100 and phospholipids. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/795808 ;","Parameter set information":"Michaelis constants for substrates were taken from (Tanaka Y. et.al., 1976; Futai M., 1973). The other parameters were estimated and/or calculated using the experimental data from (Tanaka Y. et.al., 1976; Futai M., 1973).\n","Parameter set links":" ID: Futai M (1973) Membrane D-lactate dehydrogenase from Escherichia coli. Purification and properties. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4575624 ; ID: Tanaka Y. et.al. (1976) Escherichia coli membrane D-lactate dehydrogenase. Isolation of the enzyme in aggregated from and its activation by Triton X-100 and phospholipids ; Value:http://www.ncbi.nlm.nih.gov/pubmed/795808 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=DLACTDEHYDROGFAD-MONOMER ;"},"mmid":"MM0000148","psid":"PS0000140","gnid":"GN0000162","reversible":false,"information":{"Mathematical model information":"There are three regulators (cardiolipin, phospholipid,phosphatidyl ethanolamine) considered in this model. Product inhibition is constructed basing on the structure logic of the reaction.There are three regulators (cardiolipin, phospholipid,phosphatidyl ethanolamine) considered in this model in simple Hill form. \r\nProduct inhibition is constructed basing on the structure logic of the reaction and written in Michaelis form. \r\nPhospholipid is known to affect Michaelis constant for D-lactate [Futai, 1973; Tanaka et al., 1976] and considered in simple Hill form. ","Mathematical model links":" ID: Futai M (1973) Membrane D-lactate dehydrogenase from Escherichia coli. Purification and properties. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4575624 ; ID: Tanaka Y. et.al. (1976) Escherichia coli membrane D-lactate dehydrogenase. Isolation of the enzyme in aggregated from and its activation by Triton X-100 and phospholipids. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/795808 ;","Parameter set information":"Michaelis constants for substrates were taken from (Tanaka Y. et.al., 1976; Futai M., 1973). The other parameters were estimated and/or calculated using the experimental data from (Tanaka Y. et.al., 1976; Futai M., 1973).\n","Parameter set links":" ID: Futai M (1973) Membrane D-lactate dehydrogenase from Escherichia coli. Purification and properties. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4575624 ; ID: Tanaka Y. et.al. (1976) Escherichia coli membrane D-lactate dehydrogenase. Isolation of the enzyme in aggregated from and its activation by Triton X-100 and phospholipids ; Value:http://www.ncbi.nlm.nih.gov/pubmed/795808 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=DLACTDEHYDROGFAD-MONOMER ;"},"parameters":[{"units":"mM","information":"","name":"k1","value":"0.8"},{"units":"mM","information":"","name":"k11","value":"3.35"},{"units":"mM","information":"","name":"k2","value":"0.5"},{"units":"mM","information":"","name":"k21","value":"2.05"},{"units":"mM","information":"","name":"k22","value":"11.5"},{"units":"mM","information":"","name":"k3","value":"3"},{"units":"mM","information":"","name":"k31","value":"0.5"},{"units":"1/s","information":"","name":"kf","value":"0.128"},{"units":"mM","information":"","name":"kmp1","value":"60"},{"units":"mM","information":"","name":"kmp2","value":"300"},{"units":"mM","information":"","name":"kms1","value":"0.6"},{"units":"mM","information":"","name":"kms2","value":"10"}]},{"scheme":"a quinol + HEXT <=> a quinone + H+","substrates":{"s1":{"theSubstance":{"name":"a quinol","type":"substance","synonyms":["a hydroquinone","a quinol","a reduced quinone","QH2"],"links":[],"id":"SS0000147"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"HEXT","type":"substance","synonyms":["external H+","external hydrogen ion","HEXT","H+ external","hydrogen ion external"],"links":[],"id":"SS0000279"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"a quinone","type":"substance","synonyms":["a quinone","Q","quinone"],"links":[],"id":"SS0000146"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"HYD1","type":"protein","synonyms":["ec:1.12.99.6","HYD1","Hydrogenase I","NiFe hydrogenase"],"links":[],"id":"SS0000344"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"Cu2+","type":"substance","synonyms":["Cu++","Cu2+","Cu(II)","cupric copper","cupric ion"],"links":[],"id":"SS0000312"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"NaN3","type":"substance","synonyms":["azide","hydrazoic acid","NaN3"],"links":[],"id":"SS0000283"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"N3H","type":"substance","synonyms":["N3H","N-bromosuccinimide"],"links":[],"id":"SS0000343"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"Co2+","type":"substance","synonyms":["Co++","Co2+","cobalt","cobalt ion","Co(II)"],"links":[],"id":"SS0000296"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"r1*(kcatf*(s1/kms1)*(s2/kms2) - kcatr*(p1/kmp1)*(p2/kmp2))/((1 + s1/kms1 + p1/kmp1)*(1 + s2/kms2 + p2/kmp2))*((1 + r2/kiCu)/(1 + liCu*r2/kiCu))*((1 + r3/kiNaN3)/(1 + liNaN3*r3/kiNaN3))*((1 + r4/kiNB)/(1 + liNB*r4/kiNB))* ((1 + r5/kiCo)/(1 + liCo*r5/kiCo))","theSubMathModel":null,"theInformation":{"Mathematical model information":"This model is written in the form of reversible reaction equation with additional inhibition part.This model is written as the product of two parts:\r\n1) standard reversible reaction equation.\r\n2) additional inhibitory part for Cu2+ and Co2+ ions, and NaN3, N-bromosuccinimide written in terms of simple Hill functions [Sawers RG, Boxer DH, 1986].","Mathematical model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=FORMHYDROGI-CPLX ; ID: Sawers RG, Boxer DH (1986) Purification and properties of membrane-bound hydrogenase isoenzyme 1 from anaerobically grown Escherichia coli K12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3516689 ;","Parameter set information":"Only three parameters were verified for this model: kmp2 (taken from Sawers, Boxer, 1986); kiCu, liCu (verified using experimental data from the same paper). The rest parameters remained undefined.","Parameter set links":" ID: Sawers RG, Boxer DH (1986) Purification and properties of membrane-bound hydrogenase isoenzyme 1 from anaerobically grown Escherichia coli K12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3516689 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=FORMHYDROGI-CPLX ; ID: Sawers RG, Boxer DH (1986) Purification and properties of membrane-bound hydrogenase isoenzyme 1 from anaerobically grown Escherichia coli K12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3516689 ;"},"mmid":"MM0000157","psid":"PS0000149","gnid":"GN0000171","reversible":true,"information":{"Mathematical model information":"This model is written in the form of reversible reaction equation with additional inhibition part.This model is written as the product of two parts:\r\n1) standard reversible reaction equation.\r\n2) additional inhibitory part for Cu2+ and Co2+ ions, and NaN3, N-bromosuccinimide written in terms of simple Hill functions [Sawers RG, Boxer DH, 1986].","Mathematical model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=FORMHYDROGI-CPLX ; ID: Sawers RG, Boxer DH (1986) Purification and properties of membrane-bound hydrogenase isoenzyme 1 from anaerobically grown Escherichia coli K12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3516689 ;","Parameter set information":"Only three parameters were verified for this model: kmp2 (taken from Sawers, Boxer, 1986); kiCu, liCu (verified using experimental data from the same paper). The rest parameters remained undefined.","Parameter set links":" ID: Sawers RG, Boxer DH (1986) Purification and properties of membrane-bound hydrogenase isoenzyme 1 from anaerobically grown Escherichia coli K12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3516689 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=FORMHYDROGI-CPLX ; ID: Sawers RG, Boxer DH (1986) Purification and properties of membrane-bound hydrogenase isoenzyme 1 from anaerobically grown Escherichia coli K12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3516689 ;"},"parameters":[{"units":"1/s","information":"","name":"kcatf","value":"1"},{"units":"1/s","information":"","name":"kcatr","value":"1"},{"units":"mcM","information":"","name":"kiCo","value":"1"},{"units":"mcM","information":"","name":"kiCu","value":"100"},{"units":"mcM","information":"","name":"kiNB","value":"1"},{"units":"mcM","information":"","name":"kiNaN3","value":"1"},{"units":"mcM","information":"","name":"kmp1","value":"1"},{"units":"mcM","information":"","name":"kmp2","value":"2"},{"units":"mcM","information":"","name":"kms1","value":"1"},{"units":"mcM","information":"","name":"kms2","value":"1"},{"units":"","information":"","name":"liCo","value":"1"},{"units":"","information":"","name":"liCu","value":"20"},{"units":"","information":"","name":"liNB","value":"1"},{"units":"","information":"","name":"liNaN3","value":"1"}]},{"scheme":"a quinol + HEXT <=> a quinone + H+","substrates":{"s1":{"theSubstance":{"name":"a quinol","type":"substance","synonyms":["a hydroquinone","a quinol","a reduced quinone","QH2"],"links":[],"id":"SS0000147"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"HEXT","type":"substance","synonyms":["external H+","external hydrogen ion","HEXT","H+ external","hydrogen ion external"],"links":[],"id":"SS0000279"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"a quinone","type":"substance","synonyms":["a quinone","Q","quinone"],"links":[],"id":"SS0000146"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"HYD2","type":"protein","synonyms":["ec:1.12.99.6","HYD2","Hydrogenase-2","Transporter: hydrogenase 2"],"links":[],"id":"SS0000345"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"Cu2+","type":"substance","synonyms":["Cu++","Cu2+","Cu(II)","cupric copper","cupric ion"],"links":[],"id":"SS0000312"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"Co2+","type":"substance","synonyms":["Co++","Co2+","cobalt","cobalt ion","Co(II)"],"links":[],"id":"SS0000296"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"N3H","type":"substance","synonyms":["N3H","N-bromosuccinimide"],"links":[],"id":"SS0000343"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"r1*(kcatf*(s1/kms1)*(s2/kms2) - kcatr*(p1/kmp1)*(p2/kmp2))/((1 + s1/kms1 + p1/kmp1)*(1 + s2/kms2 + p2/kmp2)*(1 + r2/kiCu)* (1 + r3/kiCo)* (1 + r4/kiNB))","theSubMathModel":null,"theInformation":{"Mathematical model information":"This simple model is written in the form of reversible reaction with additional inhibition part.This model is written as the product of two parts: \r\n1) standard reversible reaction equation.\r\n2) additional inhibitory part for Cu2+ and Co2+ ions, N-bromosuccinimide written in terms of simple Hill functions [Sawers RG, Boxer DH, 1986].","Mathematical model links":" ID: Sawers RG, Boxer DH (1986) Purification and properties of membrane-bound hydrogenase isoenzyme 1 from anaerobically grown Escherichia coli K12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3516689 ;","Parameter set information":"Only two parameters were identified for this model: kmp2 (taken from Sawers RG, Boxer DH, 1986), and kiCu (verified using experimental data from the same paper). The rest parameters remained undefined.","Parameter set links":" ID: Sawers RG, Boxer DH (1986) Purification and properties of membrane-bound hydrogenase isoenzyme 1 from anaerobically grown Escherichia coli K12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3516689 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=FORMHYDROG2-CPLX ; ID: Sawers RG, Boxer DH (1986) Purification and properties of membrane-bound hydrogenase isoenzyme 1 from anaerobically grown Escherichia coli K12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3516689 ;"},"mmid":"MM0000158","psid":"PS0000150","gnid":"GN0000172","reversible":true,"information":{"Mathematical model information":"This simple model is written in the form of reversible reaction with additional inhibition part.This model is written as the product of two parts: \r\n1) standard reversible reaction equation.\r\n2) additional inhibitory part for Cu2+ and Co2+ ions, N-bromosuccinimide written in terms of simple Hill functions [Sawers RG, Boxer DH, 1986].","Mathematical model links":" ID: Sawers RG, Boxer DH (1986) Purification and properties of membrane-bound hydrogenase isoenzyme 1 from anaerobically grown Escherichia coli K12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3516689 ;","Parameter set information":"Only two parameters were identified for this model: kmp2 (taken from Sawers RG, Boxer DH, 1986), and kiCu (verified using experimental data from the same paper). The rest parameters remained undefined.","Parameter set links":" ID: Sawers RG, Boxer DH (1986) Purification and properties of membrane-bound hydrogenase isoenzyme 1 from anaerobically grown Escherichia coli K12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3516689 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=FORMHYDROG2-CPLX ; ID: Sawers RG, Boxer DH (1986) Purification and properties of membrane-bound hydrogenase isoenzyme 1 from anaerobically grown Escherichia coli K12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3516689 ;"},"parameters":[{"units":"1/s","information":"","name":"kcatf","value":"1"},{"units":"1/s","information":"","name":"kcatr","value":"1"},{"units":"mcM","information":"","name":"kiCo","value":"1000"},{"units":"mcM","information":"","name":"kiCu","value":"100"},{"units":"mcM","information":"","name":"kiNB","value":"1000"},{"units":"mcM","information":"","name":"kmp1","value":"1"},{"units":"mcM","information":"","name":"kmp2","value":"3.7"},{"units":"mcM","information":"","name":"kms1","value":"1"},{"units":"mcM","information":"","name":"kms2","value":"1"}]},{"scheme":"ATP <=> ADP + Pi + HEXT","substrates":{"s1":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"Pi","type":"substance","synonyms":["H3PO4","Orthophosphate","Orthophosphoric acid","Phosphate","Phosphoric acid","Pi"],"links":[],"id":"SS0000070"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"HEXT","type":"substance","synonyms":["external H+","external hydrogen ion","HEXT","H+ external","hydrogen ion external"],"links":[],"id":"SS0000279"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"ATP synthase","type":"protein","synonyms":["adenosinetriphosphatase","ATP synthase","ATP synthase F1F0","EC:3.6.3.14","F0 complex","F0F1-ATPase","F-1F-0-type ATPase","FoF1-ATPase"],"links":[],"id":"SS0000202"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"Mg","type":"substance","synonyms":["Magnesium","Magnesium ion","Mg","Mg++","Mg2+"],"links":[],"id":"SS0000277"},"theState":null,"compartment":"","theInfluence":"complex regulator"},"r3":{"theSubstance":{"name":"Co2+","type":"substance","synonyms":["Co++","Co2+","cobalt","cobalt ion","Co(II)"],"links":[],"id":"SS0000296"},"theState":null,"compartment":"","theInfluence":"complex regulator"},"r4":{"theSubstance":{"name":"Ca2+","type":"substance","synonyms":["Ca++","Ca2+","calcium","calcium ion"],"links":[],"id":"SS0000346"},"theState":null,"compartment":"","theInfluence":"complex regulator"},"r5":{"theSubstance":{"name":"Mn2+","type":"substance","synonyms":["manganese (II) ion","manganese ion","Mn++","Mn2+","Mn(II)"],"links":[],"id":"SS0000294"},"theState":null,"compartment":"","theInfluence":"complex regulator"},"r6":{"theSubstance":{"name":"Cu2+","type":"substance","synonyms":["Cu++","Cu2+","Cu(II)","cupric copper","cupric ion"],"links":[],"id":"SS0000312"},"theState":null,"compartment":"","theInfluence":"complex regulator"},"r7":{"theSubstance":{"name":"Zn2+","type":"substance","synonyms":["Zinc","zinc ion","Zn","Zn++","Zn2+","Zn(II)"],"links":[],"id":"SS0000311"},"theState":null,"compartment":"","theInfluence":"complex regulator"},"r8":{"theSubstance":{"name":"Na+","type":"substance","synonyms":["Na+","Sodium","sodium ion"],"links":[],"id":"SS0000347"},"theState":null,"compartment":"","theInfluence":"complex regulator"},"r9":{"theSubstance":{"name":"K+","type":"substance","synonyms":["K+","potassium","potassium ion"],"links":[],"id":"SS0000348"},"theState":null,"compartment":"","theInfluence":"complex regulator"}},"theMathModel":"(kf*r1*(s1/kmATP)-kr*r1*(p1/kiADP)*(p2/kmPI)*(p3/kmHEXT)^4)/((1+p3/kmHEXT)^4*(1 +p2/kmPI+ s1/kmATP + p1/kiADP))* (((k0Mg/(1 + s1/kiMg0ATP) + (ilaMg*(1 + s1/klaMg)/(1 + llaMg*s1/klaMg))*r2/(ikaMg*(1 + (lkaMg*s1/kkaMg)^nkaMg)/(1 + (s1/kkaMg)^nkaMg)))/(1 + r2/(ikaMg*(1 + (lkaMg*s1/kkaMg)^nkaMg)/(1 + (s1/kkaMg)^nkaMg))*(1 + (r2/(ikiMg*(1 + (lkiMg*s1/kkiMg)^nkiMg)/(1 +(s1/kkiMg)^nkiMg)))^ (iniMg*(1 + (lniMg*s1/kniMg)^nniMg)/(1 +(s1/kniMg)^nniMg)))))*((1 + (s1/kiATP)^niATP)/ (1 + (liATP*s1/kiATP)^niATP))*((1 + (laNa*r8/kaNa)^naNa*(1 + (r8/kiNa)^niNa))/(1 + (r8/kaNa)^naNa*(1 + (liNa*r8/kiNa)^niNa)))*((1 + (r9/(ikiK*(1 + r8/kNaK)/(1 + lNaK*r8/kNaK)))^niK)/(1 + (((1 + lNaliK*r8/kNaliK)/(1 + r8/kNaliK))*r9/(ikiK*(1 + r8/kNaK)/(1 + lNaK*r8/kNaK)))^niK)))","theSubMathModel":null,"theInformation":{"Mathematical model information":" The following factors are taken into account in this model: 1) ADP is a concurent inhibitor; 2) Mg2+ activates reaction, but it is affected by ATP to play various roles, including inhibitory; 3) Na+ is an activator at lesser concentrations, and an inhibitor at more concentrations; 4) K+ is inhibitor and its influence is regulated by N+. ","Mathematical model links":" ID: Khlebodarova TM et al (2006) Gene network reconstruction and mathematical modeling of E. coli respiration: regulation of f0f1-atp synthase by metal ions ; Value:http://www.bionet.nsc.ru/meeting/bgrs2006/BGRS_2006_V2.pdf ;","Parameter set information":" The model is described in detail in (Khlebodarova et al, 2006). Only 4 parameters remained undefined due to the lack of experimental data (kf, kr, kmPI, kmHEXT). The other parameters vere determined using experimental data from (Weber et al, 1996; Koebmann et al, 2002). ","Parameter set links":" ID: Khlebodarova TM et al (2006) Gene network reconstruction and mathematical modeling of E. coli respiration: regulation of f0f1-atp synthase by metal ions ; Value:http://www.bionet.nsc.ru/meeting/bgrs2006/BGRS_2006_V2.pdf ; ID: Koebmann BJ et al (2002) The glycolytic flux in Escherichia coli is controlled by the demand for ATP. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12081962 ; ID: Weber J et al (1996) Specific tryptophan substitution in catalytic sites of Escherichia coli F1-ATPase allows differentiation between bound substrate ATP and product ADP in steady-state catalysis. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8702526 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=ATPSYN-RXN ;"},"mmid":"MM0000159","psid":"PS0000151","gnid":"GN0000173","reversible":true,"information":{"Mathematical model information":" The following factors are taken into account in this model: 1) ADP is a concurent inhibitor; 2) Mg2+ activates reaction, but it is affected by ATP to play various roles, including inhibitory; 3) Na+ is an activator at lesser concentrations, and an inhibitor at more concentrations; 4) K+ is inhibitor and its influence is regulated by N+. ","Mathematical model links":" ID: Khlebodarova TM et al (2006) Gene network reconstruction and mathematical modeling of E. coli respiration: regulation of f0f1-atp synthase by metal ions ; Value:http://www.bionet.nsc.ru/meeting/bgrs2006/BGRS_2006_V2.pdf ;","Parameter set information":" The model is described in detail in (Khlebodarova et al, 2006). Only 4 parameters remained undefined due to the lack of experimental data (kf, kr, kmPI, kmHEXT). The other parameters vere determined using experimental data from (Weber et al, 1996; Koebmann et al, 2002). ","Parameter set links":" ID: Khlebodarova TM et al (2006) Gene network reconstruction and mathematical modeling of E. coli respiration: regulation of f0f1-atp synthase by metal ions ; Value:http://www.bionet.nsc.ru/meeting/bgrs2006/BGRS_2006_V2.pdf ; ID: Koebmann BJ et al (2002) The glycolytic flux in Escherichia coli is controlled by the demand for ATP. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12081962 ; ID: Weber J et al (1996) Specific tryptophan substitution in catalytic sites of Escherichia coli F1-ATPase allows differentiation between bound substrate ATP and product ADP in steady-state catalysis. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8702526 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=ATPSYN-RXN ;"},"parameters":[{"units":"","information":"","name":"ikaMg","value":"1.1"},{"units":"","information":"","name":"ikiK","value":"50"},{"units":"","information":"","name":"ikiMg","value":"1.1"},{"units":"","information":"","name":"ilaMg","value":"1.2"},{"units":"","information":"","name":"iniMg","value":"1.5"},{"units":"mM","information":"","name":"k0Mg","value":"0.005"},{"units":"mM","information":"","name":"kNaK","value":"36"},{"units":"mM","information":"","name":"kNaliK","value":"7"},{"units":"mM","information":"","name":"kaNa","value":"19"},{"units":"1/s","information":"","name":"kf","value":"1"},{"units":"mM","information":"","name":"kiADP","value":"0.3"},{"units":"mM","information":"","name":"kiATP","value":"8"},{"units":"mM","information":"","name":"kiMg0ATP","value":"0.1"},{"units":"mM","information":"","name":"kiNa","value":"26"},{"units":"mM","information":"","name":"kkaMg","value":"8.3"},{"units":"mM","information":"","name":"kkiMg","value":"8.3"},{"units":"mM","information":"","name":"klaMg","value":"16"},{"units":"mM","information":"","name":"kmATP","value":"0.6"},{"units":"mM","information":"","name":"kmHEXT","value":"10000"},{"units":"mM","information":"","name":"kmPI","value":"100"},{"units":"mM","information":"","name":"kniMg","value":"3.9"},{"units":"1/s","information":"","name":"kr","value":"1"},{"units":"","information":"","name":"lNaK","value":"2.56"},{"units":"","information":"","name":"lNaliK","value":"1.15"},{"units":"","information":"","name":"laNa","value":"1.29"},{"units":"","information":"","name":"liATP","value":"1.06"},{"units":"","information":"","name":"liNa","value":"1.32"},{"units":"","information":"","name":"lkaMg","value":"1.78"},{"units":"","information":"","name":"lkiMg","value":"1.86"},{"units":"","information":"","name":"llaMg","value":"8"},{"units":"","information":"","name":"lniMg","value":"1.05"},{"units":"","information":"","name":"naNa","value":"1.5"},{"units":"","information":"","name":"niATP","value":"8"},{"units":"","information":"","name":"niK","value":"3"},{"units":"","information":"","name":"niNa","value":"2"},{"units":"","information":"","name":"nkaMg","value":"3.55"},{"units":"","information":"","name":"nkiMg","value":"3.55"},{"units":"","information":"","name":"nniMg","value":"12"}]},{"scheme":"-> CarA","substrates":null,"products":{"p1":{"theSubstance":{"name":"CarA","type":"protein","synonyms":["a chain","arg","CarA","PyrA","small chain"],"links":[],"id":"SS0000350"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"carA","type":"gene","synonyms":["b0032","carA"],"links":[],"id":"SS0000206"},"theState":null,"compartment":"","theInfluence":""},"r10":{"theSubstance":{"name":"PepA","type":"protein","synonyms":["aminopeptidase A/I","PepA"],"links":[],"id":"SS0000354"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r2":{"theSubstance":{"name":"UTP","type":"substance","synonyms":["Uridine 5'-triphosphate","Uridine triphosphate","UTP"],"links":[],"id":"SS0000026"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"RutR","type":"protein","synonyms":["RutR","RutR DNA-binding transcriptional dual regulator"],"links":[],"id":"SS0000357"},"theState":null,"compartment":"","theInfluence":"activator"},"r4":{"theSubstance":{"name":"Ura","type":"substance","synonyms":["Ura","Uracil"],"links":[],"id":"SS0000040"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"Thy","type":"substance","synonyms":["5-Methyluracil","Thy","Thymine"],"links":[],"id":"SS0000056"},"theState":null,"compartment":"","theInfluence":"activator"},"r6":{"theSubstance":{"name":"PurR","type":"protein","synonyms":["PurR","PurR transcriptional repressor"],"links":[],"id":"SS0000358"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r7":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r8":{"theSubstance":{"name":"G","type":"substance","synonyms":["2-Amino-6-hydroxypurine","G","Guanine"],"links":[],"id":"SS0000114"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r9":{"theSubstance":{"name":"IHF","type":"protein","synonyms":["IHF"],"links":[],"id":"SS0000353"},"theState":null,"compartment":"","theInfluence":"complex regulator"}},"theMathModel":"ks*(1/(1+(r2/kUTP)^hUTP))*((1+(((r3-(((r3*(r4^2))/(kdisRutRura^2))/(1+((2*r3*r4+r4^2)/(kdisRutRura^2))+((2*r3*r5+r5^2)/(kdisRutRthy^2))))-(((r3*(r5^2))/(kdisRutRthy^2))/(1+((2*r3*r4+r4^2)/(kdisRutRura^2))+((2*r3*r5+r5^2)/(kdisRutRthy^2)))))+(((r3*(r5^2))/(kdisRutRthy^2))/(1+((2*r3*r4+r4^2)/(kdisRutRura^2))+((2*r3*r5+r5^2)/(kdisRutRthy^2)))))/kRutR))/(1+(1+((((r6*(r7^2))/(kdisPurRhyp^2))/(1+((2*r6*r7+r7^2)/(kdisPurRhyp^2))+((2*r6*r8+r8^2)/(kdisPurRgua^2))))/k1PurR)+((((r6*(r8^2))/(kdisPurRgua^2))/(1+((2*r6*r7+r7^2)/(kdisPurRhyp^2))+((2*r6*r8+r8^2)/(kdisPurRgua^2))))/k2PurR)+((r6-(((r6*(r7^2))/(kdisPurRhyp^2))/(1+((2*r6*r7+r7^2)/(kdisPurRhyp^2))+((2*r6*r8+r8^2)/(kdisPurRgua^2))))-(((r6*(r8^2))/(kdisPurRgua^2))/(1+((2*r6*r7+r7^2)/(kdisPurRhyp^2))+((2*r6*r8+r8^2)/(kdisPurRgua^2))))))/k3PurR)*(1+(r4/k1ura)+(r4/k2ura)*(r9/kIHF))*(r10/kPepA)+(((r3-(((r3*(r4^2))/(kdisRutRura^2))/(1+((2*r3*r4+r4^2)/(kdisRutRura^2))+((2*r3*r5+r5^2)/(kdisRutRthy^2))))-(((r3*(r5^2))/(kdisRutRthy^2))/(1+((2*r3*r4+r4^2)/(kdisRutRura^2))+((2*r3*r5+r5^2)/(kdisRutRthy^2)))))+(((r3*(r5^2))/(kdisRutRthy^2))/(1+((2*r3*r4+r4^2)/(kdisRutRura^2))+((2*r3*r5+r5^2)/(kdisRutRthy^2)))))/kRutR)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Devroede N., 2006].","Mathematical model links":" ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ;","Parameter set information":"Parameter ks (ks1) was obtained from the algebraic equation of the form: ks1*f1+ks2*f2-kd*CarA = 0, where CarA - concentration of the protein, kd - the constant of degradation, f1,f2 - the proportion of transcripts from the promoter carAp1 and carAp2.ks1,ks2 - protein synthesis generalized constant from the promoter carAp1 and carAp2. kd = 0.008 [1/sec],CarA = 0.4 [mM].ks2=0.01*ks1. Parameters kUTP and hUTP were evaluated basing on [Han et al., 1998] experimental data. Parameters kRutR, k1PurR, k2PurR, k3PurR, k1Ura, k2Ura, kIHF and kPepA were evaluated basing on [Devroede et al., 2006] experimental data. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994].","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ;","Structural model information":"    Genes carA and carB are part of an operon carAB and encode structure of the subunits of the enzyme carbamoyl phosphate synthetase  (EC 6.3.5.5).\nExpression of the operon carAB is controlled purines and pyrimidines by promoter carAp1, and arginine - a promoter carAp2. Here we consider the process of synthesis protein CarA with the promoter carAp1. In the proposed regulatory mechanism, increased intracellular levels of UTP promote reiterative transcription, which results in the synthesis of transcripts with the sequence GUUUUn (where n = 1 to 30). These transcripts are not extended downstream to include structural gene sequences. In contrast, lower levels of UTP enhance normal template-directed addition of a G residue at position 5 of the nascent transcript. This addition precludes reiterative transcription and permits normal transcript elongation capable of producing translatable carAB transcripts. Thus, carAB expression, which is necessary for pyrimidine nucleotide (and arginine) biosynthesis, increases in proportion to the cellular need for UTP. Therefore,this model describes the process of inhibition. To describe the model we have used the generalized Hill function. There are several binding sites for proteins - integration host factor (IHF), PepA, PurR, and RutR. cc ","Structural model links":" ID: Ali Azam et al., 1999 Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10515926 ; ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10134 ; ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Shimada et al., 2007 RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17919280 ;"},"mmid":"MM0000220","psid":"PS0000212","gnid":"GN0000213","reversible":false,"information":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Devroede N., 2006].","Mathematical model links":" ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ;","Parameter set information":"Parameter ks (ks1) was obtained from the algebraic equation of the form: ks1*f1+ks2*f2-kd*CarA = 0, where CarA - concentration of the protein, kd - the constant of degradation, f1,f2 - the proportion of transcripts from the promoter carAp1 and carAp2.ks1,ks2 - protein synthesis generalized constant from the promoter carAp1 and carAp2. kd = 0.008 [1/sec],CarA = 0.4 [mM].ks2=0.01*ks1. Parameters kUTP and hUTP were evaluated basing on [Han et al., 1998] experimental data. Parameters kRutR, k1PurR, k2PurR, k3PurR, k1Ura, k2Ura, kIHF and kPepA were evaluated basing on [Devroede et al., 2006] experimental data. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994].","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ;","Structural model information":"    Genes carA and carB are part of an operon carAB and encode structure of the subunits of the enzyme carbamoyl phosphate synthetase  (EC 6.3.5.5).\nExpression of the operon carAB is controlled purines and pyrimidines by promoter carAp1, and arginine - a promoter carAp2. Here we consider the process of synthesis protein CarA with the promoter carAp1. In the proposed regulatory mechanism, increased intracellular levels of UTP promote reiterative transcription, which results in the synthesis of transcripts with the sequence GUUUUn (where n = 1 to 30). These transcripts are not extended downstream to include structural gene sequences. In contrast, lower levels of UTP enhance normal template-directed addition of a G residue at position 5 of the nascent transcript. This addition precludes reiterative transcription and permits normal transcript elongation capable of producing translatable carAB transcripts. Thus, carAB expression, which is necessary for pyrimidine nucleotide (and arginine) biosynthesis, increases in proportion to the cellular need for UTP. Therefore,this model describes the process of inhibition. To describe the model we have used the generalized Hill function. There are several binding sites for proteins - integration host factor (IHF), PepA, PurR, and RutR. cc ","Structural model links":" ID: Ali Azam et al., 1999 Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10515926 ; ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10134 ; ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Shimada et al., 2007 RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17919280 ;"},"parameters":[{"units":"","information":"","name":"hUTP","value":"1.5"},{"units":"mM","information":"","name":"k1PurR","value":"0.000185"},{"units":"mM","information":"","name":"k1ura","value":"0.7"},{"units":"mM","information":"","name":"k2PurR","value":"0.000185"},{"units":"mM","information":"","name":"k2ura","value":"0.005"},{"units":"mM","information":"","name":"k3PurR","value":"0.0008"},{"units":"mM","information":"","name":"kIHF","value":"0.09"},{"units":"mM","information":"","name":"kPepA","value":"0.00033"},{"units":"mM","information":"","name":"kRutR","value":"0.0001136"},{"units":"mM","information":"","name":"kUTP","value":"0.7"},{"units":"mM","information":"","name":"kdisPurRgua","value":"0.0015"},{"units":"mM","information":"","name":"kdisPurRhyp","value":"0.0093"},{"units":"mM","information":"","name":"kdisRutRthy","value":"0.001"},{"units":"mM","information":"","name":"kdisRutRura","value":"0.001"},{"units":"mM/sec","information":"","name":"ks","value":"0.0123"}]},{"scheme":"UMP + ATP <=> UDP + ADP + H+","substrates":{"s1":{"theSubstance":{"name":"UMP","type":"substance","synonyms":["5'Uridylic acid","UMP","Uridine 5'-monophosphate","Uridine monophosphate","Uridylic acid"],"links":[],"id":"SS0000024"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"UDP","type":"substance","synonyms":["UDP","Uridine 5'-diphosphate"],"links":[],"id":"SS0000025"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PyrH","type":"protein","synonyms":["PyrH","SmbA","Umk","UMP kinase","uridylate kinase"],"links":[],"id":"SS0000153"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"GTP","type":"substance","synonyms":["GTP","Guanosine 5'-triphosphate"],"links":[],"id":"SS0000140"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"UTP","type":"substance","synonyms":["Uridine 5'-triphosphate","Uridine triphosphate","UTP"],"links":[],"id":"SS0000026"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"((r1*kcat*(s1/kmump)*(s2/kmatp))/((1+(s1/kmump))*(1+(s2/kmatp))))*((1+((r2/kgtp1)^hgtp))/(1+((r2/kgtp2)^hgtp)))*(1/(1+(r3/kutp)^hutp))","theSubMathModel":null,"theInformation":{"Mathematical model information":"The reaction follows Michaelis-Menten kinetics. The model equation is based on the data that UTP and GTP are non- competitive effectors (Serina et al., 1995).","Mathematical model links":" ID: Serina et al., 1995 Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7711027 ;","Parameter set information":"Parameter kcat was extracted from Serina et al., 1996 data. Parameters kmump, kmatp, kgtp1, kgtp2, hgtp, kutp and hutp were evaluated on basis of the experimental data (Serina et al., 1995). Moreover, to simulate the enzymatic kinetics you can use steady-state concentration for ATP=9.6 mM (Bennett et al., 2009). The model was simulated upon steady state concentration of PyrF enzyme, which equals 0.0007 mM (Lu et al., 2007).","Parameter set links":" ID: Bennett et al. 2009 Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol. 2009 Aug;5(8):593-599. doi: 10.1038/nchembio.186. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=19561621 ; ID: Lu et al. 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol. 2007 Jan;25(1):117-124. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=17187058 ; ID: Serina et al. 1996 Structural properties of UMP-kinase from Escherichia coli: modulation of protein solubility by pH and UTP. Biochemistry. 1996 Jun 4;35(22):7003-11. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=8679525 ; ID: Serina et al., 1995 Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7711027 ;","Structural model information":"UMP kinase (PyrH) is an essential enzyme in the de novo pyrimidines’ biosynthesis that catalyzes the chemical reaction ATP + UMP (reversible) ADP + UDP.  The enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with a phosphate group as acceptor. The systematic name of this enzyme class is ATP:UMP phosphotransferase. The enzyme is subject to complex regulatory control by GTP and UTP (Serina et al., 1995). Crystal structures of PyrH bound to its substrate, product, competitive inhibitor UTP (Briozzo et al., 2005, that contradicts to earlier data (Serina et al., 1995)) and allosteric regulator GTP (Meyer et al., 2008) have been solved. The GTP and UTP binding sites do not overlap (Meyer et al., 2008, Marco-Marin and Rubio., 2009).","Structural model links":" ID: Briozzo et al. 2005 Structure of Escherichia coli UMP kinase differs from that of other nucleoside monophosphate kinases and sheds new light on enzyme regulation. J Biol Chem. 2005 Jul 8;280(27):25533-25540. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=15857829 ; ID: EcoCyc ; Value:http://biocyc.org/NEW-IMAGE?type=EC-NUMBER&object=EC-2.7.4.22 ; ID: Marco-Marín and Rubio 2009 The site for the allosteric activator GTP of Escherichia coli UMP kinase. FEBS Lett. 2009 Jan 5;583(1):185-9. doi: 10.1016/j.febslet.2008.11.043. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=19071117 ; ID: Meyer et al. 2008 Structural and functional characterization of Escherichia coli UMP kinase in complex with its allosteric regulator GTP. J Biol Chem. 2008 Dec 19;283(51):36011-36018. doi: 10.1074/jbc.M802614200. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=18945668 ; ID: Serina et al. 1995 Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP. Biochemistry. 1995 Apr 18;34(15):5066-5074. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=7711027 ;"},"mmid":"MM0000125","psid":"PS0000119","gnid":"GN0000064","reversible":true,"information":{"Mathematical model information":"The reaction follows Michaelis-Menten kinetics. The model equation is based on the data that UTP and GTP are non- competitive effectors (Serina et al., 1995).","Mathematical model links":" ID: Serina et al., 1995 Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7711027 ;","Parameter set information":"Parameter kcat was extracted from Serina et al., 1996 data. Parameters kmump, kmatp, kgtp1, kgtp2, hgtp, kutp and hutp were evaluated on basis of the experimental data (Serina et al., 1995). Moreover, to simulate the enzymatic kinetics you can use steady-state concentration for ATP=9.6 mM (Bennett et al., 2009). The model was simulated upon steady state concentration of PyrF enzyme, which equals 0.0007 mM (Lu et al., 2007).","Parameter set links":" ID: Bennett et al. 2009 Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol. 2009 Aug;5(8):593-599. doi: 10.1038/nchembio.186. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=19561621 ; ID: Lu et al. 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol. 2007 Jan;25(1):117-124. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=17187058 ; ID: Serina et al. 1996 Structural properties of UMP-kinase from Escherichia coli: modulation of protein solubility by pH and UTP. Biochemistry. 1996 Jun 4;35(22):7003-11. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=8679525 ; ID: Serina et al., 1995 Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7711027 ;","Structural model information":"UMP kinase (PyrH) is an essential enzyme in the de novo pyrimidines’ biosynthesis that catalyzes the chemical reaction ATP + UMP (reversible) ADP + UDP.  The enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with a phosphate group as acceptor. The systematic name of this enzyme class is ATP:UMP phosphotransferase. The enzyme is subject to complex regulatory control by GTP and UTP (Serina et al., 1995). Crystal structures of PyrH bound to its substrate, product, competitive inhibitor UTP (Briozzo et al., 2005, that contradicts to earlier data (Serina et al., 1995)) and allosteric regulator GTP (Meyer et al., 2008) have been solved. The GTP and UTP binding sites do not overlap (Meyer et al., 2008, Marco-Marin and Rubio., 2009).","Structural model links":" ID: Briozzo et al. 2005 Structure of Escherichia coli UMP kinase differs from that of other nucleoside monophosphate kinases and sheds new light on enzyme regulation. J Biol Chem. 2005 Jul 8;280(27):25533-25540. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=15857829 ; ID: EcoCyc ; Value:http://biocyc.org/NEW-IMAGE?type=EC-NUMBER&object=EC-2.7.4.22 ; ID: Marco-Marín and Rubio 2009 The site for the allosteric activator GTP of Escherichia coli UMP kinase. FEBS Lett. 2009 Jan 5;583(1):185-9. doi: 10.1016/j.febslet.2008.11.043. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=19071117 ; ID: Meyer et al. 2008 Structural and functional characterization of Escherichia coli UMP kinase in complex with its allosteric regulator GTP. J Biol Chem. 2008 Dec 19;283(51):36011-36018. doi: 10.1074/jbc.M802614200. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=18945668 ; ID: Serina et al. 1995 Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP. Biochemistry. 1995 Apr 18;34(15):5066-5074. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=7711027 ;"},"parameters":[{"units":"","information":"","name":"hgtp","value":"1.6"},{"units":"","information":"","name":"hutp","value":"2.4"},{"units":"1/sec","information":"","name":"kcat","value":"332"},{"units":"mM","information":"","name":"kgtp1","value":"0.05"},{"units":"mM","information":"","name":"kgtp2","value":"0.07"},{"units":"mM","information":"","name":"kmatp","value":"0.12"},{"units":"mM","information":"","name":"kmump","value":"0.05"},{"units":"mM","information":"","name":"kutp","value":"0.54"}]},{"scheme":"-> CarA","substrates":null,"products":{"p1":{"theSubstance":{"name":"CarA","type":"protein","synonyms":["a chain","arg","CarA","PyrA","small chain"],"links":[],"id":"SS0000350"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"carA","type":"gene","synonyms":["b0032","carA"],"links":[],"id":"SS0000206"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"ArgR","type":"protein","synonyms":["ArgR"],"links":[],"id":"SS0000386"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"arg","type":"substance","synonyms":["2-amino-5-guanidinovaleric acid","arg","arginine","L-arginine","R"],"links":[],"id":"SS0000387"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"ks*(1/(1+((((r2*(r3^6))/(kdisArgRarg^6))/(1+((6*r2*(r3^5)+(r3^6))/(kdisArgRarg^6))))/kArgR)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Caldara et al., 2006].","Mathematical model links":" ID: Caldara et al., 2006 The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17074904 ;","Parameter set information":"Parameter ks (ks2) was obtained from the algebraic equation of the form: ks1*f1+ks2*f2-kd*CarA = 0, where CarA - concentration of the protein, kd - the constant of degradation, f1,f2 - the proportion of transcripts from the promoter carAp1 and carAp2.ks1,ks2 - protein synthesis generalized constant from the promoter carAp1 and carAp2. kd = 0.008 [1/sec],CarA = 0.4 [mM]. ks2=0.01*ks1. Parameter kArgR was evaluated basing on [Caldara et al., 2006] experimental data.","Parameter set links":" ID: Caldara et al., 2006 The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17074904 ;","Structural model information":"Genes carA and carB are part of an operon carAB and encode structure of the subunits of the enzyme carbamoyl phosphate synthetase (EC 6.3.5.5). Expression of the operon carAB is controlled purines and pyrimidines by promoter carAp1, and arginine - a promoter carAp2.Here we consider the process of synthesis protein CarA with the promoter carAp2.","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10134 ;"},"mmid":"MM0000222","psid":"PS0000213","gnid":"GN0000214","reversible":false,"information":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Caldara et al., 2006].","Mathematical model links":" ID: Caldara et al., 2006 The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17074904 ;","Parameter set information":"Parameter ks (ks2) was obtained from the algebraic equation of the form: ks1*f1+ks2*f2-kd*CarA = 0, where CarA - concentration of the protein, kd - the constant of degradation, f1,f2 - the proportion of transcripts from the promoter carAp1 and carAp2.ks1,ks2 - protein synthesis generalized constant from the promoter carAp1 and carAp2. kd = 0.008 [1/sec],CarA = 0.4 [mM]. ks2=0.01*ks1. Parameter kArgR was evaluated basing on [Caldara et al., 2006] experimental data.","Parameter set links":" ID: Caldara et al., 2006 The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17074904 ;","Structural model information":"Genes carA and carB are part of an operon carAB and encode structure of the subunits of the enzyme carbamoyl phosphate synthetase (EC 6.3.5.5). Expression of the operon carAB is controlled purines and pyrimidines by promoter carAp1, and arginine - a promoter carAp2.Here we consider the process of synthesis protein CarA with the promoter carAp2.","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10134 ;"},"parameters":[{"units":"mM","information":"","name":"kArgR","value":"0.0317"},{"units":"mM","information":"","name":"kdisArgRarg","value":"0.001"},{"units":"mM/sec","information":"","name":"ks","value":"0.000123"}]},{"scheme":"-> PyrD","substrates":null,"products":{"p1":{"theSubstance":{"name":"PyrD","type":"protein","synonyms":["dihydroorotate dehydrogenase","PyrD"],"links":[],"id":"SS0000367"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"pyrD","type":"gene","synonyms":["b0945","pyrD"],"links":[],"id":"SS0000210"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"GTP","type":"substance","synonyms":["GTP","Guanosine 5'-triphosphate"],"links":[],"id":"SS0000140"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"CTP","type":"substance","synonyms":["CTP","Cytidine 5'-triphosphate","Cytidine triphosphate"],"links":[],"id":"SS0000027"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"PurR","type":"protein","synonyms":["PurR","PurR transcriptional repressor"],"links":[],"id":"SS0000358"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"Gua","type":"substance","synonyms":["Gua","Guanosine"],"links":[],"id":"SS0000113"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r6":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r7":{"theSubstance":{"name":"Fis","type":"protein","synonyms":["Fis"],"links":[],"id":"SS0000389"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"ks*(((r2/kGTP)^hGTP)/(1+((r2/kGTP)^hGTP)+((r3/kCTP)^hCTP)+w*((r2/kGTP)^hGTP)*((r3/kCTP)^hCTP)))*((1+((r4-(((r4*(r5^2))/(kdisPurRhyp^2))/(1+((2*r4*r5+r5^2)/(kdisPurRhyp^2))+((2*r4*r6+r6^2)/(kdisPurRgua^2))))-(((r4*(r6^2))/(kdisPurRgua^2))/(1+((2*r4*r5+r5^2)/(kdisPurRhyp^2))+((2*r4*r6+r6^2)/(kdisPurRgua^2)))))/k3PurR))/(1+((((r4*(r5^2))/(kdisPurRhyp^2))/(1+((2*r4*r5+r5^2)/(kdisPurRhyp^2))+((2*r4*r6+r6^2)/(kdisPurRgua^2))))/k1PurR)+((((r4*(r6^2))/(kdisPurRgua^2))/(1+((2*r4*r5+r5^2)/(kdisPurRhyp^2))+((2*r4*r6+r6^2)/(kdisPurRgua^2))))/k2PurR)+((r4-(((r4*(r5^2))/(kdisPurRhyp^2))/(1+((2*r4*r5+r5^2)/(kdisPurRhyp^2))+((2*r4*r6+r6^2)/(kdisPurRgua^2))))-(((r4*(r6^2))/(kdisPurRgua^2))/(1+((2*r4*r5+r5^2)/(kdisPurRhyp^2))+((2*r4*r6+r6^2)/(kdisPurRgua^2)))))/k3PurR)))*(1/(1+r7/kFis))","theSubMathModel":null,"theInformation":{"Mathematical model information":"The mathematical model describes the regulation of gene pyrD.The model is similar to the model describing the regulation of pyrC. To describe the model we have used the generalized Hill function.","Mathematical model links":" ID: Likhoshvai et al., 2010 Metabolic Engineering in Silico. ; Value:http://www.springerlink.com/content/51438683725255u1/ ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PyrD = 0, where PyrD - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter pyrDp. ks - protein synthesis generalized constant from the promoter pyrDp. kd = 0.002 [1/sec],PyrD = 0.0050073 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters kGTP, hGTP, kCTP,hCTP and w were evaluated basing on [Wilson et al., 1992, Likhoshvai et al., 2010] experimental data. Parameter kFis was evaluated basing on [Bradley et al., 2007] experimental data. Parameters k1PurR and k2PurR were evaluated basing on [Wilson et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Bradley M.D. et al., 2007 Effects of Fis on Escherichia coli gene expression during different growth stages. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17768236 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Likhoshvai et al., 2010 Metabolic Engineering in Silico. ; Value:http://www.springerlink.com/content/51438683725255u1/ ; ID: Wilson HR, Turnbough CL Jr., 1990 Role of the purine repressor in the regulation of pyrimidine gene expression in Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1971621 ; ID: Wilson et al., 1992 Translational control of pyrC expression mediated by nucleotide-sensitive selection of transcriptional start sites in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1345912 ;","Structural model information":" Results from [Wilson et al., 1992] laboratory indicate that the expression of the pyrD gene of E. coli is similarly regulated  CTP, GTP and PurR as pyrC. Using microarray Bradley et al (2007) showed that in the early exponential growth phase cells Fis inhibits gene expression pyrD 2.6 times. They also predicted the binding site for Fis, which overlaps with the start of transcription, but experimentally, this site has not been confirmed. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]; The concentration of Fis (dimer) = 0.05 mM [Ali Azam et al., 1999]. ","Structural model links":" ID: Ali Azam et al., 1999 Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10515926 ; ID: Bradley M.D. et al., 2007 Effects of Fis on Escherichia coli gene expression during different growth stages. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17768236 ; ID: Wilson et al., 1992 Translational control of pyrC expression mediated by nucleotide-sensitive selection of transcriptional start sites in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1345912 ;"},"mmid":"MM0000228","psid":"PS0000219","gnid":"GN0000220","reversible":false,"information":{"Mathematical model information":"The mathematical model describes the regulation of gene pyrD.The model is similar to the model describing the regulation of pyrC. To describe the model we have used the generalized Hill function.","Mathematical model links":" ID: Likhoshvai et al., 2010 Metabolic Engineering in Silico. ; Value:http://www.springerlink.com/content/51438683725255u1/ ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PyrD = 0, where PyrD - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter pyrDp. ks - protein synthesis generalized constant from the promoter pyrDp. kd = 0.002 [1/sec],PyrD = 0.0050073 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters kGTP, hGTP, kCTP,hCTP and w were evaluated basing on [Wilson et al., 1992, Likhoshvai et al., 2010] experimental data. Parameter kFis was evaluated basing on [Bradley et al., 2007] experimental data. Parameters k1PurR and k2PurR were evaluated basing on [Wilson et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Bradley M.D. et al., 2007 Effects of Fis on Escherichia coli gene expression during different growth stages. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17768236 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Likhoshvai et al., 2010 Metabolic Engineering in Silico. ; Value:http://www.springerlink.com/content/51438683725255u1/ ; ID: Wilson HR, Turnbough CL Jr., 1990 Role of the purine repressor in the regulation of pyrimidine gene expression in Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1971621 ; ID: Wilson et al., 1992 Translational control of pyrC expression mediated by nucleotide-sensitive selection of transcriptional start sites in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1345912 ;","Structural model information":" Results from [Wilson et al., 1992] laboratory indicate that the expression of the pyrD gene of E. coli is similarly regulated  CTP, GTP and PurR as pyrC. Using microarray Bradley et al (2007) showed that in the early exponential growth phase cells Fis inhibits gene expression pyrD 2.6 times. They also predicted the binding site for Fis, which overlaps with the start of transcription, but experimentally, this site has not been confirmed. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]; The concentration of Fis (dimer) = 0.05 mM [Ali Azam et al., 1999]. ","Structural model links":" ID: Ali Azam et al., 1999 Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10515926 ; ID: Bradley M.D. et al., 2007 Effects of Fis on Escherichia coli gene expression during different growth stages. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17768236 ; ID: Wilson et al., 1992 Translational control of pyrC expression mediated by nucleotide-sensitive selection of transcriptional start sites in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1345912 ;"},"parameters":[{"units":"","information":"","name":"hCTP","value":"2.5"},{"units":"","information":"","name":"hGTP","value":"1.7"},{"units":"mM","information":"","name":"k1PurR","value":"0.001"},{"units":"mM","information":"","name":"k2PurR","value":"0.001"},{"units":"mM","information":"","name":"k3PurR","value":"0.0008"},{"units":"mM","information":"","name":"kCTP","value":"0.025"},{"units":"mM","information":"","name":"kFis","value":"0.032"},{"units":"mM","information":"","name":"kGTP","value":"0.06"},{"units":"mM","information":"","name":"kdisPurRgua","value":"0.0015"},{"units":"mM","information":"","name":"kdisPurRhyp","value":"0.0093"},{"units":"mM/sec","information":"","name":"ks","value":"0.0016"},{"units":"","information":"","name":"w","value":"0.002"}]},{"scheme":"N-CAIR -> CAIR","substrates":{"s1":{"theSubstance":{"name":"N-CAIR","type":"substance","synonyms":["5-phosphoribosyl-5-carboxyaminoimidazole","N-CAIR"],"links":[],"id":"SS0000196"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"CAIR","type":"substance","synonyms":["1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate","1-(5'-Phosphoribosyl)-4-carboxy-5-aminoimidazole","1-(5'-Phosphoribosyl)-5-amino-4-carboxyimidazole","1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxylate","5-Amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate","5'-Phosphoribosyl-4-carboxy-5-aminoimidazole","5'-Phosphoribosyl-5-amino-4-imidazolecarboxylate","CAIR"],"links":[],"id":"SS0000100"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PurE","type":"protein","synonyms":["PurE"],"links":[],"id":"SS0000379"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"(((r1^8)/((kdis^7)+8*r1^7))*kcat*s1)/(KmNCAIR+s1)","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Mueller et al., 1994 N5-carboxyaminoimidazole ribonucleotide: evidence for a new intermediate and two new enzymatic activities in the de novo purine biosynthetic pathway of Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8117684 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration). Parameters were evaluated basing on [Mueller et al., 1994] experimental data. can be calculated from the whole model basing on the flow rate magnitude. can be calculated from the whole model basing on the flow rate magnitude.","Parameter set links":" ID: Mueller et al., 1994 N5-carboxyaminoimidazole ribonucleotide: evidence for a new intermediate and two new enzymatic activities in the de novo purine biosynthetic pathway of Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8117684 ;","Structural model information":" In enzymology, a 5-(carboxyamino)imidazole ribonucleotide mutase (EC 5.4.99.18) is an enzyme that catalyzes the chemical reaction\n5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole &lt;-&gt;  5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate\nHence, this enzyme has one substrate, 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole, and one product, 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate. This enzyme belongs to the family of isomerases, specifically those intramolecular transferases transferring other groups. The systematic name of this enzyme class is 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole carboxymutase. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=RXN0-743 ;"},"mmid":"MM0000212","psid":"PS0000204","gnid":"GN0000203","reversible":false,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Mueller et al., 1994 N5-carboxyaminoimidazole ribonucleotide: evidence for a new intermediate and two new enzymatic activities in the de novo purine biosynthetic pathway of Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8117684 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration). Parameters were evaluated basing on [Mueller et al., 1994] experimental data. can be calculated from the whole model basing on the flow rate magnitude. can be calculated from the whole model basing on the flow rate magnitude.","Parameter set links":" ID: Mueller et al., 1994 N5-carboxyaminoimidazole ribonucleotide: evidence for a new intermediate and two new enzymatic activities in the de novo purine biosynthetic pathway of Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8117684 ;","Structural model information":" In enzymology, a 5-(carboxyamino)imidazole ribonucleotide mutase (EC 5.4.99.18) is an enzyme that catalyzes the chemical reaction\n5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole &lt;-&gt;  5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate\nHence, this enzyme has one substrate, 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole, and one product, 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate. This enzyme belongs to the family of isomerases, specifically those intramolecular transferases transferring other groups. The systematic name of this enzyme class is 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole carboxymutase. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=RXN0-743 ;"},"parameters":[{"units":"mM","information":"","name":"KmNCAIR","value":"0.14"},{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kdis","value":"0.001"}]},{"scheme":"CAIR + ATP + asp -> SAICAR + ADP + Pi + H+","substrates":{"s1":{"theSubstance":{"name":"CAIR","type":"substance","synonyms":["1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate","1-(5'-Phosphoribosyl)-4-carboxy-5-aminoimidazole","1-(5'-Phosphoribosyl)-5-amino-4-carboxyimidazole","1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxylate","5-Amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate","5'-Phosphoribosyl-4-carboxy-5-aminoimidazole","5'-Phosphoribosyl-5-amino-4-imidazolecarboxylate","CAIR"],"links":[],"id":"SS0000100"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""},"s3":{"theSubstance":{"name":"asp","type":"substance","synonyms":["2-Aminosuccinic acid","asp","L-Asp","L-Aspartate","L-Aspartic acid"],"links":[],"id":"SS0000059"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"SAICAR","type":"substance","synonyms":["1-(5'-Phosphoribosyl)-4-(N-succinocarboxamide)-5-aminoimidazole","1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole","5'-Phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole","(S)-2-[5-Amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido]succinate","SAICAR"],"links":[],"id":"SS0000101"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"Pi","type":"substance","synonyms":["H3PO4","Orthophosphate","Orthophosphoric acid","Phosphate","Phosphoric acid","Pi"],"links":[],"id":"SS0000070"},"theState":null,"compartment":""},"p4":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PurC","type":"protein","synonyms":["PurC"],"links":[],"id":"SS0000380"},"theState":null,"compartment":"","theInfluence":"activator"},"r2":{"theSubstance":{"name":"IMP","type":"substance","synonyms":["5'-IMP","5'-Inosinate","5'-Inosine monophosphate","5'-Inosinic acid","IMP","Inosine 5'-monophosphate","Inosine 5'-phosphate","Inosine monophosphate","Inosinic acid"],"links":[],"id":"SS0000104"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"(((r1^3)/((kdis^2)+3*r1^2))*kcat*(s1/KmCAIR)*(s2/KmATP))/((1+(s1/KmCAIR)+(r2/kIMP))*(1+(s2/KmATP)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Nelson et al., 2005 Mechanism of action of Escherichia coli phosphoribosylaminoimidazolesuccinocarboxamide synthetase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/15641804 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration). Parameter were evaluated basing on [Nelson et al., 2005] experimental data. can be calculated from the whole model basing on the flow rate magnitude.","Parameter set links":" ID: Nelson et al., 2005 Mechanism of action of Escherichia coli phosphoribosylaminoimidazolesuccinocarboxamide synthetase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/15641804 ;","Structural model information":" In enzymology, a phosphoribosylaminoimidazolesuccinocarboxamide synthase (EC 6.3.2.6) is an enzyme that catalyzes the chemical reaction\nATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate &lt;-&gt;  ADP + phosphate + (S)-2-[5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxamido]succinate. The 3 substrates of this enzyme are ATP, 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate, and L-aspartate, where as its 4 products are ADP, phosphate, [[(S)-2-[5-amino-1-(5-phospho-D-ribosyl)imidazole-4-]], and [[carboxamido]succinate]]. This enzyme belongs to the family of ligases, to be specific those forming carbon-nitrogen bonds as acid-D-amino-acid ligases (peptide synthases). The systematic name of this enzyme class is 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate:L-aspartate ligase (ADP-forming). This enzyme participates in purine metabolism. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=SAICARSYN-RXN ;"},"mmid":"MM0000213","psid":"PS0000205","gnid":"GN0000205","reversible":false,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Nelson et al., 2005 Mechanism of action of Escherichia coli phosphoribosylaminoimidazolesuccinocarboxamide synthetase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/15641804 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration). Parameter were evaluated basing on [Nelson et al., 2005] experimental data. can be calculated from the whole model basing on the flow rate magnitude.","Parameter set links":" ID: Nelson et al., 2005 Mechanism of action of Escherichia coli phosphoribosylaminoimidazolesuccinocarboxamide synthetase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/15641804 ;","Structural model information":" In enzymology, a phosphoribosylaminoimidazolesuccinocarboxamide synthase (EC 6.3.2.6) is an enzyme that catalyzes the chemical reaction\nATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate &lt;-&gt;  ADP + phosphate + (S)-2-[5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxamido]succinate. The 3 substrates of this enzyme are ATP, 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate, and L-aspartate, where as its 4 products are ADP, phosphate, [[(S)-2-[5-amino-1-(5-phospho-D-ribosyl)imidazole-4-]], and [[carboxamido]succinate]]. This enzyme belongs to the family of ligases, to be specific those forming carbon-nitrogen bonds as acid-D-amino-acid ligases (peptide synthases). The systematic name of this enzyme class is 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate:L-aspartate ligase (ADP-forming). This enzyme participates in purine metabolism. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=SAICARSYN-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmATP","value":"0.019"},{"units":"mM","information":"","name":"KmCAIR","value":"8.7"},{"units":"mM","information":"","name":"kIMP","value":"0.12"},{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kdis","value":"0.001"}]},{"scheme":"NADH + a quinone -> a quinol + NAD+","substrates":{"s1":{"theSubstance":{"name":"NADH","type":"substance","synonyms":["DPNH","NADH","Nicotinamide adenine dinucleotide"],"links":[],"id":"SS0000064"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"a quinone","type":"substance","synonyms":["a quinone","Q","quinone"],"links":[],"id":"SS0000146"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"a quinol","type":"substance","synonyms":["a hydroquinone","a quinol","a reduced quinone","QH2"],"links":[],"id":"SS0000147"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"NAD+","type":"substance","synonyms":["NAD+"],"links":[],"id":"SS0000188"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"NAD+","type":"substance","synonyms":["NAD+"],"links":[],"id":"SS0000188"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r2":{"theSubstance":{"name":"Mg","type":"substance","synonyms":["Magnesium","Magnesium ion","Mg","Mg++","Mg2+"],"links":[],"id":"SS0000277"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"AMP","type":"substance","synonyms":["5'-Adenosine monophosphate","5'-Adenylic acid","5'-AMP","Adenosine 5'-monophosphate","Adenosine 5'-phosphate","Adenylate","Adenylic acid","AMP"],"links":[],"id":"SS0000073"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r6":{"theSubstance":{"name":"NDH-2","type":"protein","synonyms":["ec:1.6.1.-","ec:1.6.5.9","NADH dehydrogenase II","NADH dhII","NADH:ubiquinone oxidoreductase II","Ndh","NDH-2","NQR"],"links":[],"id":"SS0000278"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"kf*r6*(s1/kmNADH)^nmNADH/(1 + (s1/kmNADH)^nmNADH + p2/kiNAD + r3/kiAMP + r5/kiADP + r4/kiATP)* (s2/kmQ/(1 + s2/kmQ))*((1 + (laMg*r2/kaMg)^naMg)/(1 + (r2/kaMg)^naMg))*((1 + (s1/kiNADH)^niNADH)/(1 + (liNADH*s1/kiNADH)^niNADH))","theSubMathModel":null,"theInformation":{"Mathematical model information":"NADH has complex influence: at lower concentrations it activates reaction rate with nonlinear effect (nmNADH), at higher concentrations (about 1000 mM) it inhibits reaction. NADH has also some competitive inhibitors - NAD, AMP, ADP and ATP [Sheppard et. al, 1999], which are included into model in simple Michaelis form. \r\nRegulation part (both activation with Mg2+ and inhibition with NADH) are added into model in simple Hill form. ","Mathematical model links":" ID: Sheppard et. al, 1999. Purification and properties of NADH-dependent 5,10-methylenetetrahydrofolate reductase (MetF) from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9922232 ;","Parameter set information":"  The model parameters were verified using the experimental data from (Sheppard et. al, 1999). \n\nOnly one parameter (kf) remains unverified. However, the Vmax value for this enzyme was estimated in the same paper for alternative units (100 units/mg). ","Parameter set links":" ID: Sheppard et. al, 1999. Purification and properties of NADH-dependent 5,10-methylenetetrahydrofolate reductase (MetF) from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9922232 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10649 ;"},"mmid":"MM0000138","psid":"PS0000129","gnid":"GN0000155","reversible":false,"information":{"Mathematical model information":"NADH has complex influence: at lower concentrations it activates reaction rate with nonlinear effect (nmNADH), at higher concentrations (about 1000 mM) it inhibits reaction. NADH has also some competitive inhibitors - NAD, AMP, ADP and ATP [Sheppard et. al, 1999], which are included into model in simple Michaelis form. \r\nRegulation part (both activation with Mg2+ and inhibition with NADH) are added into model in simple Hill form. ","Mathematical model links":" ID: Sheppard et. al, 1999. Purification and properties of NADH-dependent 5,10-methylenetetrahydrofolate reductase (MetF) from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9922232 ;","Parameter set information":"  The model parameters were verified using the experimental data from (Sheppard et. al, 1999). \n\nOnly one parameter (kf) remains unverified. However, the Vmax value for this enzyme was estimated in the same paper for alternative units (100 units/mg). ","Parameter set links":" ID: Sheppard et. al, 1999. Purification and properties of NADH-dependent 5,10-methylenetetrahydrofolate reductase (MetF) from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9922232 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10649 ;"},"parameters":[{"units":"mM","information":"","name":"kaMg","value":"700"},{"units":"1/s","information":"","name":"kf","value":"1"},{"units":"mM","information":"","name":"kiADP","value":"700"},{"units":"mM","information":"","name":"kiAMP","value":"500"},{"units":"mM","information":"","name":"kiATP","value":"0.009"},{"units":"mM","information":"","name":"kiNAD","value":"20"},{"units":"mM","information":"","name":"kiNADH","value":"1000"},{"units":"mM","information":"","name":"kmNADH","value":"50"},{"units":"mM","information":"","name":"kmQ","value":"40"},{"units":"","information":"","name":"laMg","value":"4"},{"units":"","information":"","name":"liNADH","value":"2"},{"units":"","information":"","name":"naMg","value":"1"},{"units":"","information":"","name":"niNADH","value":"3"},{"units":"","information":"","name":"nmNADH","value":"1.6"}]},{"scheme":"a quinol + Oxygen -> a quinone + HEXT","substrates":{"s1":{"theSubstance":{"name":"a quinol","type":"substance","synonyms":["a hydroquinone","a quinol","a reduced quinone","QH2"],"links":[],"id":"SS0000147"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"O2","type":"substance","synonyms":["O2","Oxygen"],"links":[],"id":"SS0000068"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"a quinone","type":"substance","synonyms":["a quinone","Q","quinone"],"links":[],"id":"SS0000146"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"HEXT","type":"substance","synonyms":["external H+","external hydrogen ion","HEXT","H+ external","hydrogen ion external"],"links":[],"id":"SS0000279"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"CyoABCD","type":"protein","synonyms":["CyoABCD","cytochrome b562-o complex","cytochrome bo complex","cytochrome o complex","cytochrome o ubiquinol oxidase","Cytochrome oxidase bo3","ec:1.10.3.10"],"links":[],"id":"SS0000325"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r10":{"theSubstance":{"name":"Mn2+","type":"substance","synonyms":["manganese (II) ion","manganese ion","Mn++","Mn2+","Mn(II)"],"links":[],"id":"SS0000294"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r11":{"theSubstance":{"name":"cardiolipin","type":"substance","synonyms":["cardiolipin","diphosphatidylglycerol"],"links":[],"id":"SS0000301"},"theState":null,"compartment":"","theInfluence":"activator"},"r12":{"theSubstance":{"name":"PS","type":"substance","synonyms":["phosphatidyl-L-serine","phosphatidylserine","phosphatidyl serine","PS"],"links":[],"id":"SS0000300"},"theState":null,"compartment":"","theInfluence":"activator"},"r13":{"theSubstance":{"name":"phospholipid","type":"substance","synonyms":["phospholipid","Plip","PLip"],"links":[],"id":"SS0000298"},"theState":null,"compartment":"","theInfluence":"activator"},"r14":{"theSubstance":{"name":"asolectin","type":"substance","synonyms":["ASO","asolectin"],"links":[],"id":"SS0000324"},"theState":null,"compartment":"","theInfluence":"activator"},"r2":{"theSubstance":{"name":"Cd2+","type":"substance","synonyms":["Cadmium","Cadmium ion","Cd++","Cd2+"],"links":[],"id":"SS0000319"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"Zn2+","type":"substance","synonyms":["Zinc","zinc ion","Zn","Zn++","Zn2+","Zn(II)"],"links":[],"id":"SS0000311"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"Co2+","type":"substance","synonyms":["Co++","Co2+","cobalt","cobalt ion","Co(II)"],"links":[],"id":"SS0000296"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"NaN3","type":"substance","synonyms":["azide","hydrazoic acid","NaN3"],"links":[],"id":"SS0000283"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r6":{"theSubstance":{"name":"KCN","type":"substance","synonyms":["kalium cyanid","KCN","potassium cyanide"],"links":[],"id":"SS0000320"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r7":{"theSubstance":{"name":"H2O2","type":"substance","synonyms":["H2O2","hydrogen peroxide","hydroperoxide","perhydrol"],"links":[],"id":"SS0000321"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r8":{"theSubstance":{"name":"HQNO","type":"substance","synonyms":["2-heptyl-4-hydroxyquinoline n-oxide","2-Heptyl-4-quinolinol 1-oxide","2-heptylquinolin-4-ol 1-oxide","2-n-heptyl-4-hydroxyquinoline-N-oxide","HOQNO","HQNO"],"links":[],"id":"SS0000322"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r9":{"theSubstance":{"name":"NH2OH","type":"substance","synonyms":["hydroxylamine","NH2OH"],"links":[],"id":"SS0000323"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"kf*r1*(s1/kmQH2)/(1 + s1/kmQH2+p1/kmQ)*(s2/kmO2/((1 + s2/kmO2)*(1 + r3/kiZn)))*((1 + (r2/kiCd)^niCd)/(1 + (liCd*r2/kiCd)^niCd))*((1 + (r4/kiCo)^niCo)/(1 + (liCo*r4/kiCo)^niCo))*((1 + r10/kiMn)/(1 + liMn* r10/kiMn))*((1 + r8/kiHQNO)/(1 + liHQNO*r8/kiHQNO))*((1 + (r7/kiH2O2)^niH2O2)/(1 + (liH2O2*r7/kiH2O2)^niH2O2))*((1 + r6/kiKCN)/(1 + liKCN*r6/kiKCN))*((1 + r9/kiNH2OH)/(1 + liNH2OH*r9/kiNH2OH))*((1 + r5/kiNaN3)/(1 + liNaN3*r5/kiNaN3))*((1 + laASO*r14/kaASO)/(1 + r14/kaASO))","theSubMathModel":null,"theInformation":{"Mathematical model information":"This model is a product of four main parts: \r\n1) Michaelis-Mentent part with product competitive inhibition by a quinone (for a quinol). \r\n2) Metal ions (Zn2+, Cd2+, Co2+, Mn2+) inhibition part written in simple Hill form. \r\n3) Other substances (NaN3, KCN, H2O2, HQNQ, NH2OH) inhibition part written in simple Hill form. \r\n4) Asolectin activation part written in simple Hill form. \r\nHowever this model doesn't consider activation by cardiolipin, phosphatidyl serine, and phospholipid.","Mathematical model links":" ID: Kita K et al (1984) Terminal oxidases of Escherichia coli aerobic respiratory chain. I. Purification and properties of cytochrome b562-o complex from cells in the early exponential phase of aerobic growth. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6365921 ; ID: Kita K et al (1986) Purification and properties of two terminal oxidase complexes of Escherichia coli aerobic respiratory chain. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2856144 ;","Parameter set information":"  All parameters (except two ones) were verified using experimental data (Kita et al, 1984, 1986).\nThe parameter kf was not verified due to the alternative measurement units (Vmax = 150,O2/min/nmol). KmQ was estimated taking into account biochemical sence of the specie.  ","Parameter set links":" ID: Kita K et al (1984) Terminal oxidases of Escherichia coli aerobic respiratory chain. I. Purification and properties of cytochrome b562-o complex from cells in the early exponential phase of aerobic growth. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6365921 ; ID: Kita K et al (1986) Purification and properties of two terminal oxidase complexes of Escherichia coli aerobic respiratory chain. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2856144 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=CYT-O-UBIOX-CPLX ;"},"mmid":"MM0000151","psid":"PS0000143","gnid":"GN0000165","reversible":false,"information":{"Mathematical model information":"This model is a product of four main parts: \r\n1) Michaelis-Mentent part with product competitive inhibition by a quinone (for a quinol). \r\n2) Metal ions (Zn2+, Cd2+, Co2+, Mn2+) inhibition part written in simple Hill form. \r\n3) Other substances (NaN3, KCN, H2O2, HQNQ, NH2OH) inhibition part written in simple Hill form. \r\n4) Asolectin activation part written in simple Hill form. \r\nHowever this model doesn't consider activation by cardiolipin, phosphatidyl serine, and phospholipid.","Mathematical model links":" ID: Kita K et al (1984) Terminal oxidases of Escherichia coli aerobic respiratory chain. I. Purification and properties of cytochrome b562-o complex from cells in the early exponential phase of aerobic growth. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6365921 ; ID: Kita K et al (1986) Purification and properties of two terminal oxidase complexes of Escherichia coli aerobic respiratory chain. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2856144 ;","Parameter set information":"  All parameters (except two ones) were verified using experimental data (Kita et al, 1984, 1986).\nThe parameter kf was not verified due to the alternative measurement units (Vmax = 150,O2/min/nmol). KmQ was estimated taking into account biochemical sence of the specie.  ","Parameter set links":" ID: Kita K et al (1984) Terminal oxidases of Escherichia coli aerobic respiratory chain. I. Purification and properties of cytochrome b562-o complex from cells in the early exponential phase of aerobic growth. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6365921 ; ID: Kita K et al (1986) Purification and properties of two terminal oxidase complexes of Escherichia coli aerobic respiratory chain. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2856144 ;","Structural model links":" ID: Ecocyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=CYT-O-UBIOX-CPLX ;"},"parameters":[{"units":"mcM","information":"","name":"kaASO","value":"72"},{"units":"1/s","information":"","name":"kf","value":"1"},{"units":"mcM","information":"","name":"kiCd","value":"350"},{"units":"mcM","information":"","name":"kiCo","value":"100"},{"units":"mM","information":"","name":"kiH2O2","value":"110"},{"units":"mcM","information":"","name":"kiHQNO","value":"20"},{"units":"mcM","information":"","name":"kiKCN","value":"100"},{"units":"mcM","information":"","name":"kiMn","value":"300"},{"units":"mcM","information":"","name":"kiNH2OH","value":"18"},{"units":"mM","information":"","name":"kiNaN3","value":"2500"},{"units":"mcM","information":"","name":"kiZn","value":"5"},{"units":"mcM","information":"","name":"kmO2","value":"2.9"},{"units":"mcM","information":"","name":"kmQ","value":"4800"},{"units":"mcM","information":"","name":"kmQH2","value":"48"},{"units":"","information":"","name":"laASO","value":"18"},{"units":"","information":"","name":"liCd","value":"47"},{"units":"","information":"","name":"liCo","value":"25"},{"units":"","information":"","name":"liH2O2","value":"1.29"},{"units":"","information":"","name":"liHQNO","value":"9"},{"units":"","information":"","name":"liKCN","value":"7"},{"units":"","information":"","name":"liMn","value":"1.9"},{"units":"","information":"","name":"liNH2OH","value":"7"},{"units":"","information":"","name":"liNaN3","value":"100"},{"units":"","information":"","name":"niCd","value":"0.7"},{"units":"","information":"","name":"niCo","value":"0.7"},{"units":"","information":"","name":"niH2O2","value":"2.4"}]},{"scheme":"-> PyrE","substrates":null,"products":{"p1":{"theSubstance":{"name":"PyrE","type":"protein","synonyms":["orotate phosphoribosyltransferase","PyrE"],"links":[],"id":"SS0000368"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"pyrE","type":"gene","synonyms":["b3642","pyrE"],"links":[],"id":"SS0000211"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"UTP","type":"substance","synonyms":["Uridine 5'-triphosphate","Uridine triphosphate","UTP"],"links":[],"id":"SS0000026"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"GTP","type":"substance","synonyms":["GTP","Guanosine 5'-triphosphate"],"links":[],"id":"SS0000140"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"NusA","type":"protein","synonyms":["NusA","Transcription termination/antitermination L factor"],"links":[],"id":"SS0000208"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"ks*((1+k1UTP*(r2/k2UTP)^hUTP)/(1+(r2/k2UTP)^hUTP))*((1+k1GTP*(r3/k2GTP)^hGTP)/(1+(r3/k2GTP)^hGTP))*((1+k1NusA*(r4/k2NusA))/(1+(r4/k2NusA))) ","theSubMathModel":null,"theInformation":{"Mathematical model information":"When pools of both UTP and GTP were high only 5%-6% of the mRNA chains were continued into the pyrE gene. However, when the UTP pool was reduced (from 1.3 to 0.2 micromol/g dry weight) nearly 100% of transcription passed the attenuator.Likewise, a reductionin the GTP pool(from 3.2 to 0.8 micromol/g dry weight)r esulted in 25%-30% escape of attenuation. The mathematical model describes the regulation of gene pyrE. UTP and GTP are inhibitors of gene expression pyrE. To describe the model we have used the generalized Hill function.","Mathematical model links":" ID: Poulsen et al., 1987 Effect of UTP and GTP pools on attenuation at the pyrE gene of Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3302606 ;","Parameter set information":"Parameters k1UTP, k2UTP, hUTP, k1GTP, k2GTP, hGTP, k1NusA and k2NusA were evaluated basing on [Poulsen et al., 1987] experimental data.Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PyrE = 0, where PyrE - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter rphp1. ks - protein synthesis generalized constant from the promoter rphp1. kd = 0.002 [1/sec],PyrE = 0.0204881 [mM].","Parameter set links":" ID: Poulsen et al., 1987 Effect of UTP and GTP pools on attenuation at the pyrE gene of Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3302606 ;","Structural model information":" Expression of the hybrid genes was studied in a bacterium with mutations that permit changes in the UTP and GTP pools during exponential growth. It was found that the greater part of pyrE gene regulation by the nucleotides takes place at the intercistronic attenuator and that promoter control contributes only little, ca. twofold. When pools of both UTP and GTP were high only 5%-6% of the mRNA chains were continued into the pyrE gene. However, when the UTP pool was reduced (from 1.3 to 0.2 mumol/g dry weight) nearly 100% of transcription passed the attenuator. Likewise, a reduction in the GTP pool (from 3.2 to 0.8 mumol/g dry weight) resulted in 25%-30% escape of attenuation. The concentration of NusA (monomer) = 0.00242 mM [calculation from the work of Lu, 2007]. ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Poulsen et al., 1987 Effect of UTP and GTP pools on attenuation at the pyrE gene of Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3302606 ;"},"mmid":"MM0000230","psid":"PS0000220","gnid":"GN0000221","reversible":false,"information":{"Mathematical model information":"When pools of both UTP and GTP were high only 5%-6% of the mRNA chains were continued into the pyrE gene. However, when the UTP pool was reduced (from 1.3 to 0.2 micromol/g dry weight) nearly 100% of transcription passed the attenuator.Likewise, a reductionin the GTP pool(from 3.2 to 0.8 micromol/g dry weight)r esulted in 25%-30% escape of attenuation. The mathematical model describes the regulation of gene pyrE. UTP and GTP are inhibitors of gene expression pyrE. To describe the model we have used the generalized Hill function.","Mathematical model links":" ID: Poulsen et al., 1987 Effect of UTP and GTP pools on attenuation at the pyrE gene of Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3302606 ;","Parameter set information":"Parameters k1UTP, k2UTP, hUTP, k1GTP, k2GTP, hGTP, k1NusA and k2NusA were evaluated basing on [Poulsen et al., 1987] experimental data.Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PyrE = 0, where PyrE - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter rphp1. ks - protein synthesis generalized constant from the promoter rphp1. kd = 0.002 [1/sec],PyrE = 0.0204881 [mM].","Parameter set links":" ID: Poulsen et al., 1987 Effect of UTP and GTP pools on attenuation at the pyrE gene of Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3302606 ;","Structural model information":" Expression of the hybrid genes was studied in a bacterium with mutations that permit changes in the UTP and GTP pools during exponential growth. It was found that the greater part of pyrE gene regulation by the nucleotides takes place at the intercistronic attenuator and that promoter control contributes only little, ca. twofold. When pools of both UTP and GTP were high only 5%-6% of the mRNA chains were continued into the pyrE gene. However, when the UTP pool was reduced (from 1.3 to 0.2 mumol/g dry weight) nearly 100% of transcription passed the attenuator. Likewise, a reduction in the GTP pool (from 3.2 to 0.8 mumol/g dry weight) resulted in 25%-30% escape of attenuation. The concentration of NusA (monomer) = 0.00242 mM [calculation from the work of Lu, 2007]. ","Structural model links":" ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Poulsen et al., 1987 Effect of UTP and GTP pools on attenuation at the pyrE gene of Escherichia coli ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3302606 ;"},"parameters":[{"units":"","information":"","name":"hGTP","value":"1.79"},{"units":"","information":"","name":"hUTP","value":"1.4"},{"units":"","information":"","name":"k1GTP","value":"0.005"},{"units":"","information":"","name":"k1NusA","value":"4.1"},{"units":"","information":"","name":"k1UTP","value":"0.005"},{"units":"mM","information":"","name":"k2GTP","value":"0.2"},{"units":"mM","information":"","name":"k2NusA","value":"0.0001"},{"units":"mM","information":"","name":"k2UTP","value":"0.2"},{"units":"mM/sec","information":"","name":"ks","value":"0.002"}]},{"scheme":"-> CarB","substrates":null,"products":{"p1":{"theSubstance":{"name":"CarB","type":"protein","synonyms":["CarB","? chain","large chain"],"links":[],"id":"SS0000360"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"carB","type":"gene","synonyms":["b0033","carB"],"links":[],"id":"SS0000362"},"theState":null,"compartment":"","theInfluence":""},"r10":{"theSubstance":{"name":"PepA","type":"protein","synonyms":["aminopeptidase A/I","PepA"],"links":[],"id":"SS0000354"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r2":{"theSubstance":{"name":"UTP","type":"substance","synonyms":["Uridine 5'-triphosphate","Uridine triphosphate","UTP"],"links":[],"id":"SS0000026"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"RutR","type":"protein","synonyms":["RutR","RutR DNA-binding transcriptional dual regulator"],"links":[],"id":"SS0000357"},"theState":null,"compartment":"","theInfluence":"activator"},"r4":{"theSubstance":{"name":"Ura","type":"substance","synonyms":["Ura","Uracil"],"links":[],"id":"SS0000040"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"Thy","type":"substance","synonyms":["5-Methyluracil","Thy","Thymine"],"links":[],"id":"SS0000056"},"theState":null,"compartment":"","theInfluence":"activator"},"r6":{"theSubstance":{"name":"PurR","type":"protein","synonyms":["PurR","PurR transcriptional repressor"],"links":[],"id":"SS0000358"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r7":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r8":{"theSubstance":{"name":"Gua","type":"substance","synonyms":["Gua","Guanosine"],"links":[],"id":"SS0000113"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r9":{"theSubstance":{"name":"IHF","type":"protein","synonyms":["IHF"],"links":[],"id":"SS0000353"},"theState":null,"compartment":"","theInfluence":"complex regulator"}},"theMathModel":"ks*(1/(1+(r2/kUTP)^hUTP))*((1+(((r3-(((r3*(r4^2))/(kdisRutRura^2))/(1+((2*r3*r4+r4^2)/(kdisRutRura^2))+((2*r3*r5+r5^2)/(kdisRutRthy^2))))-(((r3*(r5^2))/(kdisRutRthy^2))/(1+((2*r3*r4+r4^2)/(kdisRutRura^2))+((2*r3*r5+r5^2)/(kdisRutRthy^2)))))+(((r3*(r5^2))/(kdisRutRthy^2))/(1+((2*r3*r4+r4^2)/(kdisRutRura^2))+((2*r3*r5+r5^2)/(kdisRutRthy^2)))))/kRutR))/(1+(1+((((r6*(r7^2))/(kdisPurRhyp^2))/(1+((2*r6*r7+r7^2)/(kdisPurRhyp^2))+((2*r6*r8+r8^2)/(kdisPurRgua^2))))/k1PurR)+((((r6*(r8^2))/(kdisPurRgua^2))/(1+((2*r6*r7+r7^2)/(kdisPurRhyp^2))+((2*r6*r8+r8^2)/(kdisPurRgua^2))))/k2PurR)+((r6-(((r6*(r7^2))/(kdisPurRhyp^2))/(1+((2*r6*r7+r7^2)/(kdisPurRhyp^2))+((2*r6*r8+r8^2)/(kdisPurRgua^2))))-(((r6*(r8^2))/(kdisPurRgua^2))/(1+((2*r6*r7+r7^2)/(kdisPurRhyp^2))+((2*r6*r8+r8^2)/(kdisPurRgua^2))))))/k3PurR)*(1+(r4/k1ura)+(r4/k2ura)*(r9/kIHF))*(r10/kPepA)+(((r3-(((r3*(r4^2))/(kdisRutRura^2))/(1+((2*r3*r4+r4^2)/(kdisRutRura^2))+((2*r3*r5+r5^2)/(kdisRutRthy^2))))-(((r3*(r5^2))/(kdisRutRthy^2))/(1+((2*r3*r4+r4^2)/(kdisRutRura^2))+((2*r3*r5+r5^2)/(kdisRutRthy^2)))))+(((r3*(r5^2))/(kdisRutRthy^2))/(1+((2*r3*r4+r4^2)/(kdisRutRura^2))+((2*r3*r5+r5^2)/(kdisRutRthy^2)))))/kRutR)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Devroede N., 2006].","Mathematical model links":" ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ;","Parameter set information":"Parameter ks (ks1) was obtained from the algebraic equation of the form: ks1*f1+ks2*f2-kd*CarA = 0, where CarA - concentration of the protein, kd - the constant of degradation, f1,f2 - the proportion of transcripts from the promoter carAp1 and carAp2.ks1,ks2 - protein synthesis generalized constant from the promoter carAp1 and carAp2. kd = 0.008 [1/sec],CarA = 0.4 [mM].ks2=0.01*ks1. Parameters kUTP and hUTP were evaluated basing on [Han et al., 1998] experimental data. Parameters kRutR, k1PurR, k2PurR, k3PurR, k1Ura, k2Ura, kIHF and kPepA were evaluated basing on [Devroede et al., 2006] experimental data. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994].","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ;","Structural model information":"  Genes carA and carB are part of an operon carAB and encode structure of the subunits of the enzyme carbamoyl phosphate synthetase (EC 6.3.5.5). Expression of the operon carAB is controlled purines and pyrimidines by promoter carAp1, and arginine - a promoter carAp2.Here we consider the process of synthesis protein CarB with the promoter carAp1. In the proposed regulatory mechanism, increased intracellular levels of UTP promote reiterative transcription, which results in the synthesis of transcripts with the sequence GUUUUn (where n = 1 to 30). These transcripts are not extended downstream to include structural gene sequences. In contrast, lower levels of UTP enhance normal template-directed addition of a G residue at position 5 of the nascent transcript. This addition precludes reiterative transcription and permits normal transcript elongation capable of producing translatable carAB transcripts. Thus, carAB expression, which is necessary for pyrimidine nucleotide (and arginine) biosynthesis, increases in proportion to the cellular need for UTP. Therefore,this model describes the process of inhibition. To describe the model we have used the generalized Hill function. There are several binding sites for proteins - integration host factor (IHF), PepA, PurR, and RutR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]; The concentration of PepA (homohexamer) = 0.00057 mM [calculation from the work of Lu, 2007]; The concentration of IHF (dimer) = 0.01 mM [Ali Azam et al., 1999]; The concentration of RutR (dimer) = 0.00025 [Shimada et al., 2007];   ","Structural model links":" ID: Ali Azam et al., 1999 Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10515926 ; ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10134 ; ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Shimada et al., 2007 RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17919280 ;"},"mmid":"MM0000223","psid":"PS0000214","gnid":"GN0000215","reversible":false,"information":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Devroede N., 2006].","Mathematical model links":" ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ;","Parameter set information":"Parameter ks (ks1) was obtained from the algebraic equation of the form: ks1*f1+ks2*f2-kd*CarA = 0, where CarA - concentration of the protein, kd - the constant of degradation, f1,f2 - the proportion of transcripts from the promoter carAp1 and carAp2.ks1,ks2 - protein synthesis generalized constant from the promoter carAp1 and carAp2. kd = 0.008 [1/sec],CarA = 0.4 [mM].ks2=0.01*ks1. Parameters kUTP and hUTP were evaluated basing on [Han et al., 1998] experimental data. Parameters kRutR, k1PurR, k2PurR, k3PurR, k1Ura, k2Ura, kIHF and kPepA were evaluated basing on [Devroede et al., 2006] experimental data. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994].","Parameter set links":" ID: Choi, Zalkin, 1994, Role of the purine repressor hinge sequence in repressor function. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8132474 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ;","Structural model information":"  Genes carA and carB are part of an operon carAB and encode structure of the subunits of the enzyme carbamoyl phosphate synthetase (EC 6.3.5.5). Expression of the operon carAB is controlled purines and pyrimidines by promoter carAp1, and arginine - a promoter carAp2.Here we consider the process of synthesis protein CarB with the promoter carAp1. In the proposed regulatory mechanism, increased intracellular levels of UTP promote reiterative transcription, which results in the synthesis of transcripts with the sequence GUUUUn (where n = 1 to 30). These transcripts are not extended downstream to include structural gene sequences. In contrast, lower levels of UTP enhance normal template-directed addition of a G residue at position 5 of the nascent transcript. This addition precludes reiterative transcription and permits normal transcript elongation capable of producing translatable carAB transcripts. Thus, carAB expression, which is necessary for pyrimidine nucleotide (and arginine) biosynthesis, increases in proportion to the cellular need for UTP. Therefore,this model describes the process of inhibition. To describe the model we have used the generalized Hill function. There are several binding sites for proteins - integration host factor (IHF), PepA, PurR, and RutR. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]; The concentration of PepA (homohexamer) = 0.00057 mM [calculation from the work of Lu, 2007]; The concentration of IHF (dimer) = 0.01 mM [Ali Azam et al., 1999]; The concentration of RutR (dimer) = 0.00025 [Shimada et al., 2007];   ","Structural model links":" ID: Ali Azam et al., 1999 Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10515926 ; ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10134 ; ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Shimada et al., 2007 RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17919280 ;"},"parameters":[{"units":"","information":"","name":"hUTP","value":"1.5"},{"units":"mM","information":"","name":"k1PurR","value":"0.000185"},{"units":"mM","information":"","name":"k1ura","value":"0.7"},{"units":"mM","information":"","name":"k2PurR","value":"0.000185"},{"units":"mM","information":"","name":"k2ura","value":"0.005"},{"units":"mM","information":"","name":"k3PurR","value":"0.0008"},{"units":"mM","information":"","name":"kIHF","value":"0.09"},{"units":"mM","information":"","name":"kPepA","value":"0.00033"},{"units":"mM","information":"","name":"kRutR","value":"0.0001136"},{"units":"mM","information":"","name":"kUTP","value":"0.7"},{"units":"mM","information":"","name":"kdisPurRgua","value":"0.0015"},{"units":"mM","information":"","name":"kdisPurRhyp","value":"0.0093"},{"units":"mM","information":"","name":"kdisRutRthy","value":"0.001"},{"units":"mM","information":"","name":"kdisRutRura","value":"0.001"},{"units":"mM/sec","information":"","name":"ks","value":"0.0123"}]},{"scheme":"-> CarB","substrates":null,"products":{"p1":{"theSubstance":{"name":"CarB","type":"protein","synonyms":["CarB","? chain","large chain"],"links":[],"id":"SS0000360"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"carB","type":"gene","synonyms":["b0033","carB"],"links":[],"id":"SS0000362"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"ArgR","type":"protein","synonyms":["ArgR"],"links":[],"id":"SS0000386"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"arg","type":"substance","synonyms":["2-amino-5-guanidinovaleric acid","arg","arginine","L-arginine","R"],"links":[],"id":"SS0000387"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"ks*(1/(1+((((r2*(r3^6))/(kdisArgRarg^6))/(1+((6*r2*(r3^5)+(r3^6))/(kdisArgRarg^6))))/kArgR)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Caldara et al., 2006].","Mathematical model links":" ID: Caldara et al., 2006 The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17074904 ;","Parameter set information":"Parameter ks (ks2) was obtained from the algebraic equation of the form: ks1*f1+ks2*f2-kd*CarB = 0, where CarB - concentration of the protein, kd - the constant of degradation, f1,f2 - the proportion of transcripts from the promoter carAp1 and carAp2.ks1,ks2 - protein synthesis generalized constant from the promoter carAp1 and carAp2. kd = 0.008 [1/sec],CarB = 0.4 [mM]. ks2=0.01*ks1. Parameter kArgR was evaluated basing on [Caldara et al., 2006] experimental data.","Parameter set links":" ID: Caldara et al., 2006 The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17074904 ;","Structural model information":"Genes carA and carB are part of an operon carAB and encode structure of the subunits of the enzyme carbamoyl phosphate synthetase (EC 6.3.5.5). Expression of the operon carAB is controlled purines and pyrimidines by promoter carAp1, and arginine - a promoter carAp2.Here we consider the process of synthesis protein CarB with the promoter carAp2.","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10134 ;"},"mmid":"MM0000224","psid":"PS0000215","gnid":"GN0000216","reversible":false,"information":{"Mathematical model information":"The structural model is developed on the basis of kinetic data from the article [Caldara et al., 2006].","Mathematical model links":" ID: Caldara et al., 2006 The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17074904 ;","Parameter set information":"Parameter ks (ks2) was obtained from the algebraic equation of the form: ks1*f1+ks2*f2-kd*CarB = 0, where CarB - concentration of the protein, kd - the constant of degradation, f1,f2 - the proportion of transcripts from the promoter carAp1 and carAp2.ks1,ks2 - protein synthesis generalized constant from the promoter carAp1 and carAp2. kd = 0.008 [1/sec],CarB = 0.4 [mM]. ks2=0.01*ks1. Parameter kArgR was evaluated basing on [Caldara et al., 2006] experimental data.","Parameter set links":" ID: Caldara et al., 2006 The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17074904 ;","Structural model information":"Genes carA and carB are part of an operon carAB and encode structure of the subunits of the enzyme carbamoyl phosphate synthetase (EC 6.3.5.5). Expression of the operon carAB is controlled purines and pyrimidines by promoter carAp1, and arginine - a promoter carAp2.Here we consider the process of synthesis protein CarB with the promoter carAp2.","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10134 ;"},"parameters":[{"units":"mM","information":"","name":"kArgR","value":"0.0317"},{"units":"mM","information":"","name":"kdisArgRarg","value":"0.001"},{"units":"mM/sec","information":"","name":"ks","value":"0.000123"}]},{"scheme":"-> PyrB","substrates":null,"products":{"p1":{"theSubstance":{"name":"PyrB","type":"protein","synonyms":["aspartate carbamoyltransferase, catalytic subunit","PyrB"],"links":[],"id":"SS0000363"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"pyrB","type":"gene","synonyms":["b4245","pyrB"],"links":[],"id":"SS0000207"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"NusA","type":"protein","synonyms":["NusA","Transcription termination/antitermination L factor"],"links":[],"id":"SS0000208"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"UTP","type":"substance","synonyms":["Uridine 5'-triphosphate","Uridine triphosphate","UTP"],"links":[],"id":"SS0000026"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"ks*((1+k1UTP*(r3/k2UTP)^hUTP)/(1+(r3/k2UTP)^hUTP))*((1+k1NusA*(r3/k2NusA))/(1+(r3/k2NusA))) ","theSubMathModel":null,"theInformation":{"Mathematical model information":"The mathematical model describes the effect of different concentrations of UTP and the regulatory protein NusA in time to stop transcription in the leader section operon pyrLBI [Donahue&amp;Turnbough,1994]. To describe the model we have used the generalized Hill function.","Mathematical model links":" ID: Donahue et al., 1994 Nucleotide-specific transcriptional pausing in the pyrBI leader region of Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7517939 ;","Parameter set information":"Parameters k1UTP, k2UTP, hUTP, k1NusA and k2NusA were evaluated basing on [Donahue et al., 1994] experimental data.Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PyrB = 0, where PyrB - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter pyrLp2. ks - protein synthesis generalized constant from the promoter pyrLp2. kd = 0.002 [1/sec],PyrB = 1.008 [mM].","Parameter set links":" ID: Donahue et al., 1994 Nucleotide-specific transcriptional pausing in the pyrBI leader region of Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7517939 ;","Structural model information":"  Genes pyrB and pyrI are part of an operon pyrBI and encode structure of the subunits of the pyrimidine biosynthetic enzyme aspartate transcarbamylase . Here we consider the process of synthesis protein PyrB. Expression of the pyrBI operon is regulated primarily through a UTP-sensitive transcriptional attenuation control mechanism in Escherichia coli. In this mechanism, the extent of coupling between transcription and translation within the pyrBI leader region determines the level of p-independent transcriptional termination at an attenuator preceding the pyrB gene. A key feature in this mechanism is transcriptional pausing that occurs before the attenuator in the pyrBI leader region when UTP concentrations are low. In this study, we characterized in detail this UTP-sensitive transcriptional pausing in vitro. NusA has been shown to enhance transcriptional pausing at a variety of DNAsites in E. coli. The concentration of NusA (monomer) = 0.00242 mM [calculation from the work of Lu, 2007].   ","Structural model links":" ID: Donahue et al., 1994 Nucleotide-specific transcriptional pausing in the pyrBI leader region of Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7517939 ; ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ;"},"mmid":"MM0000225","psid":"PS0000216","gnid":"GN0000217","reversible":false,"information":{"Mathematical model information":"The mathematical model describes the effect of different concentrations of UTP and the regulatory protein NusA in time to stop transcription in the leader section operon pyrLBI [Donahue&amp;Turnbough,1994]. To describe the model we have used the generalized Hill function.","Mathematical model links":" ID: Donahue et al., 1994 Nucleotide-specific transcriptional pausing in the pyrBI leader region of Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7517939 ;","Parameter set information":"Parameters k1UTP, k2UTP, hUTP, k1NusA and k2NusA were evaluated basing on [Donahue et al., 1994] experimental data.Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PyrB = 0, where PyrB - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter pyrLp2. ks - protein synthesis generalized constant from the promoter pyrLp2. kd = 0.002 [1/sec],PyrB = 1.008 [mM].","Parameter set links":" ID: Donahue et al., 1994 Nucleotide-specific transcriptional pausing in the pyrBI leader region of Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7517939 ;","Structural model information":"  Genes pyrB and pyrI are part of an operon pyrBI and encode structure of the subunits of the pyrimidine biosynthetic enzyme aspartate transcarbamylase . Here we consider the process of synthesis protein PyrB. Expression of the pyrBI operon is regulated primarily through a UTP-sensitive transcriptional attenuation control mechanism in Escherichia coli. In this mechanism, the extent of coupling between transcription and translation within the pyrBI leader region determines the level of p-independent transcriptional termination at an attenuator preceding the pyrB gene. A key feature in this mechanism is transcriptional pausing that occurs before the attenuator in the pyrBI leader region when UTP concentrations are low. In this study, we characterized in detail this UTP-sensitive transcriptional pausing in vitro. NusA has been shown to enhance transcriptional pausing at a variety of DNAsites in E. coli. The concentration of NusA (monomer) = 0.00242 mM [calculation from the work of Lu, 2007].   ","Structural model links":" ID: Donahue et al., 1994 Nucleotide-specific transcriptional pausing in the pyrBI leader region of Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7517939 ; ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ;"},"parameters":[{"units":"","information":"","name":"hUTP","value":"1.4"},{"units":"","information":"","name":"k1NusA","value":"4.1"},{"units":"","information":"","name":"k1UTP","value":"0.04"},{"units":"mM","information":"","name":"k2NusA","value":"0.0001"},{"units":"mM","information":"","name":"k2UTP","value":"0.01"},{"units":"mM/sec","information":"","name":"ks","value":"0.0118"}]},{"scheme":"-> PyrI","substrates":null,"products":{"p1":{"theSubstance":{"name":"PyrI","type":"protein","synonyms":["aspartate carbamoyltransferase, regulatory subunit","PyrI"],"links":[],"id":"SS0000364"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"pyrI","type":"gene","synonyms":["b4244","pyrI"],"links":[],"id":"SS0000365"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"NusA","type":"protein","synonyms":["NusA","Transcription termination/antitermination L factor"],"links":[],"id":"SS0000208"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"UTP","type":"substance","synonyms":["Uridine 5'-triphosphate","Uridine triphosphate","UTP"],"links":[],"id":"SS0000026"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"ks*((1+k1UTP*(r3/k2UTP)^hUTP)/(1+(r3/k2UTP)^hUTP))*((1+k1NusA*(r3/k2NusA))/(1+(r3/k2NusA))) ","theSubMathModel":null,"theInformation":{"Mathematical model information":"The mathematical model describes the effect of different concentrations of UTP and the regulatory protein NusA in time to stop transcription in the leader section operon pyrLBI [Donahue&Turnbough,1994]. To describe the model we have used the generalized Hill function.","Mathematical model links":" ID: Donahue et al., 1994 Nucleotide-specific transcriptional pausing in the pyrBI leader region of Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7517939 ;","Parameter set information":"Parameters k1UTP, k2UTP, hUTP, k1NusA and k2NusA were evaluated basing on [Donahue et al., 1994] experimental data.Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PyrB = 0, where PyrB - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter pyrLp2. ks - protein synthesis generalized constant from the promoter pyrLp2. kd = 0.002 [1/sec],PyrB = 1.008 [mM].","Parameter set links":" ID: Donahue et al., 1994 Nucleotide-specific transcriptional pausing in the pyrBI leader region of Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7517939 ;","Structural model information":"  Genes pyrB and pyrI are part of an operon pyrBI and encode structure of the subunits of the pyrimidine biosynthetic enzyme aspartate transcarbamylase . Here we consider the process of synthesis protein PyrI. Expression of the pyrBI operon is regulated primarily through a UTP-sensitive transcriptional attenuation control mechanism in Escherichia coli. In this mechanism, the extent of coupling between transcription and translation within the pyrBI leader region determines the level of p-independent transcriptional termination at an attenuator preceding the pyrB gene. A key feature in this mechanism is transcriptional pausing that occurs before the attenuator in the pyrBI leader region when UTP concentrations are low. In this study, we characterized in detail this UTP-sensitive transcriptional pausing in vitro. NusA has been shown to enhance transcriptional pausing at a variety of DNAsites in E. coli. The concentration of NusA (monomer) = 0.00242 mM [calculation from the work of Lu, 2007].  ","Structural model links":" ID: Donahue et al., 1994 Nucleotide-specific transcriptional pausing in the pyrBI leader region of Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7517939 ; ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ;"},"mmid":"MM0000226","psid":"PS0000217","gnid":"GN0000218","reversible":false,"information":{"Mathematical model information":"The mathematical model describes the effect of different concentrations of UTP and the regulatory protein NusA in time to stop transcription in the leader section operon pyrLBI [Donahue&Turnbough,1994]. To describe the model we have used the generalized Hill function.","Mathematical model links":" ID: Donahue et al., 1994 Nucleotide-specific transcriptional pausing in the pyrBI leader region of Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7517939 ;","Parameter set information":"Parameters k1UTP, k2UTP, hUTP, k1NusA and k2NusA were evaluated basing on [Donahue et al., 1994] experimental data.Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PyrB = 0, where PyrB - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter pyrLp2. ks - protein synthesis generalized constant from the promoter pyrLp2. kd = 0.002 [1/sec],PyrB = 1.008 [mM].","Parameter set links":" ID: Donahue et al., 1994 Nucleotide-specific transcriptional pausing in the pyrBI leader region of Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7517939 ;","Structural model information":"  Genes pyrB and pyrI are part of an operon pyrBI and encode structure of the subunits of the pyrimidine biosynthetic enzyme aspartate transcarbamylase . Here we consider the process of synthesis protein PyrI. Expression of the pyrBI operon is regulated primarily through a UTP-sensitive transcriptional attenuation control mechanism in Escherichia coli. In this mechanism, the extent of coupling between transcription and translation within the pyrBI leader region determines the level of p-independent transcriptional termination at an attenuator preceding the pyrB gene. A key feature in this mechanism is transcriptional pausing that occurs before the attenuator in the pyrBI leader region when UTP concentrations are low. In this study, we characterized in detail this UTP-sensitive transcriptional pausing in vitro. NusA has been shown to enhance transcriptional pausing at a variety of DNAsites in E. coli. The concentration of NusA (monomer) = 0.00242 mM [calculation from the work of Lu, 2007].  ","Structural model links":" ID: Donahue et al., 1994 Nucleotide-specific transcriptional pausing in the pyrBI leader region of Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7517939 ; ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ;"},"parameters":[{"units":"","information":"","name":"hUTP","value":"1.4"},{"units":"","information":"","name":"k1NusA","value":"4.1"},{"units":"","information":"","name":"k1UTP","value":"0.04"},{"units":"mM","information":"","name":"k2NusA","value":"0.0001"},{"units":"mM","information":"","name":"k2UTP","value":"0.01"},{"units":"mM/sec","information":"","name":"ks","value":"0.0118"}]},{"scheme":"ATP + gln + CO2 + H2O <=> cap + ADP + glu + Pi + H+","substrates":{"s1":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"gln","type":"substance","synonyms":["gln","L-2-Aminoglutaramic acid","L-Glutamine"],"links":[],"id":"SS0000028"},"theState":null,"compartment":""},"s3":{"theSubstance":{"name":"CO2","type":"substance","synonyms":["Carbon dioxide","CO2"],"links":[],"id":"SS0000071"},"theState":null,"compartment":""},"s4":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"cap","type":"substance","synonyms":["cap","Carbamoyl phosphate"],"links":[],"id":"SS0000029"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"glu","type":"substance","synonyms":["glu","Glutamate","L-Glutamate","L-Glutamic acid","L-Glutaminic acid"],"links":[],"id":"SS0000061"},"theState":null,"compartment":""},"p4":{"theSubstance":{"name":"Pi","type":"substance","synonyms":["H3PO4","Orthophosphate","Orthophosphoric acid","Phosphate","Phosphoric acid","Pi"],"links":[],"id":"SS0000070"},"theState":null,"compartment":""},"p5":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"CarA","type":"protein","synonyms":["a chain","arg","CarA","PyrA","small chain"],"links":[],"id":"SS0000350"},"theState":null,"compartment":"","theInfluence":"activator"},"r2":{"theSubstance":{"name":"IMP","type":"substance","synonyms":["5'-IMP","5'-Inosinate","5'-Inosine monophosphate","5'-Inosinic acid","IMP","Inosine 5'-monophosphate","Inosine 5'-phosphate","Inosine monophosphate","Inosinic acid"],"links":[],"id":"SS0000104"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"Ornithine","type":"substance","synonyms":["alpha,delta-diaminovaleric acid","L-ornithine","Ornithine","(S)-2,5-diaminopentanoate","(S)-2,5-diaminopentanoic acid","(S)-2,5-diaminovaleric acid"],"links":[],"id":"SS0000142"},"theState":null,"compartment":"","theInfluence":"activator"},"r4":{"theSubstance":{"name":"UMP","type":"substance","synonyms":["5'Uridylic acid","UMP","Uridine 5'-monophosphate","Uridine monophosphate","Uridylic acid"],"links":[],"id":"SS0000024"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"UDP","type":"substance","synonyms":["UDP","Uridine 5'-diphosphate"],"links":[],"id":"SS0000025"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r6":{"theSubstance":{"name":"UTP","type":"substance","synonyms":["Uridine 5'-triphosphate","Uridine triphosphate","UTP"],"links":[],"id":"SS0000026"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"((kcat*r1*((s1/KmATP)^2)*(s2/Kmgln)*(s3/KmCO2))/(((1+s1/KmATP)^2)*(1+s2/Kmgln)*(1+s3/KmCO2)))*((1+korn1*((r3/korn2)^horn))/(1+(r3/korn2)^horn))*((1+kIMP1*(r2/kIMP2))/(1+(r2/kIMP2)+((r4/kUMP)^hUMP )+((r5/kUDP)^hUDP)+((r6/kUTP)^hUTP)))","theSubMathModel":null,"theInformation":{"Mathematical model links":" ID: Anderson et al., 1966 Control of Escherichia coli carbamyl phosphate synthetase by purine and pyrimidine nucleotides. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5339550 ; ID: Robin et al., 1989 Carbamoyl phosphate biosynthesis and partition in pyrimidine and arginine pathways of Escherichia coli. In situ properties of carbamoyl-phosphate synthase, ornithine transcarbamylase and aspartate transcarbamylase in permeabilized cells. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2673777 ; ID: Wild et al., 1989 In the presence of CTP, UTP becomes an allosteric inhibitor of aspartate transcarbamoylase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2643106 ;","Parameter set information":"Parameters kcat and korn1 were extracted from Pierrat et al. article. Parameters hUMP, kIMP1, kIMP2, korn2 and horn were evaluated on basis of the data in Robin et al. article. Parameters kUDP,kUTP, hUDP, hUTP were evaluated on basis of the data presented in Anderson et al. paper. Parameters kUMP, KmATP, Kmgln, KmCO2 were taken from Robin et al. article. Moreover, to simulate the enzymatic kinetics you can use steady-state concentrations for CO2=10 mM (Robin et al., 1989); ATP=9.6 mM, Gln = 3.8 mM, orn = 0.01 mM and IMP = 0.27 mM (Bennett et al., 2009). The model was simulated upon steady state concentration of CarA enzyme, which equals to 0.0048 mM (Albe et al., 1990).","Parameter set links":" ID: Albe et al., 1990 Cellular concentrations of enzymes and their substrates. Journal of Theoretical Biology, 143(2), 163-195.. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2200929 ; ID: Anderson et al., 1966 Control of Escherichia coli carbamyl phosphate synthetase by purine and pyrimidine nucleotides. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5339550 ; ID: Bennett et al., 2009 Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2754216 ; ID: Pierrat et al., 2002 Dissection of the conduit for allosteric control of carbamoyl phosphate synthetase by ornithine. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11913967 ; ID: Robin et al., 1989 Carbamoyl phosphate biosynthesis and partition in pyrimidine and arginine pathways of Escherichia coli. In situ properties of carbamoyl-phosphate synthase, ornithine transcarbamylase and aspartate transcarbamylase in permeabilized cells. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2673777 ; ID: Wild et al., 1989 In the presence of CTP, UTP becomes an allosteric inhibitor of aspartate transcarbamoylase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2643106 ;","Structural model information":"Carbamoyl phosphate synthetase from E. coli catalyzes the first committed step in the separate biosynthetic pathways for the production of arginine and pyrimidine nucleotides. The enzyme is an a heterodimeric enzyme composed of a small amidotransferase subunit complexed to a larger synthetase subunit. The small subunit encoded by carA gene hydrolyzes glutamine to glutamate and ammonia. The large subunit encoded by carB gene binds the two required molecules of MgATP and catalyzes the two required phosphorylation events. Subunit composition of carbamoyl phosphate synthetase = [CarB]2[CarA]2. Since UMP, UDP and UTP are known to be competitive inhibitors [Robin et al.,1989; Anderson et al., 1966] of this reaction the equation can be written as a sum of inhibitors influences. IMP is capable of competitive activation of CASPase relative to UMP [Wild et al., 1989]. Ornithine specifically antagonizes the UMP inhibition of CPSase and is capable of independent activation [Wild et al., 1989].","Structural model links":" ID: Anderson et al., 1966 Control of Escherichia coli carbamyl phosphate synthetase by purine and pyrimidine nucleotides. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5339550 ; ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=CARBPSYN-RXN ; ID: Pierrat et al., 2002 Dissection of the conduit for allosteric control of carbamoyl phosphate synthetase by ornithine. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11913967 ; ID: Robin et al., 1989 Carbamoyl phosphate biosynthesis and partition in pyrimidine and arginine pathways of Escherichia coli. In situ properties of carbamoyl-phosphate synthase, ornithine transcarbamylase and aspartate transcarbamylase in permeabilized cells. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2673777 ; ID: Wild et al., 1989 In the presence of CTP, UTP becomes an allosteric inhibitor of aspartate transcarbamoylase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2643106 ;"},"mmid":"MM0000191","psid":"PS0000185","gnid":"GN0000182","reversible":true,"information":{"Mathematical model links":" ID: Anderson et al., 1966 Control of Escherichia coli carbamyl phosphate synthetase by purine and pyrimidine nucleotides. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5339550 ; ID: Robin et al., 1989 Carbamoyl phosphate biosynthesis and partition in pyrimidine and arginine pathways of Escherichia coli. In situ properties of carbamoyl-phosphate synthase, ornithine transcarbamylase and aspartate transcarbamylase in permeabilized cells. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2673777 ; ID: Wild et al., 1989 In the presence of CTP, UTP becomes an allosteric inhibitor of aspartate transcarbamoylase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2643106 ;","Parameter set information":"Parameters kcat and korn1 were extracted from Pierrat et al. article. Parameters hUMP, kIMP1, kIMP2, korn2 and horn were evaluated on basis of the data in Robin et al. article. Parameters kUDP,kUTP, hUDP, hUTP were evaluated on basis of the data presented in Anderson et al. paper. Parameters kUMP, KmATP, Kmgln, KmCO2 were taken from Robin et al. article. Moreover, to simulate the enzymatic kinetics you can use steady-state concentrations for CO2=10 mM (Robin et al., 1989); ATP=9.6 mM, Gln = 3.8 mM, orn = 0.01 mM and IMP = 0.27 mM (Bennett et al., 2009). The model was simulated upon steady state concentration of CarA enzyme, which equals to 0.0048 mM (Albe et al., 1990).","Parameter set links":" ID: Albe et al., 1990 Cellular concentrations of enzymes and their substrates. Journal of Theoretical Biology, 143(2), 163-195.. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2200929 ; ID: Anderson et al., 1966 Control of Escherichia coli carbamyl phosphate synthetase by purine and pyrimidine nucleotides. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5339550 ; ID: Bennett et al., 2009 Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2754216 ; ID: Pierrat et al., 2002 Dissection of the conduit for allosteric control of carbamoyl phosphate synthetase by ornithine. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11913967 ; ID: Robin et al., 1989 Carbamoyl phosphate biosynthesis and partition in pyrimidine and arginine pathways of Escherichia coli. In situ properties of carbamoyl-phosphate synthase, ornithine transcarbamylase and aspartate transcarbamylase in permeabilized cells. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2673777 ; ID: Wild et al., 1989 In the presence of CTP, UTP becomes an allosteric inhibitor of aspartate transcarbamoylase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2643106 ;","Structural model information":"Carbamoyl phosphate synthetase from E. coli catalyzes the first committed step in the separate biosynthetic pathways for the production of arginine and pyrimidine nucleotides. The enzyme is an a heterodimeric enzyme composed of a small amidotransferase subunit complexed to a larger synthetase subunit. The small subunit encoded by carA gene hydrolyzes glutamine to glutamate and ammonia. The large subunit encoded by carB gene binds the two required molecules of MgATP and catalyzes the two required phosphorylation events. Subunit composition of carbamoyl phosphate synthetase = [CarB]2[CarA]2. Since UMP, UDP and UTP are known to be competitive inhibitors [Robin et al.,1989; Anderson et al., 1966] of this reaction the equation can be written as a sum of inhibitors influences. IMP is capable of competitive activation of CASPase relative to UMP [Wild et al., 1989]. Ornithine specifically antagonizes the UMP inhibition of CPSase and is capable of independent activation [Wild et al., 1989].","Structural model links":" ID: Anderson et al., 1966 Control of Escherichia coli carbamyl phosphate synthetase by purine and pyrimidine nucleotides. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5339550 ; ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=CARBPSYN-RXN ; ID: Pierrat et al., 2002 Dissection of the conduit for allosteric control of carbamoyl phosphate synthetase by ornithine. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11913967 ; ID: Robin et al., 1989 Carbamoyl phosphate biosynthesis and partition in pyrimidine and arginine pathways of Escherichia coli. In situ properties of carbamoyl-phosphate synthase, ornithine transcarbamylase and aspartate transcarbamylase in permeabilized cells. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2673777 ; ID: Wild et al., 1989 In the presence of CTP, UTP becomes an allosteric inhibitor of aspartate transcarbamoylase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2643106 ;"},"parameters":[{"units":"mM","information":"","name":"KmATP","value":"8"},{"units":"mM","information":"","name":"KmCO2","value":"3.6"},{"units":"mM","information":"","name":"Kmgln","value":"0.22"},{"units":"","information":"","name":"hUDP","value":"1.4"},{"units":"","information":"","name":"hUMP","value":"1.4"},{"units":"","information":"","name":"hUTP","value":"1.4"},{"units":"","information":"","name":"horn","value":"2.4"},{"units":"","information":"","name":"kIMP1","value":"1.43"},{"units":"mM","information":"","name":"kIMP2","value":"0.05"},{"units":"mM","information":"","name":"kUDP","value":"0.73"},{"units":"mM","information":"","name":"kUMP","value":"0.04"},{"units":"mM","information":"","name":"kUTP","value":"1.03"},{"units":"1/sec","information":"","name":"kcat","value":"12"},{"units":"","information":"","name":"korn1","value":"3.4"},{"units":"mM","information":"","name":"korn2","value":"0.1"}]},{"scheme":"-> NrdB","substrates":null,"products":{"p1":{"theSubstance":{"name":"NrdB","type":"protein","synonyms":["NrdB","ribonucleoside diphosphate reductase 1, ? subunit dimer"],"links":[],"id":"SS0000371"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"nrdB","type":"gene","synonyms":["nrdB"],"links":[],"id":"SS0000395"},"theState":null,"compartment":"","theInfluence":""},"r10":{"theSubstance":{"name":"RutR","type":"protein","synonyms":["RutR","RutR DNA-binding transcriptional dual regulator"],"links":[],"id":"SS0000357"},"theState":null,"compartment":"","theInfluence":"activator"},"r11":{"theSubstance":{"name":"Ura","type":"substance","synonyms":["Ura","Uracil"],"links":[],"id":"SS0000040"},"theState":null,"compartment":"","theInfluence":"activator"},"r12":{"theSubstance":{"name":"Thy","type":"substance","synonyms":["5-Methyluracil","Thy","Thymine"],"links":[],"id":"SS0000056"},"theState":null,"compartment":"","theInfluence":"activator"},"r2":{"theSubstance":{"name":"DnaA","type":"protein","synonyms":["DnaA"],"links":[],"id":"SS0000390"},"theState":null,"compartment":"","theInfluence":"complex regulator"},"r3":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":"","theInfluence":"activator"},"r4":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":"","theInfluence":"activator"},"r5":{"theSubstance":{"name":"NrdR","type":"protein","synonyms":["NrdR"],"links":[],"id":"SS0000391"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r6":{"theSubstance":{"name":"dATP","type":"substance","synonyms":["2'-Deoxyadenosine 5'-triphosphate","dATP","Deoxyadenosine 5'-triphosphate","Deoxyadenosine triphosphate"],"links":[],"id":"SS0000079"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r7":{"theSubstance":{"name":"Fis","type":"protein","synonyms":["Fis"],"links":[],"id":"SS0000389"},"theState":null,"compartment":"","theInfluence":"activator"},"r8":{"theSubstance":{"name":"ArgP","type":"protein","synonyms":["ArgP"],"links":[],"id":"SS0000392"},"theState":null,"compartment":"","theInfluence":"activator"},"r9":{"theSubstance":{"name":"arg","type":"substance","synonyms":["2-amino-5-guanidinovaleric acid","arg","arginine","L-arginine","R"],"links":[],"id":"SS0000387"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"ks*((1+(k1DnaA*(((k0*(((r2*r3)/kdisDnaAATP)/(1+((r2*r3)/kdisDnaAATP)+((r2*r4)/kdisDnaAADP))))/k2DnaA)^hDnaA)))/(1+(((k0*(((r2*r3)/kdisDnaAATP)/(1+((r2*r3)/kdisDnaAATP)+((r2*r4)/kdisDnaAADP))))/k2DnaA)^hDnaA)))*(1/(1+((((k0*(((r2*r3)/kdisDnaAATP)/(1+((r2*r3)/kdisDnaAATP)+((r2*r4)/kdisDnaAADP))))^3)/((kdisDnaA^2)+3*((k0*(((r2*r3)/kdisDnaAATP)/(1+((r2*r3)/kdisDnaAATP)+((r2*r4)/kdisDnaAADP))))^2)))/k3Dna)))*((1+k1NrdR*(((((r5*r3)/kdisNrdRATP)/(1+((r5*r3)/kdisNrdRATP)+((r5*r6)/kdisNrdRdATP)))/k2NrdR)+((((r5*r6)/kdisNrdRdATP)/(1+((r5*r3)/kdisNrdRATP)+((r5*r6)/kdisNrdRdATP)))/k3NrdR)))/(1+((((r5*r3)/kdisNrdRATP)/(1+((r5*r3)/kdisNrdRATP)+((r5*r6)/kdisNrdRdATP)))/k2NrdR)+((((r5*r6)/kdisNrdRdATP)/(1+((r5*r3)/kdisNrdRATP)+((r5*r6)/kdisNrdRdATP)))/k3NrdR)))*((1+k1Fis*(r7/k2Fis))/(1+(r7/k2Fis)))*((1+k3Fis*(r7/k4Fis))/(1+(r7/k4Fis)))*((1+k1ArgP*(((((r8*(r9^2))/(kdisArgParg^2))/(1+((2*r8*r9+(r9^2))/(kdisArgParg^2))))/k2ArgP)^hArgP))/(1+(((((r8*(r9^2))/(kdisArgParg^2))/(1+((2*r8*r9+(r9^2))/(kdisArgParg^2))))/k2ArgP)^hArgP)))*((1+k1RutR*((((r10*(r11^2))/(kdisRutRura^2))/(1+((r10*(r11^2))/(kdisRutRura^2))+((r10*(r12^2))/(kdisRutRthy^2))))/k2RutR))/(1+((((r10*(r12^2))/(kdisRutRthy^2))/(1+((r10*(r11^2))/(kdisRutRura^2))+((r10*(r12^2))/(kdisRutRthy^2))))/k2RutR)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"To describe the model we have used the generalized Hill function. The efficiency of transcription of the operon nrdAB is regulated positively transcription factors Fis, ArgP and negatively NrdR [Augustin et al., 1994, Torrents et al., 2007, Han et al., 1998]. Active nrdAB operon and controls factor DnaA, but the direction of its impact depends on the concentration of its ATP-bound form [Olliver et al., 2010].","Mathematical model links":" ID: Augustin L.B., 1994 Jacobson B.A., Fuchs J.A., Escherichia coli Fis and DnaA proteins bind specifically to the nrd promoter region and affect expression of an nrd-lac fusion. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8288532 ; ID: Han J.S. et al., 1998 Effect of IciA protein on the expression of the nrd gene encoding ribonucleoside diphosphate reductase in E. coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9819053 ; ID: Olliver A. et al., 2010 DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/20487274 ; ID: Torrents E. et al., 2007 NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17496099 ;","Parameter set information":"  Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*NrdB = 0, where NrdB - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter nrdAp. ks - protein synthesis generalized constant from the promoter nrdAp. kd = 0.002 [1/sec], NrdB =0.002736 [mM]. Parameters k1DnaA, k2DnaA, k3DnaA and hDnaA were evaluated basing on [Olliver A. et al., 2010] experimental data. Parameters k1Fis, k2Fis, k3Fis and k4Fis were evaluated basing on [Augustin L.B., 1994] experimental data. Parameters k1NrdR, k2NrdR and k3NrdR were evaluated basing on [Torrents E. et al., 2007] experimental data.Parameters k1ArgP, k2ArgP, hArgP were evaluated basing on [Han J.S. et al., 1998 ] experimental data. Parameters kdisDnaAATP, and kdisDnaAADP are taken from article [Kaguni, 2006]. Parameter kdisDnaA was evaluated basing on [Olliver et al., 2010] experimental data. ","Parameter set links":" ID: Augustin L.B., 1994 Jacobson B.A., Fuchs J.A., Escherichia coli Fis and DnaA proteins bind specifically to the nrd promoter region and affect expression of an nrd-lac fusion. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8288532 ; ID: Han J.S. et al., 1998 Effect of IciA protein on the expression of the nrd gene encoding ribonucleoside diphosphate reductase in E. coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9819053 ; ID: Kaguni J.M., 2006 DnaA: controlling the initiation of bacterial DNA replication and more. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16753031 ; ID: Olliver A. et al., 2010 DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/20487274 ; ID: Torrents E. et al., 2007 NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17496099 ;","Structural model information":"Genes nrdA and nrdB are part of an operon nrdAB and encode structure of the subunits of the enzyme ribonucleoside diphosphate reductase. Here we consider the process of synthesis protein NrdB with the promoter nrdAp. The efficiency of transcription of the operon nrdAB is regulated positively transcription factors Fis, ArgP and negatively NrdR [Augustin et al., 1994, Torrents et al., 2007, Han et al., 1998]. Active nrdAB operon and controls factor DnaA, but the direction of its impact depends on the concentration of its ATP-bound form [Olliver et al., 2010].","Structural model links":" ID: Augustin L.B., 1994 Jacobson B.A., Fuchs J.A., Escherichia coli Fis and DnaA proteins bind specifically to the nrd promoter region and affect expression of an nrd-lac fusion. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8288532 ; ID: Han J.S. et al., 1998 Effect of IciA protein on the expression of the nrd gene encoding ribonucleoside diphosphate reductase in E. coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9819053 ; ID: Olliver A. et al., 2010 DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/20487274 ; ID: Torrents E. et al., 2007 NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17496099 ;"},"mmid":"MM0000232","psid":"PS0000222","gnid":"GN0000223","reversible":false,"information":{"Mathematical model information":"To describe the model we have used the generalized Hill function. The efficiency of transcription of the operon nrdAB is regulated positively transcription factors Fis, ArgP and negatively NrdR [Augustin et al., 1994, Torrents et al., 2007, Han et al., 1998]. Active nrdAB operon and controls factor DnaA, but the direction of its impact depends on the concentration of its ATP-bound form [Olliver et al., 2010].","Mathematical model links":" ID: Augustin L.B., 1994 Jacobson B.A., Fuchs J.A., Escherichia coli Fis and DnaA proteins bind specifically to the nrd promoter region and affect expression of an nrd-lac fusion. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8288532 ; ID: Han J.S. et al., 1998 Effect of IciA protein on the expression of the nrd gene encoding ribonucleoside diphosphate reductase in E. coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9819053 ; ID: Olliver A. et al., 2010 DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/20487274 ; ID: Torrents E. et al., 2007 NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17496099 ;","Parameter set information":"  Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*NrdB = 0, where NrdB - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter nrdAp. ks - protein synthesis generalized constant from the promoter nrdAp. kd = 0.002 [1/sec], NrdB =0.002736 [mM]. Parameters k1DnaA, k2DnaA, k3DnaA and hDnaA were evaluated basing on [Olliver A. et al., 2010] experimental data. Parameters k1Fis, k2Fis, k3Fis and k4Fis were evaluated basing on [Augustin L.B., 1994] experimental data. Parameters k1NrdR, k2NrdR and k3NrdR were evaluated basing on [Torrents E. et al., 2007] experimental data.Parameters k1ArgP, k2ArgP, hArgP were evaluated basing on [Han J.S. et al., 1998 ] experimental data. Parameters kdisDnaAATP, and kdisDnaAADP are taken from article [Kaguni, 2006]. Parameter kdisDnaA was evaluated basing on [Olliver et al., 2010] experimental data. ","Parameter set links":" ID: Augustin L.B., 1994 Jacobson B.A., Fuchs J.A., Escherichia coli Fis and DnaA proteins bind specifically to the nrd promoter region and affect expression of an nrd-lac fusion. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8288532 ; ID: Han J.S. et al., 1998 Effect of IciA protein on the expression of the nrd gene encoding ribonucleoside diphosphate reductase in E. coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9819053 ; ID: Kaguni J.M., 2006 DnaA: controlling the initiation of bacterial DNA replication and more. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16753031 ; ID: Olliver A. et al., 2010 DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/20487274 ; ID: Torrents E. et al., 2007 NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17496099 ;","Structural model information":"Genes nrdA and nrdB are part of an operon nrdAB and encode structure of the subunits of the enzyme ribonucleoside diphosphate reductase. Here we consider the process of synthesis protein NrdB with the promoter nrdAp. The efficiency of transcription of the operon nrdAB is regulated positively transcription factors Fis, ArgP and negatively NrdR [Augustin et al., 1994, Torrents et al., 2007, Han et al., 1998]. Active nrdAB operon and controls factor DnaA, but the direction of its impact depends on the concentration of its ATP-bound form [Olliver et al., 2010].","Structural model links":" ID: Augustin L.B., 1994 Jacobson B.A., Fuchs J.A., Escherichia coli Fis and DnaA proteins bind specifically to the nrd promoter region and affect expression of an nrd-lac fusion. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8288532 ; ID: Han J.S. et al., 1998 Effect of IciA protein on the expression of the nrd gene encoding ribonucleoside diphosphate reductase in E. coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9819053 ; ID: Olliver A. et al., 2010 DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/20487274 ; ID: Torrents E. et al., 2007 NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17496099 ;"},"parameters":[{"units":"","information":"","name":"hArgP","value":"2"},{"units":"","information":"","name":"hDnaA","value":"2"},{"units":"","information":"","name":"k0","value":"0.12"},{"units":"mM","information":"","name":"k1ArgP","value":"5"},{"units":"","information":"","name":"k1DnaA","value":"2.07"},{"units":"","information":"","name":"k1Fis","value":"2.53"},{"units":"mM","information":"","name":"k1NrdR","value":"0.228"},{"units":"","information":"","name":"k1RutR","value":"2"},{"units":"mM","information":"","name":"k2ArgP","value":"0.000167"},{"units":"mM","information":"","name":"k2DnaA","value":"0.00002"},{"units":"mM","information":"","name":"k2Fis","value":"0.001"},{"units":"mM","information":"","name":"k2NrdR","value":"0.0003"},{"units":"mM","information":"","name":"k2RutR","value":"0.0001"},{"units":"mM","information":"","name":"k3Dna","value":"0.0001"},{"units":"","information":"","name":"k3Fis","value":"6.4"},{"units":"mM","information":"","name":"k3NrdR","value":"0.0003"},{"units":"mM","information":"","name":"k4Fis","value":"0.004"},{"units":"mM","information":"","name":"kdisArgParg","value":"0.001"},{"units":"mM","information":"","name":"kdisDnaA","value":"0.00134"},{"units":"mM","information":"","name":"kdisDnaAADP","value":"0.0001"},{"units":"mM","information":"","name":"kdisDnaAATP","value":"0.00003"},{"units":"mM","information":"","name":"kdisNrdRATP","value":"0.001"},{"units":"mM","information":"","name":"kdisNrdRdATP","value":"0.001"},{"units":"mM","information":"","name":"kdisRutRthy","value":"0.001"},{"units":"mM","information":"","name":"kdisRutRura","value":"0.001"},{"units":"mM/sec","information":"","name":"ks","value":"0.000007"}]},{"scheme":"cap + asp -> caasp + Pi + H+","substrates":{"s1":{"theSubstance":{"name":"cap","type":"substance","synonyms":["cap","Carbamoyl phosphate"],"links":[],"id":"SS0000029"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"asp","type":"substance","synonyms":["2-Aminosuccinic acid","asp","L-Asp","L-Aspartate","L-Aspartic acid"],"links":[],"id":"SS0000059"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"caasp","type":"substance","synonyms":["caasp","N-Carbamoyl-L-aspartate"],"links":[],"id":"SS0000030"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"Pi","type":"substance","synonyms":["H3PO4","Orthophosphate","Orthophosphoric acid","Phosphate","Phosphoric acid","Pi"],"links":[],"id":"SS0000070"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PyrB","type":"protein","synonyms":["aspartate carbamoyltransferase, catalytic subunit","PyrB"],"links":[],"id":"SS0000363"},"theState":null,"compartment":"","theInfluence":"activator"},"r2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"CTP","type":"substance","synonyms":["CTP","Cytidine 5'-triphosphate","Cytidine triphosphate"],"links":[],"id":"SS0000027"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"UTP","type":"substance","synonyms":["Uridine 5'-triphosphate","Uridine triphosphate","UTP"],"links":[],"id":"SS0000026"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"PyrI","type":"protein","synonyms":["aspartate carbamoyltransferase, regulatory subunit","PyrI"],"links":[],"id":"SS0000364"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"((r1*kcat*((s1/Kmcap)^hcap)*((s2/Kmasp)^hasp1))/((1+ (s1/Kmcap)^hcap)*(1+(s2/Kmasp)^hasp2)))*((1+kCTP1*(r3/kCTP2)+kATP1*(r2/kATP2)+kUTP1*(r4/kUTP2))/(1+(r3/kCTP2)+(r2/kATP2)+(r4/kUTP2)+w*(r3/kCTP2)*(r4/kUTP2)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Aspartate transcarbamylase (ATCase) catalyzes the first reaction unique to the de novo biosynthesis of pyrimidine nucleotides. The ATCase holoenzyme consists of two catalytic trimers (encoded by pyrB) and three regulatory dimers (encoded by pyrI).The ATCase holoenzyme consists of two catalytic trimers (encoded by pyrB) and three regulatory dimers (encoded by pyrI).","Mathematical model links":" ID: Wales et al., 1999 Divergent allosteric patterns verify the regulatory paradigm for aspartate transcarbamylase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10600393 ; ID: Xu et al., 1991 Function of serine-52 and serine-80 in the catalytic mechanism of Escherichia coli aspartate transcarbamoylase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1900434 ;","Parameter set information":"Parameters kcat and r1 were taken from Albe et al article. Parameters kmcap and kmasp were taken from Shepherdson M. and Pardee A. B., 1962. Parameters hcap, hasp1, hasp2 were evaluated on basis of Xu et al data. Parameters kCTP1, kCTP2, kATP1, kATP2, kUTP1, kUTP2 and W were evaluated using Wales et al quantitative data. To simulate the enzymatic kinetics you can use steady-state concentrations for Asp = 4.2 mM (Bennett et al., 2009). The model was simulated upon steady state concentration of PyrB enzyme, which equals to 0.0846 mM (Albe et al., 1990).","Parameter set links":" ID: Albe et al., 1990 Cellular concentrations of enzymes and their substrates. Journal of Theoretical Biology, 143(2), 163-195.. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2200929 ; ID: Bennett et al., 2009 Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol. 2009, V.5(8),P.593-599 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2754216 ; ID: Shepherdson M. and Pardee A. B., 1962. [124b] Aspartate transcarbamylase from Escherichia coli:... Methods in Enzymology, V.5, P.925-931. ; Value:http://www.sciencedirect.com/science/article/pii/S0076687962053379 ; ID: Wales et al., 1999 Divergent allosteric patterns verify the regulatory paradigm for aspartate transcarbamylase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10600393 ; ID: Xu et al., 1991 Function of serine-52 and serine-80 in the catalytic mechanism of Escherichia coli aspartate transcarbamoylase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1900434 ;","Structural model information":"Aspartate transcarbamylase (ATCase) catalyzes the first reaction unique to the de novo biosynthesis of pyrimidine nucleotides.The ATCase holoenzyme consists of two catalytic trimers (encoded by pyrB) and three regulatory dimers (encoded by pyrI).UTP potentiates inhibition by CTP. The inhibitor CTP and the activator ATP do not simply act in inverse ways on the same equilibrium.","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=ASPCARBTRANS-RXN ; ID: Shepherdson M., Pardee A. B., 1962. [124b] Aspartate transcarbamylase from Escherichia coli:... Methods in Enzymology, V.5, P.925-931. ; Value:http://www.sciencedirect.com/science/article/pii/S0076687962053379 ;"},"mmid":"MM0000192","psid":"PS0000186","gnid":"GN0000183","reversible":false,"information":{"Mathematical model information":"Aspartate transcarbamylase (ATCase) catalyzes the first reaction unique to the de novo biosynthesis of pyrimidine nucleotides. The ATCase holoenzyme consists of two catalytic trimers (encoded by pyrB) and three regulatory dimers (encoded by pyrI).The ATCase holoenzyme consists of two catalytic trimers (encoded by pyrB) and three regulatory dimers (encoded by pyrI).","Mathematical model links":" ID: Wales et al., 1999 Divergent allosteric patterns verify the regulatory paradigm for aspartate transcarbamylase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10600393 ; ID: Xu et al., 1991 Function of serine-52 and serine-80 in the catalytic mechanism of Escherichia coli aspartate transcarbamoylase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1900434 ;","Parameter set information":"Parameters kcat and r1 were taken from Albe et al article. Parameters kmcap and kmasp were taken from Shepherdson M. and Pardee A. B., 1962. Parameters hcap, hasp1, hasp2 were evaluated on basis of Xu et al data. Parameters kCTP1, kCTP2, kATP1, kATP2, kUTP1, kUTP2 and W were evaluated using Wales et al quantitative data. To simulate the enzymatic kinetics you can use steady-state concentrations for Asp = 4.2 mM (Bennett et al., 2009). The model was simulated upon steady state concentration of PyrB enzyme, which equals to 0.0846 mM (Albe et al., 1990).","Parameter set links":" ID: Albe et al., 1990 Cellular concentrations of enzymes and their substrates. Journal of Theoretical Biology, 143(2), 163-195.. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2200929 ; ID: Bennett et al., 2009 Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol. 2009, V.5(8),P.593-599 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC2754216 ; ID: Shepherdson M. and Pardee A. B., 1962. [124b] Aspartate transcarbamylase from Escherichia coli:... Methods in Enzymology, V.5, P.925-931. ; Value:http://www.sciencedirect.com/science/article/pii/S0076687962053379 ; ID: Wales et al., 1999 Divergent allosteric patterns verify the regulatory paradigm for aspartate transcarbamylase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10600393 ; ID: Xu et al., 1991 Function of serine-52 and serine-80 in the catalytic mechanism of Escherichia coli aspartate transcarbamoylase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1900434 ;","Structural model information":"Aspartate transcarbamylase (ATCase) catalyzes the first reaction unique to the de novo biosynthesis of pyrimidine nucleotides.The ATCase holoenzyme consists of two catalytic trimers (encoded by pyrB) and three regulatory dimers (encoded by pyrI).UTP potentiates inhibition by CTP. The inhibitor CTP and the activator ATP do not simply act in inverse ways on the same equilibrium.","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=ASPCARBTRANS-RXN ; ID: Shepherdson M., Pardee A. B., 1962. [124b] Aspartate transcarbamylase from Escherichia coli:... Methods in Enzymology, V.5, P.925-931. ; Value:http://www.sciencedirect.com/science/article/pii/S0076687962053379 ;"},"parameters":[{"units":"mM","information":"","name":"Kmasp","value":"60"},{"units":"mM","information":"","name":"Kmcap","value":"0.45"},{"units":"","information":"","name":"hasp1","value":"2.3"},{"units":"","information":"","name":"hasp2","value":"3.1"},{"units":"","information":"","name":"hcap","value":"2.2"},{"units":"","information":"","name":"kATP1","value":"3.4"},{"units":"mM","information":"","name":"kATP2","value":"0.34"},{"units":"","information":"","name":"kCTP1","value":"0.22"},{"units":"mM","information":"","name":"kCTP2","value":"0.06"},{"units":"","information":"","name":"kUTP1","value":"0.9"},{"units":"mM","information":"","name":"kUTP2","value":"1"},{"units":"1/sec","information":"","name":"kcat","value":"1667"},{"units":"","information":"","name":"w","value":"3"}]},{"scheme":"-> PyrC","substrates":null,"products":{"p1":{"theSubstance":{"name":"PyrC","type":"protein","synonyms":["dihydroorotase","PyrC"],"links":[],"id":"SS0000366"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"pyrC","type":"gene","synonyms":["b1062","pyrC"],"links":[],"id":"SS0000209"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"GTP","type":"substance","synonyms":["GTP","Guanosine 5'-triphosphate"],"links":[],"id":"SS0000140"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"CTP","type":"substance","synonyms":["CTP","Cytidine 5'-triphosphate","Cytidine triphosphate"],"links":[],"id":"SS0000027"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"PurR","type":"protein","synonyms":["PurR","PurR transcriptional repressor"],"links":[],"id":"SS0000358"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"Gua","type":"substance","synonyms":["Gua","Guanosine"],"links":[],"id":"SS0000113"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r6":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r7":{"theSubstance":{"name":"Fur","type":"protein","synonyms":["Fur"],"links":[],"id":"SS0000388"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"ks*(((r2/kGTP)^hGTP)/(1+((r2/kGTP)^hGTP)+((r3/kCTP)^hCTP)+w*((r2/kGTP)^hGTP)*((r3/kCTP)^hCTP)))*((1+((r4-(((r4*(r5^2))/(kdisPurRhyp^2))/(1+((2*r4*r5+r5^2)/(kdisPurRhyp^2))+((2*r4*r6+r6^2)/(kdisPurRgua^2))))-(((r4*(r6^2))/(kdisPurRgua^2))/(1+((2*r4*r5+r5^2)/(kdisPurRhyp^2))+((2*r4*r6+r6^2)/(kdisPurRgua^2)))))/k3PurR))/(1+((((r4*(r5^2))/(kdisPurRhyp^2))/(1+((2*r4*r5+r5^2)/(kdisPurRhyp^2))+((2*r4*r6+r6^2)/(kdisPurRgua^2))))/k1PurR)+((((r4*(r6^2))/(kdisPurRgua^2))/(1+((2*r4*r5+r5^2)/(kdisPurRhyp^2))+((2*r4*r6+r6^2)/(kdisPurRgua^2))))/k2PurR)+((r4-(((r4*(r5^2))/(kdisPurRhyp^2))/(1+((2*r4*r5+r5^2)/(kdisPurRhyp^2))+((2*r4*r6+r6^2)/(kdisPurRgua^2))))-(((r4*(r6^2))/(kdisPurRgua^2))/(1+((2*r4*r5+r5^2)/(kdisPurRhyp^2))+((2*r4*r6+r6^2)/(kdisPurRgua^2)))))/k3PurR)))*(1/(1+r7/kFur))","theSubMathModel":null,"theInformation":{"Mathematical model information":" Expression of pyrC gene, encoding dihydroorotase, an enzyme involved in pyrimidine biosynthesis, is downregulated by pyrimidines. The hairpin formation is controlled via a nucleotide sensitive selection of the pyrC transcription initiation. At a high CTP concentration, the main part of pyrC transcripts is initiated from nucleotide C17, located at a distance of 17 nucleotides from the pyrC translation start site. Such transcripts are able to form a stable hairpin at the 5&amp;amp;apos;end of mRNA in the region of ribosome binding site, thereby interfering with a normal translation initiation. At a low CTP and high GTP concentrations, the main part of the pyrC transcripts is initiated from nucleotide G15, which is by two nucleotides closer to the initiation codon as compared with C17. Consequently, the synthesized transcript is by two nucleotides shorter and is unable to form a stable hairpin at the 5-end of mRNA, which provides for a normal translation initiation. A uniqueness of this locus is in that biosynthesis of the protein PyrC is regulated via negative feedback by selection of the transcription start site, which influences the possibility of translation initiation of the transcribed mRNA. In the case of excess pyrimidines, the predominantly synthesized transcripts form a hairpin at the ribosome binding site, which blocks the translation initiation. In the case of pyrimidine deficiency in the cell, truncated transcripts are synthesized, which can be translated, thereby elevating the concentration of dihydroorotase in the cell. A detailed biochemical scheme for genetic regulation of pyrC gene expression deducible from the information briefed above is exclusively intricate. The mathematical model describes the regulation of gene pyrC. To describe the model we have used the generalized Hill function. In the promoter region of the operon pyrC binds purine repressor (PurR). When binding protein PurR is not inhibiting the expression of the operon pyrC, but the addition of adenine in the medium enhances the effect of inhibiting the transcription factor PurR 2 times. Chai et al.(2007) showed that gene expression is controlled negatively pyrC transcription factor Fur. In his presence, gene expression is reduced by 17%. ","Mathematical model links":" ID: Likhoshvai et al., 2010 Metabolic Engineering in Silico. ; Value:http://www.springerlink.com/content/51438683725255u1/ ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PyrC = 0, where PyrC - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter pyrCp. ks - protein synthesis generalized constant from the promoter pyrCp. kd = 0.002 [1/sec],PyrC = 0.006371 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters kGTP, hGTP, kCTP,hCTP and w were evaluated basing on [Wilson et al., 1992, Likhoshvai et al., 2010] experimental data. Parameter kFur was evaluated basing on [Chai et al., 2007] experimental data. Parameters k1PurR and k2PurR were evaluated basing on [Wilson et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Chai et al., 2007 Effect of fur on pyrC gene expression. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/18176545 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Likhoshvai et al., 2010 Metabolic Engineering in Silico. ; Value:http://www.springerlink.com/content/51438683725255u1/ ; ID: Wilson HR, Turnbough CL Jr., 1990 Role of the purine repressor in the regulation of pyrimidine gene expression in Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1971621 ; ID: Wilson et al., 1992 Translational control of pyrC expression mediated by nucleotide-sensitive selection of transcriptional start sites in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1345912 ;","Structural model information":"   Translation of pyrC is regulated by transcription start site selection. When CTP is abundant, a site distal to the start codon is chosen, allowing formation of a hairpin that blocks ribosome binding. Otherwise, a proximal site is chosen that prevents hairpin formation, allowing translation.\nIn the promoter region of the operon pyrC binds purine repressor (PurR) and transcription factor Fur. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]; The concentration of Fur (dimer) = 0.0012 mM [calculation from the work of Lu, 2007]. ","Structural model links":" ID: Chai et al., 2007 Effect of fur on pyrC gene expression. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/18176545 ; ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Wilson et al., 1992 Translational control of pyrC expression mediated by nucleotide-sensitive selection of transcriptional start sites in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1345912 ;"},"mmid":"MM0000227","psid":"PS0000218","gnid":"GN0000219","reversible":false,"information":{"Mathematical model information":" Expression of pyrC gene, encoding dihydroorotase, an enzyme involved in pyrimidine biosynthesis, is downregulated by pyrimidines. The hairpin formation is controlled via a nucleotide sensitive selection of the pyrC transcription initiation. At a high CTP concentration, the main part of pyrC transcripts is initiated from nucleotide C17, located at a distance of 17 nucleotides from the pyrC translation start site. Such transcripts are able to form a stable hairpin at the 5&amp;amp;apos;end of mRNA in the region of ribosome binding site, thereby interfering with a normal translation initiation. At a low CTP and high GTP concentrations, the main part of the pyrC transcripts is initiated from nucleotide G15, which is by two nucleotides closer to the initiation codon as compared with C17. Consequently, the synthesized transcript is by two nucleotides shorter and is unable to form a stable hairpin at the 5-end of mRNA, which provides for a normal translation initiation. A uniqueness of this locus is in that biosynthesis of the protein PyrC is regulated via negative feedback by selection of the transcription start site, which influences the possibility of translation initiation of the transcribed mRNA. In the case of excess pyrimidines, the predominantly synthesized transcripts form a hairpin at the ribosome binding site, which blocks the translation initiation. In the case of pyrimidine deficiency in the cell, truncated transcripts are synthesized, which can be translated, thereby elevating the concentration of dihydroorotase in the cell. A detailed biochemical scheme for genetic regulation of pyrC gene expression deducible from the information briefed above is exclusively intricate. The mathematical model describes the regulation of gene pyrC. To describe the model we have used the generalized Hill function. In the promoter region of the operon pyrC binds purine repressor (PurR). When binding protein PurR is not inhibiting the expression of the operon pyrC, but the addition of adenine in the medium enhances the effect of inhibiting the transcription factor PurR 2 times. Chai et al.(2007) showed that gene expression is controlled negatively pyrC transcription factor Fur. In his presence, gene expression is reduced by 17%. ","Mathematical model links":" ID: Likhoshvai et al., 2010 Metabolic Engineering in Silico. ; Value:http://www.springerlink.com/content/51438683725255u1/ ;","Parameter set information":"Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*PyrC = 0, where PyrC - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter pyrCp. ks - protein synthesis generalized constant from the promoter pyrCp. kd = 0.002 [1/sec],PyrC = 0.006371 [mM]. Parameters kdisPurRhyp and kdisPurRgua are taken from article [Choi, Zalkin, 1994]. Parameters kGTP, hGTP, kCTP,hCTP and w were evaluated basing on [Wilson et al., 1992, Likhoshvai et al., 2010] experimental data. Parameter kFur was evaluated basing on [Chai et al., 2007] experimental data. Parameters k1PurR and k2PurR were evaluated basing on [Wilson et al., 1990] experimental data.Parameter k1PurR was evaluated basing on [Devroede et al., 2006] experimental data.","Parameter set links":" ID: Chai et al., 2007 Effect of fur on pyrC gene expression. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/18176545 ; ID: Devroede N., 2006 Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16621816 ; ID: Likhoshvai et al., 2010 Metabolic Engineering in Silico. ; Value:http://www.springerlink.com/content/51438683725255u1/ ; ID: Wilson HR, Turnbough CL Jr., 1990 Role of the purine repressor in the regulation of pyrimidine gene expression in Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1971621 ; ID: Wilson et al., 1992 Translational control of pyrC expression mediated by nucleotide-sensitive selection of transcriptional start sites in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1345912 ;","Structural model information":"   Translation of pyrC is regulated by transcription start site selection. When CTP is abundant, a site distal to the start codon is chosen, allowing formation of a hairpin that blocks ribosome binding. Otherwise, a proximal site is chosen that prevents hairpin formation, allowing translation.\nIn the promoter region of the operon pyrC binds purine repressor (PurR) and transcription factor Fur. The concentration of PurR (dimer) = 0.00097 mM [calculation from the work of Lu, 2007]; The concentration of Fur (dimer) = 0.0012 mM [calculation from the work of Lu, 2007]. ","Structural model links":" ID: Chai et al., 2007 Effect of fur on pyrC gene expression. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/18176545 ; ID: Lu et al., 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17187058 ; ID: Wilson et al., 1992 Translational control of pyrC expression mediated by nucleotide-sensitive selection of transcriptional start sites in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/1345912 ;"},"parameters":[{"units":"","information":"","name":"hCTP","value":"2.5"},{"units":"","information":"","name":"hGTP","value":"1.7"},{"units":"mM","information":"","name":"k1PurR","value":"0.001"},{"units":"mM","information":"","name":"k2PurR","value":"0.001"},{"units":"mM","information":"","name":"k3PurR","value":"0.0008"},{"units":"mM","information":"","name":"kCTP","value":"0.025"},{"units":"mM","information":"","name":"kFur","value":"0.0059"},{"units":"mM","information":"","name":"kGTP","value":"0.06"},{"units":"mM","information":"","name":"kdisPurRgua","value":"0.0015"},{"units":"mM","information":"","name":"kdisPurRhyp","value":"0.0093"},{"units":"mM/sec","information":"","name":"ks","value":"0.00096"},{"units":"","information":"","name":"w","value":"0.002"}]},{"scheme":"SAICAR -> AICAR + fumarate","substrates":{"s1":{"theSubstance":{"name":"SAICAR","type":"substance","synonyms":["1-(5'-Phosphoribosyl)-4-(N-succinocarboxamide)-5-aminoimidazole","1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole","5'-Phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole","(S)-2-[5-Amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido]succinate","SAICAR"],"links":[],"id":"SS0000101"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"AICAR","type":"substance","synonyms":["1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide","5-Amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide","5-Aminoimidazole-4-carboxamide ribotide","5-Phosphoribosyl-4-carbamoyl-5-aminoimidazole","5'-Phospho-ribosyl-5-amino-4-imidazole carboxamide","5'-Phosphoribosyl-5-amino-4-imidazolecarboxamide","AICAR"],"links":[],"id":"SS0000102"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"fumarate","type":"substance","synonyms":["fum","fumarate","fumaric acid"],"links":[],"id":"SS0000180"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PurB","type":"protein","synonyms":["PurB"],"links":[],"id":"SS0000381"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"r1*kcat*s1/(KmSAICAR+s1)","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Sivendran et al., 2008 Effect of a new non-cleavable substrate analog on wild-type and serine mutants in the signature sequence of adenylosuccinate lyase of Bacillus subtilis and Homo sapiens. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/18469177 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. Parameter was evaluated basing on [Sivendran et al., 2008] experimental data. Michaelis constant (kmsaicar) with respect to saicar of B. subtilis.","Parameter set links":" ID: Sivendran et al., 2008 Effect of a new non-cleavable substrate analog on wild-type and serine mutants in the signature sequence of adenylosuccinate lyase of Bacillus subtilis and Homo sapiens. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/18469177 ;","Structural model information":"  \nAdenylosuccinate lyase (ASL), the product of the gene purB in E. coli, catalyzes two reactions in de novo purine nucleotide biosynthesis. In addition to the removal of fumarate from 5-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole, the enzyme also converts adenylosuccinate to AMP. Subunit composition of enzyme of Adenylosuccinate lyase = [PurB].  ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=AICARSYN-RXN ;"},"mmid":"MM0000214","psid":"PS0000206","gnid":"GN0000206","reversible":false,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Sivendran et al., 2008 Effect of a new non-cleavable substrate analog on wild-type and serine mutants in the signature sequence of adenylosuccinate lyase of Bacillus subtilis and Homo sapiens. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/18469177 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. Parameter was evaluated basing on [Sivendran et al., 2008] experimental data. Michaelis constant (kmsaicar) with respect to saicar of B. subtilis.","Parameter set links":" ID: Sivendran et al., 2008 Effect of a new non-cleavable substrate analog on wild-type and serine mutants in the signature sequence of adenylosuccinate lyase of Bacillus subtilis and Homo sapiens. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/18469177 ;","Structural model information":"  \nAdenylosuccinate lyase (ASL), the product of the gene purB in E. coli, catalyzes two reactions in de novo purine nucleotide biosynthesis. In addition to the removal of fumarate from 5-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole, the enzyme also converts adenylosuccinate to AMP. Subunit composition of enzyme of Adenylosuccinate lyase = [PurB].  ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=AICARSYN-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmSAICAR","value":"0.0029"},{"units":"1/sec","information":"","name":"kcat","value":"1"}]},{"scheme":"AICAR + 10-formyl-tetrahydrofolate <=> FAICAR + tetrahydrofolate","substrates":{"s1":{"theSubstance":{"name":"AICAR","type":"substance","synonyms":["1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide","5-Amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide","5-Aminoimidazole-4-carboxamide ribotide","5-Phosphoribosyl-4-carbamoyl-5-aminoimidazole","5'-Phospho-ribosyl-5-amino-4-imidazole carboxamide","5'-Phosphoribosyl-5-amino-4-imidazolecarboxamide","AICAR"],"links":[],"id":"SS0000102"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"10-FTHF","type":"substance","synonyms":["10-formyl-tetrahydrofolate","10-formyl-THF","10-FTHF"],"links":[],"id":"SS0000172"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"FAICAR","type":"substance","synonyms":["1-(5'-Phosphoribosyl)-5-formamido-4-imidazolecarboxamide","5-Formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide","5-Formamido-1-(5-phosphoribosyl)imidazole-4-carboxamide","5'-Phosphoribosyl-5-formamido-4-imidazolecarboxamide","FAICAR"],"links":[],"id":"SS0000103"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"THF","type":"substance","synonyms":["5,6,7,8-tetrahydrofolic acid","H4PteGlu","tetrahydrofolate","tetrahydrofolic acid","THF","vitamin B9"],"links":[],"id":"SS0000173"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PurH","type":"protein","synonyms":["PurH"],"links":[],"id":"SS0000382"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"r1*kcat*s1/(KmAICAR+s1)","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Shim et al., 2001 Evaluation of the catalytic mechanism of AICAR transformylase by pH-dependent kinetics, mutagenesis, and quantum chemical calculations. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11457277 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. Michaelis constant (kmaicar) with respect to aicar of Gallus sp.[Shim et al., 2001]","Parameter set links":" ID: Shim et al., 2001 Evaluation of the catalytic mechanism of AICAR transformylase by pH-dependent kinetics, mutagenesis, and quantum chemical calculations. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11457277 ;","Structural model information":"The ninth and tenth reactions of the de novo purine biosynthetic pathway for IMP biosynthesis are sequentially catalysed by AICAR transformylase and IMP cyclohydrolase. Recent studies have concluded that AICAR transformylase and IMP cyclohydrolase form a bifunctional enzyme with both activities residing on a single polypeptide. The two activities reside in two distinct domains of a single polypeptide which requires dimerization for maximum activity of both reactions [Flannigan et al., 1990]. EC 2.1.2.3 (AICAR transformylase), EC 3.5.4.10 (IMP cyclohydrolase).Subunit composition of enzyme of AICAR transformylase / IMP cyclohydrolase = [PurH].","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=AICARTRANSFORM-RXN ; ID: Flannigan et al., 1990 Purine biosynthesis in Escherichia coli K12: structure and DNA sequence studies of the purHD locus ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2192230 ;"},"mmid":"MM0000215","psid":"PS0000207","gnid":"GN0000207","reversible":true,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Shim et al., 2001 Evaluation of the catalytic mechanism of AICAR transformylase by pH-dependent kinetics, mutagenesis, and quantum chemical calculations. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11457277 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. Michaelis constant (kmaicar) with respect to aicar of Gallus sp.[Shim et al., 2001]","Parameter set links":" ID: Shim et al., 2001 Evaluation of the catalytic mechanism of AICAR transformylase by pH-dependent kinetics, mutagenesis, and quantum chemical calculations. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11457277 ;","Structural model information":"The ninth and tenth reactions of the de novo purine biosynthetic pathway for IMP biosynthesis are sequentially catalysed by AICAR transformylase and IMP cyclohydrolase. Recent studies have concluded that AICAR transformylase and IMP cyclohydrolase form a bifunctional enzyme with both activities residing on a single polypeptide. The two activities reside in two distinct domains of a single polypeptide which requires dimerization for maximum activity of both reactions [Flannigan et al., 1990]. EC 2.1.2.3 (AICAR transformylase), EC 3.5.4.10 (IMP cyclohydrolase).Subunit composition of enzyme of AICAR transformylase / IMP cyclohydrolase = [PurH].","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=AICARTRANSFORM-RXN ; ID: Flannigan et al., 1990 Purine biosynthesis in Escherichia coli K12: structure and DNA sequence studies of the purHD locus ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2192230 ;"},"parameters":[{"units":"mM","information":"","name":"KmAICAR","value":"0.0019"},{"units":"1/sec","information":"","name":"kcat","value":"1"}]},{"scheme":"GDP + Thioredoxin -> dGDP + an oxidized thioredoxin + H2O","substrates":{"s1":{"theSubstance":{"name":"GDP","type":"substance","synonyms":["GDP","Guanosine 5'-diphosphate","Guanosine diphosphate"],"links":[],"id":"SS0000087"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"Thioredoxin","type":"protein","synonyms":["Reduced thioredoxin","Thioredoxin"],"links":[],"id":"SS0000046"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"dGDP","type":"substance","synonyms":["2'-Deoxyguanosine 5'-diphosphate","dGDP"],"links":[],"id":"SS0000120"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"TrxA","type":"protein","synonyms":["an oxidized thioredoxin","DasC","FipA","thioredoxin disulfide","TrxA","TsnC"],"links":[],"id":"SS0000369"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"NrdA","type":"protein","synonyms":["NrdA","ribonucleoside diphosphate reductase 1, a subunit dimer"],"links":[],"id":"SS0000370"},"theState":null,"compartment":"","theInfluence":"activator"},"r10":{"theSubstance":{"name":"CTP","type":"substance","synonyms":["CTP","Cytidine 5'-triphosphate","Cytidine triphosphate"],"links":[],"id":"SS0000027"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r11":{"theSubstance":{"name":"dATP","type":"substance","synonyms":["2'-Deoxyadenosine 5'-triphosphate","dATP","Deoxyadenosine 5'-triphosphate","Deoxyadenosine triphosphate"],"links":[],"id":"SS0000079"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r12":{"theSubstance":{"name":"NrdB","type":"protein","synonyms":["NrdB","ribonucleoside diphosphate reductase 1, ? subunit dimer"],"links":[],"id":"SS0000371"},"theState":null,"compartment":"","theInfluence":"activator"},"r2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":"","theInfluence":"complex regulator"},"r3":{"theSubstance":{"name":"GTP","type":"substance","synonyms":["GTP","Guanosine 5'-triphosphate"],"links":[],"id":"SS0000140"},"theState":null,"compartment":"","theInfluence":"complex regulator"},"r4":{"theSubstance":{"name":"dGTP","type":"substance","synonyms":["2'-Deoxyguanosine 5'-triphosphate","Deoxyguanosine 5'-triphosphate","Deoxyguanosine triphosphate","dGTP"],"links":[],"id":"SS0000121"},"theState":null,"compartment":"","theInfluence":"activator"},"r5":{"theSubstance":{"name":"UTP","type":"substance","synonyms":["Uridine 5'-triphosphate","Uridine triphosphate","UTP"],"links":[],"id":"SS0000026"},"theState":null,"compartment":"","theInfluence":"complex regulator"},"r6":{"theSubstance":{"name":"dCTP","type":"substance","synonyms":["2'-Deoxycytidine 5'-triphosphate","dCTP","Deoxycytidine 5'-triphosphate","Deoxycytidine triphosphate"],"links":[],"id":"SS0000043"},"theState":null,"compartment":"","theInfluence":"complex regulator"},"r7":{"theSubstance":{"name":"dTMP","type":"substance","synonyms":["Deoxythymidine 5'-phosphate","Deoxythymidylic acid","dTMP","Thymidine 5'-phosphate","Thymidine monophosphate","Thymidylate","Thymidylic acid"],"links":[],"id":"SS0000054"},"theState":null,"compartment":"","theInfluence":"activator"},"r8":{"theSubstance":{"name":"dTDP","type":"substance","synonyms":["Deoxythymidine 5'-diphosphate","dTDP"],"links":[],"id":"SS0000053"},"theState":null,"compartment":"","theInfluence":"activator"},"r9":{"theSubstance":{"name":"TTP","type":"substance","synonyms":["Deoxythymidine 5'-triphosphate","Deoxythymidine triphosphate","dTTP","TTP"],"links":[],"id":"SS0000052"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"(( (((r1^2)*(r12^2))/((kdis^3)+2*r1*(r12^2)+2*r12*(r1^2)))*kcat*s1)/(KmGDP+s1))*((1+(k1dATP*(r11/k2dATP)^hdATP)+(k1ATP*(r2/k2ATP))+(k1dGTP*(r4/k2dGTP))+(k1TTP*(r9/k2TTP))+(k1dTDP*(r8/k2dTDP))+(k1dTMP*(r7/k2dTMP)))/(1+((r11/k2dATP)^hdATP)+((r2/k2ATP)^hATP)+(r4/k2dGTP)+(r9/k2TTP)+(r8/k2dTDP)+(r7/k2dTMP)+w1*(r4/k2dGTP)*(r9/k2TTP)+w2*((r11/k2dATP)^hdATP)*((r2/k2ATP)^hATP)+w3*(r9/k2TTP)*((r11/k2dATP)^hdATP)))*((1+(k1CTP*(r10/k2CTP)^hCTP))/(1+((r10/k2CTP)^hCTP)))*((1+k1dCTP*(r6/k2dCTP))/(1+(r6/k2dCTP)^hdCTP))*((1+k1UTP*(r5/k2UTP))/(1+(r5/k2UTP)^hUTP))*((1+k1GTP*(r3/k2GTP))/(1+(r3/k2GTP)^hGTP))","theSubMathModel":null,"theInformation":{"Mathematical model information":"As ATP, dATP, dGTP, TTP, TDP and TMP are known to be noncompetitive inhibitors [Larsson et al., 1966] of this reaction the equasion can be written as a sum of inhibitors influenses. But we have the mutual influence of regulators (dATP, ATP), (dGTP,TTP) and (dATP, ATP). And we can be written as a product of inhibitors influenses.CTP,UTP,dCTP and GTP were not competitive regulators [Larsson et al., 1966]. Regulation of the nucleotides dCTP, UTP, GTP and ATP occurs by a dual mechanism activation /inhibition, depending on the concentration.","Mathematical model links":" ID: Larsson A., Reichard P., 1966 Enzymatic synthesis of deoxyribonucleotides. X. Reduction of purine ribonucleotides; allosteric behavior and substrate specificity of the enzyme system from Escherichia coli B. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5330120 ;","Parameter set information":"Parametrs evaluated basing on [Larsson et al., 1966] experimental data. kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude.","Parameter set links":" ID: Larsson A., Reichard P., 1966 Enzymatic synthesis of deoxyribonucleotides. X. Reduction of purine ribonucleotides; allosteric behavior and substrate specificity of the enzyme system from Escherichia coli B. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5330120 ;","Structural model information":" Ribonucleoside-diphosphate reductase (RDPR) catalyzes the conversion of nucleotides to deoxynucleotides, an essential step in DNA synthesis. All four ribonucleoside diphosphates are reduced by RDPR. Glutaredoxin may substitute for thioredoxin in the reaction. The enzyme consists of two non-identical subunits, proteins R1 and R2 (also called a and ? or B1 and B2). Separately the subunits are catalytically inactive, but in the presence of Mg2+ they combine to form the enzymatically active complex. The substrate specificity is regulated by allosteric effectors (dATP, ATP, dTTP, dGTP) which bind to the R1 protein. The R1 protein also contains the redox-active thiols in each of its two active sites and five cysteine residues required for activity. The R2 subunit contains a unique cofactor, a binuclear iron center and organic free radical which arises from the oxidation of a single tyrosine residue of the subunit. The tyrosyl radical is essential for activity. A multienzyme complex is needed to activate the tyrosyl radical. The activating system is composed of three proteins, FMN reductase, superoxide dismutase and protein fraction named fraction b whose function is poorly defined. Ribonucleotide reductase catalyzes the rate-limiting step in DNA biosynthesis. Its central role in DNA replication and repair makes its regulation important to ensure appropriate pools of deoxyribonucleotides for these processes. Three major classes I, II and III have been designated that share similar catalytic mechanisms. Enterobacteria, including Escherichia coli and Salmonella enterica serovar Typhimurium contain class Ia (encoded by nrdA and nrdB ), class Ib (encoded by nrdE and nrdF ) and class III (encoded by nrdD ) enzymes. Class Ia and Ib enzymes are active under aerobic conditions, while class III enzymes are inactivated by oxygen and function under strictly anaerobic conditions. Although there are differences in structure and cofactor use, their catalytic mechanisms involve a transient cysteinyl radical at the active site that inititates ribonucleotide reduction.  ","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=GDPREDUCT-RXN ;"},"mmid":"MM0000199","psid":"PS0000193","gnid":"GN0000192","reversible":false,"information":{"Mathematical model information":"As ATP, dATP, dGTP, TTP, TDP and TMP are known to be noncompetitive inhibitors [Larsson et al., 1966] of this reaction the equasion can be written as a sum of inhibitors influenses. But we have the mutual influence of regulators (dATP, ATP), (dGTP,TTP) and (dATP, ATP). And we can be written as a product of inhibitors influenses.CTP,UTP,dCTP and GTP were not competitive regulators [Larsson et al., 1966]. Regulation of the nucleotides dCTP, UTP, GTP and ATP occurs by a dual mechanism activation /inhibition, depending on the concentration.","Mathematical model links":" ID: Larsson A., Reichard P., 1966 Enzymatic synthesis of deoxyribonucleotides. X. Reduction of purine ribonucleotides; allosteric behavior and substrate specificity of the enzyme system from Escherichia coli B. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5330120 ;","Parameter set information":"Parametrs evaluated basing on [Larsson et al., 1966] experimental data. kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude.","Parameter set links":" ID: Larsson A., Reichard P., 1966 Enzymatic synthesis of deoxyribonucleotides. X. Reduction of purine ribonucleotides; allosteric behavior and substrate specificity of the enzyme system from Escherichia coli B. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5330120 ;","Structural model information":" Ribonucleoside-diphosphate reductase (RDPR) catalyzes the conversion of nucleotides to deoxynucleotides, an essential step in DNA synthesis. All four ribonucleoside diphosphates are reduced by RDPR. Glutaredoxin may substitute for thioredoxin in the reaction. The enzyme consists of two non-identical subunits, proteins R1 and R2 (also called a and ? or B1 and B2). Separately the subunits are catalytically inactive, but in the presence of Mg2+ they combine to form the enzymatically active complex. The substrate specificity is regulated by allosteric effectors (dATP, ATP, dTTP, dGTP) which bind to the R1 protein. The R1 protein also contains the redox-active thiols in each of its two active sites and five cysteine residues required for activity. The R2 subunit contains a unique cofactor, a binuclear iron center and organic free radical which arises from the oxidation of a single tyrosine residue of the subunit. The tyrosyl radical is essential for activity. A multienzyme complex is needed to activate the tyrosyl radical. The activating system is composed of three proteins, FMN reductase, superoxide dismutase and protein fraction named fraction b whose function is poorly defined. Ribonucleotide reductase catalyzes the rate-limiting step in DNA biosynthesis. Its central role in DNA replication and repair makes its regulation important to ensure appropriate pools of deoxyribonucleotides for these processes. Three major classes I, II and III have been designated that share similar catalytic mechanisms. Enterobacteria, including Escherichia coli and Salmonella enterica serovar Typhimurium contain class Ia (encoded by nrdA and nrdB ), class Ib (encoded by nrdE and nrdF ) and class III (encoded by nrdD ) enzymes. Class Ia and Ib enzymes are active under aerobic conditions, while class III enzymes are inactivated by oxygen and function under strictly anaerobic conditions. Although there are differences in structure and cofactor use, their catalytic mechanisms involve a transient cysteinyl radical at the active site that inititates ribonucleotide reduction.  ","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=GDPREDUCT-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmGDP","value":"0.8"},{"units":"","information":"","name":"hATP","value":"1.9"},{"units":"","information":"","name":"hCTP","value":"2.8"},{"units":"","information":"","name":"hGTP","value":"1.56"},{"units":"","information":"","name":"hUTP","value":"2.6"},{"units":"","information":"","name":"hdATP","value":"1.2"},{"units":"","information":"","name":"hdCTP","value":"1.58"},{"units":"","information":"","name":"k1ATP","value":"2.45"},{"units":"","information":"","name":"k1CTP","value":"0.45"},{"units":"","information":"","name":"k1GTP","value":"2"},{"units":"","information":"","name":"k1TTP","value":"10"},{"units":"","information":"","name":"k1UTP","value":"13"},{"units":"","information":"","name":"k1dATP","value":"0.1"},{"units":"","information":"","name":"k1dCTP","value":"17"},{"units":"","information":"","name":"k1dGTP","value":"11"},{"units":"","information":"","name":"k1dTDP","value":"10"},{"units":"","information":"","name":"k1dTMP","value":"5.5"},{"units":"mM","information":"","name":"k2ATP","value":"0.7"},{"units":"mM","information":"","name":"k2CTP","value":"1.5"},{"units":"mM","information":"","name":"k2GTP","value":"0.5"},{"units":"mM","information":"","name":"k2TTP","value":"0.001"},{"units":"mM","information":"","name":"k2UTP","value":"1.4"},{"units":"mM","information":"","name":"k2dATP","value":"0.0016"},{"units":"mM","information":"","name":"k2dCTP","value":"0.05"},{"units":"mM","information":"","name":"k2dGTP","value":"0.002"},{"units":"mM","information":"","name":"k2dTDP","value":"0.04"},{"units":"mM","information":"","name":"k2dTMP","value":"0.06"},{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kdis","value":"0.001"},{"units":"","information":"","name":"w1","value":"0.007"},{"units":"","information":"","name":"w2","value":"0.4"},{"units":"","information":"","name":"w3","value":"0.7"}]},{"scheme":"ADP + Thioredoxin <=> dADP + an oxidized thioredoxin + H2O","substrates":{"s1":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"Thioredoxin","type":"protein","synonyms":["Reduced thioredoxin","Thioredoxin"],"links":[],"id":"SS0000046"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"dADP","type":"substance","synonyms":["2'-Deoxyadenosine 5'-diphosphate","dADP"],"links":[],"id":"SS0000078"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"TrxA","type":"protein","synonyms":["an oxidized thioredoxin","DasC","FipA","thioredoxin disulfide","TrxA","TsnC"],"links":[],"id":"SS0000369"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"NrdA","type":"protein","synonyms":["NrdA","ribonucleoside diphosphate reductase 1, a subunit dimer"],"links":[],"id":"SS0000370"},"theState":null,"compartment":"","theInfluence":"activator"},"r2":{"theSubstance":{"name":"NrdB","type":"protein","synonyms":["NrdB","ribonucleoside diphosphate reductase 1, ? subunit dimer"],"links":[],"id":"SS0000371"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"TTP","type":"substance","synonyms":["Deoxythymidine 5'-triphosphate","Deoxythymidine triphosphate","dTTP","TTP"],"links":[],"id":"SS0000052"},"theState":null,"compartment":"","theInfluence":"activator"},"r4":{"theSubstance":{"name":"dGTP","type":"substance","synonyms":["2'-Deoxyguanosine 5'-triphosphate","Deoxyguanosine 5'-triphosphate","Deoxyguanosine triphosphate","dGTP"],"links":[],"id":"SS0000121"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"(((((r1^2)*(r2^2))/((kdis^3)+2*r1*(r2^2)+2*r2*(r1^2)))*kcat*s1)/(KmADP+s1))*((1+(k1dGTP*(r4/k2dGTP))+(k1TTP*(r3/k2TTP)))/(1+(r4/k2dGTP)+(r3/k2TTP)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics. As dCTP, dGTP and TTP are known to be noncompetetive inhibitors [Larsson et al.,1966] of this reaction the equasion can be written as a sum of inhibitors influenses.","Mathematical model links":" ID: Larsson A., Reichard P., 1966 Enzymatic synthesis of deoxyribonucleotides. X. Reduction of purine ribonucleotides; allosteric behavior and substrate specificity of the enzyme system from Escherichia coli B. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5330120 ;","Parameter set information":"Parametrs were evaluated basing on [Larsson et al., 1966] experimental data. kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude.","Parameter set links":" ID: Larsson A., Reichard P., 1966 Enzymatic synthesis of deoxyribonucleotides. X. Reduction of purine ribonucleotides; allosteric behavior and substrate specificity of the enzyme system from Escherichia coli B. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5330120 ;","Structural model information":" Ribonucleoside-diphosphate reductase (RDPR) catalyzes the conversion of nucleotides to deoxynucleotides, an essential step in DNA synthesis. All four ribonucleoside diphosphates are reduced by RDPR. Glutaredoxin may substitute for thioredoxin in the reaction. The enzyme consists of two non-identical subunits, proteins R1 and R2 (also called a and ? or B1 and B2). Separately the subunits are catalytically inactive, but in the presence of Mg2+ they combine to form the enzymatically active complex. The substrate specificity is regulated by allosteric effectors (dATP, ATP, dTTP, dGTP) which bind to the R1 protein. The R1 protein also contains the redox-active thiols in each of its two active sites and five cysteine residues required for activity. The R2 subunit contains a unique cofactor, a binuclear iron center and organic free radical which arises from the oxidation of a single tyrosine residue of the subunit. The tyrosyl radical is essential for activity. A multienzyme complex is needed to activate the tyrosyl radical. The activating system is composed of three proteins, FMN reductase, superoxide dismutase and protein fraction named fraction b whose function is poorly defined. Ribonucleotide reductase catalyzes the rate-limiting step in DNA biosynthesis. Its central role in DNA replication and repair makes its regulation important to ensure appropriate pools of deoxyribonucleotides for these processes. Three major classes I, II and III have been designated that share similar catalytic mechanisms. Enterobacteria, including Escherichia coli and Salmonella enterica serovar Typhimurium contain class Ia (encoded by nrdA and nrdB ), class Ib (encoded by nrdE and nrdF ) and class III (encoded by nrdD ) enzymes. Class Ia and Ib enzymes are active under aerobic conditions, while class III enzymes are inactivated by oxygen and function under strictly anaerobic conditions. Although there are differences in structure and cofactor use, their catalytic mechanisms involve a transient cysteinyl radical at the active site that inititates ribonucleotide reduction.  ","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=ADPREDUCT-RXN ;"},"mmid":"MM0000200","psid":"PS0000194","gnid":"GN0000193","reversible":true,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics. As dCTP, dGTP and TTP are known to be noncompetetive inhibitors [Larsson et al.,1966] of this reaction the equasion can be written as a sum of inhibitors influenses.","Mathematical model links":" ID: Larsson A., Reichard P., 1966 Enzymatic synthesis of deoxyribonucleotides. X. Reduction of purine ribonucleotides; allosteric behavior and substrate specificity of the enzyme system from Escherichia coli B. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5330120 ;","Parameter set information":"Parametrs were evaluated basing on [Larsson et al., 1966] experimental data. kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude.","Parameter set links":" ID: Larsson A., Reichard P., 1966 Enzymatic synthesis of deoxyribonucleotides. X. Reduction of purine ribonucleotides; allosteric behavior and substrate specificity of the enzyme system from Escherichia coli B. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5330120 ;","Structural model information":" Ribonucleoside-diphosphate reductase (RDPR) catalyzes the conversion of nucleotides to deoxynucleotides, an essential step in DNA synthesis. All four ribonucleoside diphosphates are reduced by RDPR. Glutaredoxin may substitute for thioredoxin in the reaction. The enzyme consists of two non-identical subunits, proteins R1 and R2 (also called a and ? or B1 and B2). Separately the subunits are catalytically inactive, but in the presence of Mg2+ they combine to form the enzymatically active complex. The substrate specificity is regulated by allosteric effectors (dATP, ATP, dTTP, dGTP) which bind to the R1 protein. The R1 protein also contains the redox-active thiols in each of its two active sites and five cysteine residues required for activity. The R2 subunit contains a unique cofactor, a binuclear iron center and organic free radical which arises from the oxidation of a single tyrosine residue of the subunit. The tyrosyl radical is essential for activity. A multienzyme complex is needed to activate the tyrosyl radical. The activating system is composed of three proteins, FMN reductase, superoxide dismutase and protein fraction named fraction b whose function is poorly defined. Ribonucleotide reductase catalyzes the rate-limiting step in DNA biosynthesis. Its central role in DNA replication and repair makes its regulation important to ensure appropriate pools of deoxyribonucleotides for these processes. Three major classes I, II and III have been designated that share similar catalytic mechanisms. Enterobacteria, including Escherichia coli and Salmonella enterica serovar Typhimurium contain class Ia (encoded by nrdA and nrdB ), class Ib (encoded by nrdE and nrdF ) and class III (encoded by nrdD ) enzymes. Class Ia and Ib enzymes are active under aerobic conditions, while class III enzymes are inactivated by oxygen and function under strictly anaerobic conditions. Although there are differences in structure and cofactor use, their catalytic mechanisms involve a transient cysteinyl radical at the active site that inititates ribonucleotide reduction.  ","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=ADPREDUCT-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmADP","value":"0.03"},{"units":"","information":"","name":"k1TTP","value":"5"},{"units":"","information":"","name":"k1dGTP","value":"9"},{"units":"mM","information":"","name":"k2TTP","value":"0.001"},{"units":"mM","information":"","name":"k2dGTP","value":"0.001"},{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kdis","value":"0.001"}]},{"scheme":"CDP + Thioredoxin -> dCDP + an oxidized thioredoxin + H2O","substrates":{"s1":{"theSubstance":{"name":"CDP","type":"substance","synonyms":["CDP","Cytidine 5'-diphosphate","Cytidine diphosphate"],"links":[],"id":"SS0000033"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"Thioredoxin","type":"protein","synonyms":["Reduced thioredoxin","Thioredoxin"],"links":[],"id":"SS0000046"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"dCDP","type":"substance","synonyms":["2'-Deoxycytidine 5'-diphosphate","2'-Deoxycytidine diphosphate","dCDP"],"links":[],"id":"SS0000044"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"TrxA","type":"protein","synonyms":["an oxidized thioredoxin","DasC","FipA","thioredoxin disulfide","TrxA","TsnC"],"links":[],"id":"SS0000369"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"NrdA","type":"protein","synonyms":["NrdA","ribonucleoside diphosphate reductase 1, a subunit dimer"],"links":[],"id":"SS0000370"},"theState":null,"compartment":"","theInfluence":"activator"},"r2":{"theSubstance":{"name":"dCTP","type":"substance","synonyms":["2'-Deoxycytidine 5'-triphosphate","dCTP","Deoxycytidine 5'-triphosphate","Deoxycytidine triphosphate"],"links":[],"id":"SS0000043"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"TTP","type":"substance","synonyms":["Deoxythymidine 5'-triphosphate","Deoxythymidine triphosphate","dTTP","TTP"],"links":[],"id":"SS0000052"},"theState":null,"compartment":"","theInfluence":"activator"},"r4":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":"","theInfluence":"activator"},"r5":{"theSubstance":{"name":"dATP","type":"substance","synonyms":["2'-Deoxyadenosine 5'-triphosphate","dATP","Deoxyadenosine 5'-triphosphate","Deoxyadenosine triphosphate"],"links":[],"id":"SS0000079"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r6":{"theSubstance":{"name":"dADP","type":"substance","synonyms":["2'-Deoxyadenosine 5'-diphosphate","dADP"],"links":[],"id":"SS0000078"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r7":{"theSubstance":{"name":"dGTP","type":"substance","synonyms":["2'-Deoxyguanosine 5'-triphosphate","Deoxyguanosine 5'-triphosphate","Deoxyguanosine triphosphate","dGTP"],"links":[],"id":"SS0000121"},"theState":null,"compartment":"","theInfluence":"activator"},"r8":{"theSubstance":{"name":"NrdB","type":"protein","synonyms":["NrdB","ribonucleoside diphosphate reductase 1, ? subunit dimer"],"links":[],"id":"SS0000371"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"((((r1^2)*(r8^2))/((kdis^3)+2*r1*(r8^2)+2*r8*(r1^2)))*kcat*s1/(KmCDP+s1))*((1+k1dCTP*(r2/k2dCTP))/(1+(r2/k2dCTP)))*((1+k1ATP*((r4/k2ATP)^hATP)+k1dATP*(r5/k2dATP)+k1TTP*(r3/k2TTP))/(1+((r4/k2ATP)^hATP)+(r5/k2dATP)+(r3/k2TTP)+w1*(r5/k2dATP)*(r3/k2TTP)+w2*(r4/k2ATP)*(r3/k2TTP)))*((1+k1dADP*(r6/k2dADP))/(1+(r6/k2dADP)))*((1+k1dGTP*(r7/k2dGTP))/(1+(r7/k2dGTP)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Enzyme activity is positively regulated by pyrimidine (TTP, dCTP) and purine nucleotides (ATP, dGTP). dATP and dADP are inhibitors [Larsson et al., 1966]. Reaction follows Michaelis Menten kinetics. dATP and TTP have a mutual influence. ATP and TTP have a mutual influence [Larsson et al., 1966].","Mathematical model links":" ID: Larsson A., Reichard P., 1966 Enzymatic synthesis of deoxyribonucleotides. IX. Allosteric effects in the reduction of pyrimidine ribonucleotides by the ribonucleoside diphosphate reductase system of Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5330119 ;","Parameter set information":"Parameters were evaluated basing on [Larsson et al., 1966] experimental data.kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is an enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude.","Parameter set links":" ID: Larsson A., Reichard P., 1966 Enzymatic synthesis of deoxyribonucleotides. IX. Allosteric effects in the reduction of pyrimidine ribonucleotides by the ribonucleoside diphosphate reductase system of Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5330119 ;","Structural model information":" Ribonucleoside-diphosphate reductase (RDPR) catalyzes the conversion of nucleotides to deoxynucleotides, an essential step in DNA synthesis. All four ribonucleoside diphosphates are reduced by RDPR. Glutaredoxin may substitute for thioredoxin in the reaction. The enzyme consists of two non-identical subunits, proteins R1 and R2 (also called a and ? or B1 and B2). Separately the subunits are catalytically inactive, but in the presence of Mg2+ they combine to form the enzymatically active complex. The substrate specificity is regulated by allosteric effectors (dATP, ATP, dTTP, dGTP) which bind to the R1 protein. The R1 protein also contains the redox-active thiols in each of its two active sites and five cysteine residues required for activity. The R2 subunit contains a unique cofactor, a binuclear iron center and organic free radical which arises from the oxidation of a single tyrosine residue of the subunit. The tyrosyl radical is essential for activity. A multienzyme complex is needed to activate the tyrosyl radical. The activating system is composed of three proteins, FMN reductase, superoxide dismutase and protein fraction named fraction b whose function is poorly defined. Ribonucleotide reductase catalyzes the rate-limiting step in DNA biosynthesis. Its central role in DNA replication and repair makes its regulation important to ensure appropriate pools of deoxyribonucleotides for these processes. Three major classes I, II and III have been designated that share similar catalytic mechanisms. Enterobacteria, including Escherichia coli and Salmonella enterica serovar Typhimurium contain class Ia (encoded by nrdA and nrdB ), class Ib (encoded by nrdE and nrdF ) and class III (encoded by nrdD ) enzymes. Class Ia and Ib enzymes are active under aerobic conditions, while class III enzymes are inactivated by oxygen and function under strictly anaerobic conditions. Although there are differences in structure and cofactor use, their catalytic mechanisms involve a transient cysteinyl radical at the active site that inititates ribonucleotide reduction.  ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=CDPREDUCT-RXN ;"},"mmid":"MM0000202","psid":"PS0000195","gnid":"GN0000194","reversible":false,"information":{"Mathematical model information":"Enzyme activity is positively regulated by pyrimidine (TTP, dCTP) and purine nucleotides (ATP, dGTP). dATP and dADP are inhibitors [Larsson et al., 1966]. Reaction follows Michaelis Menten kinetics. dATP and TTP have a mutual influence. ATP and TTP have a mutual influence [Larsson et al., 1966].","Mathematical model links":" ID: Larsson A., Reichard P., 1966 Enzymatic synthesis of deoxyribonucleotides. IX. Allosteric effects in the reduction of pyrimidine ribonucleotides by the ribonucleoside diphosphate reductase system of Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5330119 ;","Parameter set information":"Parameters were evaluated basing on [Larsson et al., 1966] experimental data.kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is an enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude.","Parameter set links":" ID: Larsson A., Reichard P., 1966 Enzymatic synthesis of deoxyribonucleotides. IX. Allosteric effects in the reduction of pyrimidine ribonucleotides by the ribonucleoside diphosphate reductase system of Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5330119 ;","Structural model information":" Ribonucleoside-diphosphate reductase (RDPR) catalyzes the conversion of nucleotides to deoxynucleotides, an essential step in DNA synthesis. All four ribonucleoside diphosphates are reduced by RDPR. Glutaredoxin may substitute for thioredoxin in the reaction. The enzyme consists of two non-identical subunits, proteins R1 and R2 (also called a and ? or B1 and B2). Separately the subunits are catalytically inactive, but in the presence of Mg2+ they combine to form the enzymatically active complex. The substrate specificity is regulated by allosteric effectors (dATP, ATP, dTTP, dGTP) which bind to the R1 protein. The R1 protein also contains the redox-active thiols in each of its two active sites and five cysteine residues required for activity. The R2 subunit contains a unique cofactor, a binuclear iron center and organic free radical which arises from the oxidation of a single tyrosine residue of the subunit. The tyrosyl radical is essential for activity. A multienzyme complex is needed to activate the tyrosyl radical. The activating system is composed of three proteins, FMN reductase, superoxide dismutase and protein fraction named fraction b whose function is poorly defined. Ribonucleotide reductase catalyzes the rate-limiting step in DNA biosynthesis. Its central role in DNA replication and repair makes its regulation important to ensure appropriate pools of deoxyribonucleotides for these processes. Three major classes I, II and III have been designated that share similar catalytic mechanisms. Enterobacteria, including Escherichia coli and Salmonella enterica serovar Typhimurium contain class Ia (encoded by nrdA and nrdB ), class Ib (encoded by nrdE and nrdF ) and class III (encoded by nrdD ) enzymes. Class Ia and Ib enzymes are active under aerobic conditions, while class III enzymes are inactivated by oxygen and function under strictly anaerobic conditions. Although there are differences in structure and cofactor use, their catalytic mechanisms involve a transient cysteinyl radical at the active site that inititates ribonucleotide reduction.  ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=CDPREDUCT-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmCDP","value":"0.5"},{"units":"","information":"","name":"hATP","value":"1.4"},{"units":"","information":"","name":"k1ATP","value":"2"},{"units":"","information":"","name":"k1TTP","value":"5"},{"units":"","information":"","name":"k1dADP","value":"0.01"},{"units":"","information":"","name":"k1dATP","value":"0.01"},{"units":"","information":"","name":"k1dCTP","value":"2"},{"units":"","information":"","name":"k1dGTP","value":"2"},{"units":"mM","information":"","name":"k2ATP","value":"0.00004"},{"units":"mM","information":"","name":"k2TTP","value":"0.001"},{"units":"mM","information":"","name":"k2dADP","value":"0.3"},{"units":"mM","information":"","name":"k2dATP","value":"0.001"},{"units":"mM","information":"","name":"k2dCTP","value":"0.0001"},{"units":"mM","information":"","name":"k2dGTP","value":"0.0002"},{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kdis","value":"0.001"},{"units":"","information":"","name":"w1","value":"0.35"},{"units":"","information":"","name":"w2","value":"20"}]},{"scheme":"UDP + Thioredoxin -> dUDP + an oxidized thioredoxin + H2O","substrates":{"s1":{"theSubstance":{"name":"UDP","type":"substance","synonyms":["UDP","Uridine 5'-diphosphate"],"links":[],"id":"SS0000025"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"Thioredoxin","type":"protein","synonyms":["Reduced thioredoxin","Thioredoxin"],"links":[],"id":"SS0000046"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"dUDP","type":"substance","synonyms":["2'-Deoxyuridine 5'-diphosphate","dUDP"],"links":[],"id":"SS0000049"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"TrxA","type":"protein","synonyms":["an oxidized thioredoxin","DasC","FipA","thioredoxin disulfide","TrxA","TsnC"],"links":[],"id":"SS0000369"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"NrdA","type":"protein","synonyms":["NrdA","ribonucleoside diphosphate reductase 1, a subunit dimer"],"links":[],"id":"SS0000370"},"theState":null,"compartment":"","theInfluence":"activator"},"r2":{"theSubstance":{"name":"TTP","type":"substance","synonyms":["Deoxythymidine 5'-triphosphate","Deoxythymidine triphosphate","dTTP","TTP"],"links":[],"id":"SS0000052"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":"","theInfluence":"activator"},"r4":{"theSubstance":{"name":"NrdB","type":"protein","synonyms":["NrdB","ribonucleoside diphosphate reductase 1, ? subunit dimer"],"links":[],"id":"SS0000371"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"(((r1^2)*(r4^2)/((kdis^3)+2*r1*(r4^2)+2*r4*(r1^2)))*kcat*s1/(KmUDP+s1))*((k0+k1ATP*((r3/k2ATP)^h1ATP)+k1TTP*(r2/k2TTP))/(1+((r3/k2ATP)^h2ATP)+(r2/k2TTP)+w*((r3/k2ATP)^h2ATP)*((r2/k2TTP)^hTTP)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis Menten kinetics. As ATP and TTP are known to be noncompetetive inhibitors[Larsson et al., 1966] of this reaction the equasion can be written as a sum of inhibitors influenses. But if we have the mutual influence of regulators the UDP reduction is down.Subunit composition of ribonucleoside diphosphate reductase 1 = [NrdA]2,[NrdB]2.","Mathematical model links":" ID: Larsson A., Reichard P., 1966 Enzymatic synthesis of deoxyribonucleotides. IX. Allosteric effects in the reduction of pyrimidine ribonucleotides by the ribonucleoside diphosphate reductase system of Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5330119 ;","Parameter set information":"Parameters were evaluated basing on [Larsson et al., 1966] experimental data.kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is an enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude.","Parameter set links":" ID: Larsson A., Reichard P., 1966 Enzymatic synthesis of deoxyribonucleotides. IX. Allosteric effects in the reduction of pyrimidine ribonucleotides by the ribonucleoside diphosphate reductase system of Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5330119 ;","Structural model information":" Ribonucleoside-diphosphate reductase (RDPR) catalyzes the conversion of nucleotides to deoxynucleotides, an essential step in DNA synthesis. All four ribonucleoside diphosphates are reduced by RDPR. Glutaredoxin may substitute for thioredoxin in the reaction. The enzyme consists of two non-identical subunits, proteins R1 and R2 (also called a and ? or B1 and B2). Separately the subunits are catalytically inactive, but in the presence of Mg2+ they combine to form the enzymatically active complex. The substrate specificity is regulated by allosteric effectors (dATP, ATP, dTTP, dGTP) which bind to the R1 protein. The R1 protein also contains the redox-active thiols in each of its two active sites and five cysteine residues required for activity. The R2 subunit contains a unique cofactor, a binuclear iron center and organic free radical which arises from the oxidation of a single tyrosine residue of the subunit. The tyrosyl radical is essential for activity. A multienzyme complex is needed to activate the tyrosyl radical. The activating system is composed of three proteins, FMN reductase, superoxide dismutase and protein fraction named fraction b whose function is poorly defined. Ribonucleotide reductase catalyzes the rate-limiting step in DNA biosynthesis. Its central role in DNA replication and repair makes its regulation important to ensure appropriate pools of deoxyribonucleotides for these processes. Three major classes I, II and III have been designated that share similar catalytic mechanisms. Enterobacteria, including Escherichia coli and Salmonella enterica serovar Typhimurium contain class Ia (encoded by nrdA and nrdB ), class Ib (encoded by nrdE and nrdF ) and class III (encoded by nrdD ) enzymes. Class Ia and Ib enzymes are active under aerobic conditions, while class III enzymes are inactivated by oxygen and function under strictly anaerobic conditions. Although there are differences in structure and cofactor use, their catalytic mechanisms involve a transient cysteinyl radical at the active site that inititates ribonucleotide reduction.  ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=UDPREDUCT-RXN ;"},"mmid":"MM0000203","psid":"PS0000196","gnid":"GN0000195","reversible":false,"information":{"Mathematical model information":"Reaction follows Michaelis Menten kinetics. As ATP and TTP are known to be noncompetetive inhibitors[Larsson et al., 1966] of this reaction the equasion can be written as a sum of inhibitors influenses. But if we have the mutual influence of regulators the UDP reduction is down.Subunit composition of ribonucleoside diphosphate reductase 1 = [NrdA]2,[NrdB]2.","Mathematical model links":" ID: Larsson A., Reichard P., 1966 Enzymatic synthesis of deoxyribonucleotides. IX. Allosteric effects in the reduction of pyrimidine ribonucleotides by the ribonucleoside diphosphate reductase system of Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5330119 ;","Parameter set information":"Parameters were evaluated basing on [Larsson et al., 1966] experimental data.kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is an enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude.","Parameter set links":" ID: Larsson A., Reichard P., 1966 Enzymatic synthesis of deoxyribonucleotides. IX. Allosteric effects in the reduction of pyrimidine ribonucleotides by the ribonucleoside diphosphate reductase system of Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5330119 ;","Structural model information":" Ribonucleoside-diphosphate reductase (RDPR) catalyzes the conversion of nucleotides to deoxynucleotides, an essential step in DNA synthesis. All four ribonucleoside diphosphates are reduced by RDPR. Glutaredoxin may substitute for thioredoxin in the reaction. The enzyme consists of two non-identical subunits, proteins R1 and R2 (also called a and ? or B1 and B2). Separately the subunits are catalytically inactive, but in the presence of Mg2+ they combine to form the enzymatically active complex. The substrate specificity is regulated by allosteric effectors (dATP, ATP, dTTP, dGTP) which bind to the R1 protein. The R1 protein also contains the redox-active thiols in each of its two active sites and five cysteine residues required for activity. The R2 subunit contains a unique cofactor, a binuclear iron center and organic free radical which arises from the oxidation of a single tyrosine residue of the subunit. The tyrosyl radical is essential for activity. A multienzyme complex is needed to activate the tyrosyl radical. The activating system is composed of three proteins, FMN reductase, superoxide dismutase and protein fraction named fraction b whose function is poorly defined. Ribonucleotide reductase catalyzes the rate-limiting step in DNA biosynthesis. Its central role in DNA replication and repair makes its regulation important to ensure appropriate pools of deoxyribonucleotides for these processes. Three major classes I, II and III have been designated that share similar catalytic mechanisms. Enterobacteria, including Escherichia coli and Salmonella enterica serovar Typhimurium contain class Ia (encoded by nrdA and nrdB ), class Ib (encoded by nrdE and nrdF ) and class III (encoded by nrdD ) enzymes. Class Ia and Ib enzymes are active under aerobic conditions, while class III enzymes are inactivated by oxygen and function under strictly anaerobic conditions. Although there are differences in structure and cofactor use, their catalytic mechanisms involve a transient cysteinyl radical at the active site that inititates ribonucleotide reduction.  ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=UDPREDUCT-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmUDP","value":"0.22"},{"units":"","information":"","name":"h1ATP","value":"1.2"},{"units":"","information":"","name":"h2ATP","value":"1.7"},{"units":"","information":"","name":"hTTP","value":"2.4"},{"units":"","information":"","name":"k0","value":"0.25"},{"units":"","information":"","name":"k1ATP","value":"2.4"},{"units":"","information":"","name":"k1TTP","value":"1.4"},{"units":"mM","information":"","name":"k2ATP","value":"0.2"},{"units":"mM","information":"","name":"k2TTP","value":"0.001"},{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kdis","value":"0.001"},{"units":"","information":"","name":"w","value":"0.0004"}]},{"scheme":"prpp + gln + H2O -> PRA + glu + ppi","substrates":{"s1":{"theSubstance":{"name":"prpp","type":"substance","synonyms":["5-Phospho-alpha-D-ribose 1-diphosphate","5-Phosphoribosyl 1-pyrophosphate","5-Phosphoribosyl diphosphate","prpp"],"links":[],"id":"SS0000021"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"gln","type":"substance","synonyms":["gln","L-2-Aminoglutaramic acid","L-Glutamine"],"links":[],"id":"SS0000028"},"theState":null,"compartment":""},"s3":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"PRA","type":"substance","synonyms":["5-Phospho-beta-D-ribosylamine","5-Phospho-D-ribosylamine","5-Phosphoribosyl-1-amine","5-Phosphoribosylamine","PRA"],"links":[],"id":"SS0000094"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"glu","type":"substance","synonyms":["glu","Glutamate","L-Glutamate","L-Glutamic acid","L-Glutaminic acid"],"links":[],"id":"SS0000061"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"ppi","type":"substance","synonyms":["Diphosphate","PP","ppi","pyrophosphate"],"links":[],"id":"SS0000023"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PurF","type":"protein","synonyms":["PurF"],"links":[],"id":"SS0000372"},"theState":null,"compartment":"","theInfluence":"activator"},"r2":{"theSubstance":{"name":"IMP","type":"substance","synonyms":["5'-IMP","5'-Inosinate","5'-Inosine monophosphate","5'-Inosinic acid","IMP","Inosine 5'-monophosphate","Inosine 5'-phosphate","Inosine monophosphate","Inosinic acid"],"links":[],"id":"SS0000104"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"AMP","type":"substance","synonyms":["5'-Adenosine monophosphate","5'-Adenylic acid","5'-AMP","Adenosine 5'-monophosphate","Adenosine 5'-phosphate","Adenylate","Adenylic acid","AMP"],"links":[],"id":"SS0000073"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"GMP","type":"substance","synonyms":["GMP","Guanosine 5'-monophosphate","Guanosine 5'-phosphate","Guanosine monophosphate","Guanylic acid"],"links":[],"id":"SS0000112"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"XMP","type":"substance","synonyms":["(9-D-Ribosylxanthine)-5'-phosphate","Xanthosine 5'-phosphate","Xanthylic acid","XMP"],"links":[],"id":"SS0000109"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r6":{"theSubstance":{"name":"GTP","type":"substance","synonyms":["GTP","Guanosine 5'-triphosphate"],"links":[],"id":"SS0000140"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"((((r1^4)/((kdis^3)+4*r1^3))*kcat*(s1/Kmprpp)*(s2/Kmgln))/((1+(s1/Kmprpp))*(1+(s2/Kmgln))))*(1/(1+((r3/kamp1)^hamp1)+((r4/kgmp1)^hgmp1)+((r6/kgtp1)^hgtp1)+((r2/kimp1)^himp1)+((r5/kxmp1)^hxmp1)+w1*((r3/kamp1)^hamp1)*((r4/kgmp1)^hgmp1)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis Menten kinetics. The enzyme is sensitive to end product inhibition by AMP and GMP. GMP is a more effective inhibitor of the enzyme than is AMP. GMP and AMP added together in equivalent amounts function synergistically. The inhibition is seen to be much greater than that calculated for additive inhibition by these concentrations of the inhibitors. GMP and AMP together has a synergistic effect on inhibition of both activities [Messenger et al., 1979]. When adding 5 mM IMP or XMP or GTP enzyme activity decreased on 86% or 51% or 79%[Messenger et al., 1979]. Subunit composition of enzyme of amidophosphoribosyl transferase = [PurF]4.","Mathematical model links":" ID: Messenger et al., 1979 Glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli. Purification and properties. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/372191 ;","Parameter set information":" kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is an enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. Parameters were evaluated basing on [Messenger et al., 1979] experimental data. We believe that the mechanism of action of regulatory molecules (IMP, GTP, XMP) on the enzyme activity is similar to GMP, then hGMP1 = hIMP1 = hGTP1 = hXMP1 = 4.6 ","Parameter set links":" ID: Messenger et al., 1979 Glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli. Purification and properties. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/372191 ;","Structural model information":"  Aminophosphoribosyltransferase is one enzyme in a family of 13 glutamine amidotransferases. Like other glutamine amidotransferases this enzyme has distinct sites for glutamine and NH3 utilization. All glutamine amidotransferases thus far studied contain a cysteine residue essential for the glutamine-dependent activity. Alkylation of this cysteine residue leads to selective loss of glutamine-dependent activity while the NH3 dependent activity is generally unaffected, suggesting distinct sites for glutamine binding and NH3 utilization. According to the proposed mechanism, glutamine binds and then forms a covalent intermediate with an active site cysteine. A glutamyl thioester is formed upon transfer of the amide, either directly to the second substrate or to the NH3 site. Hydrolysis of the thioester releases glutamate. Whereas in some glutamine amidotransferases, such as anthranilate synthase, the glutamine and NH3 sites are on distinct subunits, in other enyzmes including amidophosphoribosyltransferase, both functions are on a single subunit. It appears that the NH3 site can utilize exogenous NH3 when the enzyme functions as an aminase or the transferred amide of glutamine when the enzyme functions as an amidotransferase. In contrast to other amidophosphoribosyltransferases, nonheme iron is not present in significant amounts. In addition to its capacity to utilize NH3 in place of glutamine, the enzyme also has glutaminase activity whch is stimulated by the substrate analogs ribose 5-phosphate plus pyrophosphate. The glutamine dependent activity was inactiviated by affinity labeling with structural analogs of glutamine, L-2-amino-4-oxo-5-chloropentanoic acid and 6-diazo-5-oxo-L-norleucine and by iodoacetamide, suggesting that an active site cysteine residue may be required for the glutamine amide transfer function.\n\nThe enzyme is sensitive to end product inhibition by AMP and GMP. GMP is a more effective inhibitor of the enzyme than is AMP. GMP and AMP added together in equivalent amounts function synergistically. The inhibition is seen to be much greater than that calculated for additive inhibition by these concentrations of the inhibitors. GMP and AMP together has a synergistic effect on inhibition of both activities. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=PRPPAMIDOTRANS-RXN ;"},"mmid":"MM0000205","psid":"PS0000197","gnid":"GN0000196","reversible":false,"information":{"Mathematical model information":"Reaction follows Michaelis Menten kinetics. The enzyme is sensitive to end product inhibition by AMP and GMP. GMP is a more effective inhibitor of the enzyme than is AMP. GMP and AMP added together in equivalent amounts function synergistically. The inhibition is seen to be much greater than that calculated for additive inhibition by these concentrations of the inhibitors. GMP and AMP together has a synergistic effect on inhibition of both activities [Messenger et al., 1979]. When adding 5 mM IMP or XMP or GTP enzyme activity decreased on 86% or 51% or 79%[Messenger et al., 1979]. Subunit composition of enzyme of amidophosphoribosyl transferase = [PurF]4.","Mathematical model links":" ID: Messenger et al., 1979 Glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli. Purification and properties. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/372191 ;","Parameter set information":" kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is an enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. Parameters were evaluated basing on [Messenger et al., 1979] experimental data. We believe that the mechanism of action of regulatory molecules (IMP, GTP, XMP) on the enzyme activity is similar to GMP, then hGMP1 = hIMP1 = hGTP1 = hXMP1 = 4.6 ","Parameter set links":" ID: Messenger et al., 1979 Glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli. Purification and properties. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/372191 ;","Structural model information":"  Aminophosphoribosyltransferase is one enzyme in a family of 13 glutamine amidotransferases. Like other glutamine amidotransferases this enzyme has distinct sites for glutamine and NH3 utilization. All glutamine amidotransferases thus far studied contain a cysteine residue essential for the glutamine-dependent activity. Alkylation of this cysteine residue leads to selective loss of glutamine-dependent activity while the NH3 dependent activity is generally unaffected, suggesting distinct sites for glutamine binding and NH3 utilization. According to the proposed mechanism, glutamine binds and then forms a covalent intermediate with an active site cysteine. A glutamyl thioester is formed upon transfer of the amide, either directly to the second substrate or to the NH3 site. Hydrolysis of the thioester releases glutamate. Whereas in some glutamine amidotransferases, such as anthranilate synthase, the glutamine and NH3 sites are on distinct subunits, in other enyzmes including amidophosphoribosyltransferase, both functions are on a single subunit. It appears that the NH3 site can utilize exogenous NH3 when the enzyme functions as an aminase or the transferred amide of glutamine when the enzyme functions as an amidotransferase. In contrast to other amidophosphoribosyltransferases, nonheme iron is not present in significant amounts. In addition to its capacity to utilize NH3 in place of glutamine, the enzyme also has glutaminase activity whch is stimulated by the substrate analogs ribose 5-phosphate plus pyrophosphate. The glutamine dependent activity was inactiviated by affinity labeling with structural analogs of glutamine, L-2-amino-4-oxo-5-chloropentanoic acid and 6-diazo-5-oxo-L-norleucine and by iodoacetamide, suggesting that an active site cysteine residue may be required for the glutamine amide transfer function.\n\nThe enzyme is sensitive to end product inhibition by AMP and GMP. GMP is a more effective inhibitor of the enzyme than is AMP. GMP and AMP added together in equivalent amounts function synergistically. The inhibition is seen to be much greater than that calculated for additive inhibition by these concentrations of the inhibitors. GMP and AMP together has a synergistic effect on inhibition of both activities. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=PRPPAMIDOTRANS-RXN ;"},"parameters":[{"units":"mM","information":"","name":"Kmgln","value":"1.7"},{"units":"mM","information":"","name":"Kmprpp","value":"0.067"},{"units":"","information":"","name":"hamp1","value":"2"},{"units":"","information":"","name":"hgmp1","value":"4.6"},{"units":"","information":"","name":"hgtp1","value":"4.6"},{"units":"","information":"","name":"himp1","value":"4.6"},{"units":"","information":"","name":"hxmp1","value":"4.6"},{"units":"mM","information":"","name":"kamp1","value":"3.5"},{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kdis","value":"0.001"},{"units":"mM","information":"","name":"kgmp1","value":"1.1"},{"units":"mM","information":"","name":"kgtp1","value":"3.8"},{"units":"mM","information":"","name":"kimp1","value":"3.4"},{"units":"mM","information":"","name":"kxmp1","value":"4.9"},{"units":"","information":"","name":"w1","value":"30"}]},{"scheme":"ATP + PRA + glycine <=> ADP + GAR + Pi + H+","substrates":{"s1":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"PRA","type":"substance","synonyms":["5-Phospho-beta-D-ribosylamine","5-Phospho-D-ribosylamine","5-Phosphoribosyl-1-amine","5-Phosphoribosylamine","PRA"],"links":[],"id":"SS0000094"},"theState":null,"compartment":""},"s3":{"theSubstance":{"name":"glycine","type":"substance","synonyms":["aminoacetic acid","gly","glycine"],"links":[],"id":"SS0000168"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"GAR","type":"substance","synonyms":["5'-Phosphoribosylglycinamide","GAR","Glycinamide ribonucleotide","N1-(5-Phospho-D-ribosyl)glycinamide"],"links":[],"id":"SS0000095"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"Pi","type":"substance","synonyms":["H3PO4","Orthophosphate","Orthophosphoric acid","Phosphate","Phosphoric acid","Pi"],"links":[],"id":"SS0000070"},"theState":null,"compartment":""},"p4":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PurD","type":"protein","synonyms":["PurD"],"links":[],"id":"SS0000373"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"(r1*kcat*(s2/KmPRA)*(s1/KmATP))/((1+(s2/KmPRA))*(1+(s1/KmATP)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Shen et al., 1990 Glycinamide ribonucleotide synthetase from Escherichia coli: cloning, overproduction, sequencing, isolation, and characterization. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2182115 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1(where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. Parameters KmPRA and KmATP were taken from Shen et al. article.","Parameter set links":" ID: Shen et al., 1990 Glycinamide ribonucleotide synthetase from Escherichia coli: cloning, overproduction, sequencing, isolation, and characterization. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2182115 ;","Structural model information":" In enzymology, a phosphoribosylamine-glycine ligase (EC 6.3.4.13) is an enzyme that catalyzes the chemical reaction\nATP + 5-phospho-D-ribosylamine + glycine  &lt;-&gt; ADP + phosphate + N-(5-phospho-D-ribosyl)glycinamide\nThe 3 substrates of this enzyme are ATP, 5-phospho-D-ribosylamine, and glycine, whereas its 3 products are ADP, phosphate and N-(5-phospho-D-ribosyl)glycinamide.\nThis enzyme belongs to the family of ligases, specifically those forming generic carbon-nitrogen bonds. This enzyme participates in purine metabolism.\nBacterial genes that encode this enzyme are often named purD.  ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=GLYRIBONUCSYN-RXN ;"},"mmid":"MM0000206","psid":"PS0000198","gnid":"GN0000197","reversible":true,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Shen et al., 1990 Glycinamide ribonucleotide synthetase from Escherichia coli: cloning, overproduction, sequencing, isolation, and characterization. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2182115 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1(where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. Parameters KmPRA and KmATP were taken from Shen et al. article.","Parameter set links":" ID: Shen et al., 1990 Glycinamide ribonucleotide synthetase from Escherichia coli: cloning, overproduction, sequencing, isolation, and characterization. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2182115 ;","Structural model information":" In enzymology, a phosphoribosylamine-glycine ligase (EC 6.3.4.13) is an enzyme that catalyzes the chemical reaction\nATP + 5-phospho-D-ribosylamine + glycine  &lt;-&gt; ADP + phosphate + N-(5-phospho-D-ribosyl)glycinamide\nThe 3 substrates of this enzyme are ATP, 5-phospho-D-ribosylamine, and glycine, whereas its 3 products are ADP, phosphate and N-(5-phospho-D-ribosyl)glycinamide.\nThis enzyme belongs to the family of ligases, specifically those forming generic carbon-nitrogen bonds. This enzyme participates in purine metabolism.\nBacterial genes that encode this enzyme are often named purD.  ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=GLYRIBONUCSYN-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmATP","value":"0.17"},{"units":"mM","information":"","name":"KmPRA","value":"0.07"},{"units":"1/sec","information":"","name":"kcat","value":"1"}]},{"scheme":"UTP + ATP + gln + H2O -> CTP + ADP + Pi + glu + H+","substrates":{"s1":{"theSubstance":{"name":"UTP","type":"substance","synonyms":["Uridine 5'-triphosphate","Uridine triphosphate","UTP"],"links":[],"id":"SS0000026"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""},"s3":{"theSubstance":{"name":"gln","type":"substance","synonyms":["gln","L-2-Aminoglutaramic acid","L-Glutamine"],"links":[],"id":"SS0000028"},"theState":null,"compartment":""},"s4":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"CTP","type":"substance","synonyms":["CTP","Cytidine 5'-triphosphate","Cytidine triphosphate"],"links":[],"id":"SS0000027"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"Pi","type":"substance","synonyms":["H3PO4","Orthophosphate","Orthophosphoric acid","Phosphate","Phosphoric acid","Pi"],"links":[],"id":"SS0000070"},"theState":null,"compartment":""},"p4":{"theSubstance":{"name":"glu","type":"substance","synonyms":["glu","Glutamate","L-Glutamate","L-Glutamic acid","L-Glutaminic acid"],"links":[],"id":"SS0000061"},"theState":null,"compartment":""},"p5":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PyrG","type":"protein","synonyms":["CTPase","CTP synthase","CTP synthetase","PyrG"],"links":[],"id":"SS0000155"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"GTP","type":"substance","synonyms":["GTP","Guanosine 5'-triphosphate"],"links":[],"id":"SS0000140"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"(r1*kcat*((s1^hutp)/((kms1^hutp)*(1+p1/kctp)+s1^hutp))*((s2^hatp)/((kms2^hatp)+(s2^hutp)*(1+s2/katp)))*(k0GTP+(kGTP1*(r2/kgtp2))+(kGTP3*(r2/kgtp4)^hgtp)))/(1+(r2/kgtp2)+(r2/kgtp4)^hgtp)","theSubMathModel":null,"theInformation":{"Mathematical model information":"The product CTP has been found to inhibit competitively with UTP (Long et al., 1967). GTP actually behaves as a negative allosteric effector of E. coli CTP synthase at high concentrations, inhibiting glutamine-dependent CTP formation. In addition, GTP inhibits NH3-dependent CTP formation in a concentration dependent manner (MacDonell et al., 2004).","Mathematical model links":" ID: Long et al., 1967 Cytidine triphosphate synthetase of Escherichia coli B. I. Purification and kinetics ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4862983 ; ID: MacDonnell et al., 2004 Inhibition of E. coli CTP synthase by the \"positive\" allosteric effector GTP ; Value:http://www.ncbi.nlm.nih.gov/pubmed/15158730 ;","Parameter set information":"Parameters hutp, kms1, hatp, kms2, katp, k0GTP, kGTP1, kGTP3, kgtp2, kgtp4 and hgtp were evaluated on basis of MacDonell et al., 2004 experimental data. Parameter kctp was extracted from Long and Pardee, 1967 data. Moreover, to simulate the enzymatic kinetics you can use steady-state concentrations for ATP=9.6 mM and GTP = 4.9 mM (Bennett et al., 2009). The model was simulated upon steady state concentration of PyrG enzyme, which equals 0.0014 mM (Lu et al., 2007).","Parameter set links":" ID: Bennett et al. 2009 Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol. 2009 Aug;5(8):593-599. doi: 10.1038/nchembio.186. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=19561621 ; ID: Long and Pardee 1967 Cytidine triphosphate synthetase of Escherichia coli B. I. Purification and kinetics ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4862983 ; ID: Lu et al. 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol. 2007 Jan;25(1):117-124. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=17187058 ; ID: MacDonnell et al., 2004 Inhibition of E. coli CTP synthase by the \"positive\" allosteric effector GTP ; Value:http://www.ncbi.nlm.nih.gov/pubmed/15158730 ;","Structural model information":"CTP synthetase catalyzes the glutamine- or ammonia-dependent synthesis of CTP from UTP, the final step in the de novo biosynthesis of CTP. The enzyme is inhibited by its product, CTP, shows positive cooperativity for its substrates, ATP and UTP, and is allosterically activated by GTP (Long and Pardee, 1967; Levitzki and Koshland, 1972). The tetrameric structure provides insight into the observed negative cooperativity for glutamine and the effector GTP (Levitzki and Koshland, 1969) and the observation that high concentrations of GTP inhibit CTP formation, but not glutamine hydrolysis (MacDonnell et al., 2004).","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=CTPSYN-RXN ; ID: Levitzki and Koshland 1969 Negative cooperativity in regulatory enzymes. Proc Natl Acad Sci U S A. 1969 Apr;62(4):1121-1128. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=5256410 ; ID: Levitzki and Koshland 1972 Role of an allosteric effector. Guanosine triphosphate activation in cytosine triphosphate synthetase. Biochemistry. 1972 Jan 18;11(2):241-246. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=4550559 ; ID: Long and Pardee 1967 Cytidine triphosphate synthetase of Escherichia coli B. I. Purification and kinetics. J Biol Chem. 1967 Oct 25;242(20):4715-4721. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=4862983 ; ID: MacDonnell et al. 2004 Inhibition of E. coli CTP synthase by the positive allosteric effector GTP.Biochim Biophys Acta. 2004 Jun 1;1699(1-2):213-220. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=15158730 ;"},"mmid":"MM0000170","psid":"PS0000166","gnid":"GN0000081","reversible":false,"information":{"Mathematical model information":"The product CTP has been found to inhibit competitively with UTP (Long et al., 1967). GTP actually behaves as a negative allosteric effector of E. coli CTP synthase at high concentrations, inhibiting glutamine-dependent CTP formation. In addition, GTP inhibits NH3-dependent CTP formation in a concentration dependent manner (MacDonell et al., 2004).","Mathematical model links":" ID: Long et al., 1967 Cytidine triphosphate synthetase of Escherichia coli B. I. Purification and kinetics ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4862983 ; ID: MacDonnell et al., 2004 Inhibition of E. coli CTP synthase by the \"positive\" allosteric effector GTP ; Value:http://www.ncbi.nlm.nih.gov/pubmed/15158730 ;","Parameter set information":"Parameters hutp, kms1, hatp, kms2, katp, k0GTP, kGTP1, kGTP3, kgtp2, kgtp4 and hgtp were evaluated on basis of MacDonell et al., 2004 experimental data. Parameter kctp was extracted from Long and Pardee, 1967 data. Moreover, to simulate the enzymatic kinetics you can use steady-state concentrations for ATP=9.6 mM and GTP = 4.9 mM (Bennett et al., 2009). The model was simulated upon steady state concentration of PyrG enzyme, which equals 0.0014 mM (Lu et al., 2007).","Parameter set links":" ID: Bennett et al. 2009 Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol. 2009 Aug;5(8):593-599. doi: 10.1038/nchembio.186. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=19561621 ; ID: Long and Pardee 1967 Cytidine triphosphate synthetase of Escherichia coli B. I. Purification and kinetics ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4862983 ; ID: Lu et al. 2007 Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol. 2007 Jan;25(1):117-124. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=17187058 ; ID: MacDonnell et al., 2004 Inhibition of E. coli CTP synthase by the \"positive\" allosteric effector GTP ; Value:http://www.ncbi.nlm.nih.gov/pubmed/15158730 ;","Structural model information":"CTP synthetase catalyzes the glutamine- or ammonia-dependent synthesis of CTP from UTP, the final step in the de novo biosynthesis of CTP. The enzyme is inhibited by its product, CTP, shows positive cooperativity for its substrates, ATP and UTP, and is allosterically activated by GTP (Long and Pardee, 1967; Levitzki and Koshland, 1972). The tetrameric structure provides insight into the observed negative cooperativity for glutamine and the effector GTP (Levitzki and Koshland, 1969) and the observation that high concentrations of GTP inhibit CTP formation, but not glutamine hydrolysis (MacDonnell et al., 2004).","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=CTPSYN-RXN ; ID: Levitzki and Koshland 1969 Negative cooperativity in regulatory enzymes. Proc Natl Acad Sci U S A. 1969 Apr;62(4):1121-1128. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=5256410 ; ID: Levitzki and Koshland 1972 Role of an allosteric effector. Guanosine triphosphate activation in cytosine triphosphate synthetase. Biochemistry. 1972 Jan 18;11(2):241-246. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=4550559 ; ID: Long and Pardee 1967 Cytidine triphosphate synthetase of Escherichia coli B. I. Purification and kinetics. J Biol Chem. 1967 Oct 25;242(20):4715-4721. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=4862983 ; ID: MacDonnell et al. 2004 Inhibition of E. coli CTP synthase by the positive allosteric effector GTP.Biochim Biophys Acta. 2004 Jun 1;1699(1-2):213-220. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/?term=15158730 ;"},"parameters":[{"units":"","information":"","name":"hatp","value":"2.1"},{"units":"","information":"","name":"hgtp","value":"4"},{"units":"","information":"","name":"hutp","value":"1.8"},{"units":"","information":"","name":"k0GTP","value":"0.27"},{"units":"","information":"","name":"kGTP1","value":"10.3"},{"units":"","information":"","name":"kGTP3","value":"0"},{"units":"mM","information":"","name":"katp","value":"7"},{"units":"1/sec","information":"","name":"kcat","value":"5.9"},{"units":"mM","information":"","name":"kctp","value":"0.11"},{"units":"mM","information":"","name":"kgtp2","value":"0.023"},{"units":"mM","information":"","name":"kgtp4","value":"0.19"},{"units":"mM","information":"","name":"kms1","value":"0.2"},{"units":"mM","information":"","name":"kms2","value":"0.6"}]},{"scheme":"CTP + ADP + H+ <=> CDP + ATP","substrates":{"s1":{"theSubstance":{"name":"CTP","type":"substance","synonyms":["CTP","Cytidine 5'-triphosphate","Cytidine triphosphate"],"links":[],"id":"SS0000027"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""},"s3":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"CDP","type":"substance","synonyms":["CDP","Cytidine 5'-diphosphate","Cytidine diphosphate"],"links":[],"id":"SS0000033"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Ndk","type":"protein","synonyms":["Ndk","NDP kinase","nucleoside diphosphate kinase"],"links":[],"id":"SS0000154"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"r1*kcat*s1*s2/((kms1+s1)*(kms2+s2))","theSubMathModel":null,"theInformation":{"Mathematical model information":"ADP is phosphorylated to ATP [Roisin, 1978]. We proposed a simple model without competitive substrates such as CDP,GDP,ADP... as they are rapidly consumed in their reactions.","Mathematical model links":" ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Parameter set information":"Parameters kmadp and kmctp were evaluated basing on [Roisin, 1978] data.","Parameter set links":" ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Structural model information":" Nucleoside diphosphate kinase catalyzes the reaction in which the terminal phosphate of a nucleoside-triphosphate is transferred to a nucleoside-diphosphate. \nThe enzyme exhibits broad substrate specificity. The reaction mechanism is an ordered bi-molecular ping-pong type. The intracellular levels of ATP are considerably \nhigher than other nucleoside triphosphates. In addition, ATP is far more abundant than ADP or AMP, so there is a strong thermodynamic tendency for the potential energy \nof ATP to be used in the synthesis of other high-energy compounds. Therefore nucleoside diphosphate kinase is \nunlikely to be involved in the synthesis of ATP. The purified enzyme is tetrameric and was detected in the periplasmic fraction after cold osmotic shock. \nA periplasmic location for the enzyme appears inconsistent with its function. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=CDPKIN-RXN ; ID: PubMed ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;"},"mmid":"MM0000171","psid":"PS0000167","gnid":"GN0000086","reversible":true,"information":{"Mathematical model information":"ADP is phosphorylated to ATP [Roisin, 1978]. We proposed a simple model without competitive substrates such as CDP,GDP,ADP... as they are rapidly consumed in their reactions.","Mathematical model links":" ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Parameter set information":"Parameters kmadp and kmctp were evaluated basing on [Roisin, 1978] data.","Parameter set links":" ID: Roisin et al., 1978 Nucleosidediphosphate kinase of Escherichia coli, a periplasmic enzyme ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;","Structural model information":" Nucleoside diphosphate kinase catalyzes the reaction in which the terminal phosphate of a nucleoside-triphosphate is transferred to a nucleoside-diphosphate. \nThe enzyme exhibits broad substrate specificity. The reaction mechanism is an ordered bi-molecular ping-pong type. The intracellular levels of ATP are considerably \nhigher than other nucleoside triphosphates. In addition, ATP is far more abundant than ADP or AMP, so there is a strong thermodynamic tendency for the potential energy \nof ATP to be used in the synthesis of other high-energy compounds. Therefore nucleoside diphosphate kinase is \nunlikely to be involved in the synthesis of ATP. The purified enzyme is tetrameric and was detected in the periplasmic fraction after cold osmotic shock. \nA periplasmic location for the enzyme appears inconsistent with its function. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=CDPKIN-RXN ; ID: PubMed ; Value:http://www.ncbi.nlm.nih.gov/pubmed/214126 ;"},"parameters":[{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kms1","value":"1.43"},{"units":"mM","information":"","name":"kms2","value":"0.25"}]},{"scheme":"dCTP + H2O -> NH3 + dUTP","substrates":{"s1":{"theSubstance":{"name":"dCTP","type":"substance","synonyms":["2'-Deoxycytidine 5'-triphosphate","dCTP","Deoxycytidine 5'-triphosphate","Deoxycytidine triphosphate"],"links":[],"id":"SS0000043"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"NH3","type":"substance","synonyms":["Ammonia","NH3"],"links":[],"id":"SS0000060"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"dUTP","type":"substance","synonyms":["2'-Deoxyuridine 5'-triphosphate","dUTP"],"links":[],"id":"SS0000048"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Dcd","type":"protein","synonyms":["Dcd","dCTPase","dCTP deaminase","Dus","EC:3.5.4.13","PaxA"],"links":[],"id":"SS0000162"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"Pi","type":"substance","synonyms":["H3PO4","Orthophosphate","Orthophosphoric acid","Phosphate","Phosphoric acid","Pi"],"links":[],"id":"SS0000070"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"TTP","type":"substance","synonyms":["Deoxythymidine 5'-triphosphate","Deoxythymidine triphosphate","dTTP","TTP"],"links":[],"id":"SS0000052"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"(r1*kcat*(s1^(hr3+(r3/kttp))))/(((kms1*(1+(r3/kttp)))^(hr3+(r3/kttp)))+(s1^(hr3+(r3/kttp))))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis Menten kinetics. TTP is a competitive inhibitor of dCTP relative to the enzyme [Johansson et al., 2007]","Mathematical model links":" ID: Johansson et al., 2007 Regulation of dCTP deaminase from Escherichia coli by nonallosteric dTTP binding to an inactive form of the enzyme ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17651436 ;","Parameter set information":"Parameters hr3, kttp and kms1 were evaluated basing on (Johansson et al., 2007) data.","Parameter set links":" ID: Johansson et al., 2007 Regulation of dCTP deaminase from Escherichia coli by nonallosteric dTTP binding to an inactive form of the enzyme ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17651436 ;","Structural model information":"The reaction product is auto-inhibitor dUTP","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=DCTP-DEAM-RXN ;"},"mmid":"MM0000172","psid":"PS0000168","gnid":"GN0000069","reversible":false,"information":{"Mathematical model information":"Reaction follows Michaelis Menten kinetics. TTP is a competitive inhibitor of dCTP relative to the enzyme [Johansson et al., 2007]","Mathematical model links":" ID: Johansson et al., 2007 Regulation of dCTP deaminase from Escherichia coli by nonallosteric dTTP binding to an inactive form of the enzyme ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17651436 ;","Parameter set information":"Parameters hr3, kttp and kms1 were evaluated basing on (Johansson et al., 2007) data.","Parameter set links":" ID: Johansson et al., 2007 Regulation of dCTP deaminase from Escherichia coli by nonallosteric dTTP binding to an inactive form of the enzyme ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17651436 ;","Structural model information":"The reaction product is auto-inhibitor dUTP","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=DCTP-DEAM-RXN ;"},"parameters":[{"units":"","information":"","name":"hr3","value":"1.5"},{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kms1","value":"0.066"},{"units":"mM","information":"","name":"kttp","value":"0.059"}]},{"scheme":"GAR + formate + ATP -> FGAR + ADP + Pi + H+","substrates":{"s1":{"theSubstance":{"name":"GAR","type":"substance","synonyms":["5'-Phosphoribosylglycinamide","GAR","Glycinamide ribonucleotide","N1-(5-Phospho-D-ribosyl)glycinamide"],"links":[],"id":"SS0000095"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"formate","type":"substance","synonyms":["formate","formic acid"],"links":[],"id":"SS0000170"},"theState":null,"compartment":""},"s3":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"FGAR","type":"substance","synonyms":["5'-Phosphoribosyl-N-formylglycinamide","FGAR","N2-Formyl-N1-(5-phospho-D-ribosyl)glycinamide","N-Formyl-GAR","N-Formylglycinamide ribonucleotide"],"links":[],"id":"SS0000096"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"Pi","type":"substance","synonyms":["H3PO4","Orthophosphate","Orthophosphoric acid","Phosphate","Phosphoric acid","Pi"],"links":[],"id":"SS0000070"},"theState":null,"compartment":""},"p4":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PurT","type":"protein","synonyms":["PurT"],"links":[],"id":"SS0000374"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":" (r1*kcat*(s1/KmGAR)*(s3/KmATP))/((1+(s1/KmGAR))*(1+(s3/KmATP)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Marolewski et al., 1994 Cloning and characterization of a new purine biosynthetic enzyme: a non-folate glycinamide ribonucleotide transformylase from E. coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8117714 ;","Parameter set information":"Parameters were evaluated basing on [Marolewski et al., 1994] experimental data.","Parameter set links":" ID: Marolewski et al., 1994 Cloning and characterization of a new purine biosynthetic enzyme: a non-folate glycinamide ribonucleotide transformylase from E. coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8117714 ;","Structural model information":" E. coli contains two different GAR transformylases, both catalyzing the third step in purine biosynthesis. The transformylase coded for by the purN gene requires formyl folate for the reaction. The second transformylase, coded for by the purT gene, utilizes formate. There is no significant homology between the two transformylases. This reaction is catalyzed second transformylase. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=GARTRANSFORMYL2-RXN ;"},"mmid":"MM0000207","psid":"PS0000199","gnid":"GN0000198","reversible":false,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Marolewski et al., 1994 Cloning and characterization of a new purine biosynthetic enzyme: a non-folate glycinamide ribonucleotide transformylase from E. coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8117714 ;","Parameter set information":"Parameters were evaluated basing on [Marolewski et al., 1994] experimental data.","Parameter set links":" ID: Marolewski et al., 1994 Cloning and characterization of a new purine biosynthetic enzyme: a non-folate glycinamide ribonucleotide transformylase from E. coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8117714 ;","Structural model information":" E. coli contains two different GAR transformylases, both catalyzing the third step in purine biosynthesis. The transformylase coded for by the purN gene requires formyl folate for the reaction. The second transformylase, coded for by the purT gene, utilizes formate. There is no significant homology between the two transformylases. This reaction is catalyzed second transformylase. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=GARTRANSFORMYL2-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmATP","value":"0.045"},{"units":"mM","information":"","name":"KmGAR","value":"0.011"},{"units":"1/sec","information":"","name":"kcat","value":"37.6"}]},{"scheme":"GAR + 10-formyl-tetrahydrofolate <=> FGAR + tetrahydrofolate + H+","substrates":{"s1":{"theSubstance":{"name":"GAR","type":"substance","synonyms":["5'-Phosphoribosylglycinamide","GAR","Glycinamide ribonucleotide","N1-(5-Phospho-D-ribosyl)glycinamide"],"links":[],"id":"SS0000095"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"10-FTHF","type":"substance","synonyms":["10-formyl-tetrahydrofolate","10-formyl-THF","10-FTHF"],"links":[],"id":"SS0000172"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"FGAR","type":"substance","synonyms":["5'-Phosphoribosyl-N-formylglycinamide","FGAR","N2-Formyl-N1-(5-phospho-D-ribosyl)glycinamide","N-Formyl-GAR","N-Formylglycinamide ribonucleotide"],"links":[],"id":"SS0000096"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"THF","type":"substance","synonyms":["5,6,7,8-tetrahydrofolic acid","H4PteGlu","tetrahydrofolate","tetrahydrofolic acid","THF","vitamin B9"],"links":[],"id":"SS0000173"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PurN","type":"protein","synonyms":["PurN"],"links":[],"id":"SS0000375"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"r1*kcat*s1/(KmGAR+s1)","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis Menten kinetics.","Mathematical model links":" ID: Inglese et al., 1990 Active-site mapping and site-specific mutagenesis of glycinamide ribonucleotide transformylase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2204419 ;","Parameter set information":"Parameters kcat, kms1 were taken from [Inglese et al., 1990] article.","Parameter set links":" ID: Inglese et al., 1990 Active-site mapping and site-specific mutagenesis of glycinamide ribonucleotide transformylase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2204419 ;","Structural model information":" E. coli contains two different GAR transformylases, both catalyzing the third step in purine biosynthesis. The transformylase coded for by the purN gene requires formyl folate for the reaction. The second transformylase, coded for by the purT gene, utilizes formate. There is no significant homology between the two transformylases. This reaction is catalyzed first transformylase. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=GART-RXN ;"},"mmid":"MM0000208","psid":"PS0000200","gnid":"GN0000199","reversible":true,"information":{"Mathematical model information":"Reaction follows Michaelis Menten kinetics.","Mathematical model links":" ID: Inglese et al., 1990 Active-site mapping and site-specific mutagenesis of glycinamide ribonucleotide transformylase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2204419 ;","Parameter set information":"Parameters kcat, kms1 were taken from [Inglese et al., 1990] article.","Parameter set links":" ID: Inglese et al., 1990 Active-site mapping and site-specific mutagenesis of glycinamide ribonucleotide transformylase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2204419 ;","Structural model information":" E. coli contains two different GAR transformylases, both catalyzing the third step in purine biosynthesis. The transformylase coded for by the purN gene requires formyl folate for the reaction. The second transformylase, coded for by the purT gene, utilizes formate. There is no significant homology between the two transformylases. This reaction is catalyzed first transformylase. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=GART-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmGAR","value":"0.0122"},{"units":"1/sec","information":"","name":"kcat","value":"13.5"}]},{"scheme":"FGAR + ATP + gln + H2O -> FGAM + glu + ADP + Pi","substrates":{"s1":{"theSubstance":{"name":"FGAR","type":"substance","synonyms":["5'-Phosphoribosyl-N-formylglycinamide","FGAR","N2-Formyl-N1-(5-phospho-D-ribosyl)glycinamide","N-Formyl-GAR","N-Formylglycinamide ribonucleotide"],"links":[],"id":"SS0000096"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""},"s3":{"theSubstance":{"name":"gln","type":"substance","synonyms":["gln","L-2-Aminoglutaramic acid","L-Glutamine"],"links":[],"id":"SS0000028"},"theState":null,"compartment":""},"s4":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"FGAM","type":"substance","synonyms":["1-(5'-Phosphoribosyl)-N-formylglycinamidine","2-(Formamido)-N1-(5-phospho-D-ribosyl)acetamidine","2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine","5'-Phosphoribosylformylglycinamidine","5'-Phosphoribosyl-N-formylglycinamidine","FGAM"],"links":[],"id":"SS0000097"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"glu","type":"substance","synonyms":["glu","Glutamate","L-Glutamate","L-Glutamic acid","L-Glutaminic acid"],"links":[],"id":"SS0000061"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""},"p4":{"theSubstance":{"name":"Pi","type":"substance","synonyms":["H3PO4","Orthophosphate","Orthophosphoric acid","Phosphate","Phosphoric acid","Pi"],"links":[],"id":"SS0000070"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PurL","type":"protein","synonyms":["PurL"],"links":[],"id":"SS0000376"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"(r1*kcat*(s1/KmFGAR)*(s2/KmATP))/((1+(s1/KmFGAR))*(1+(s2/KmATP)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Schendel et al., 1989 Formylglycinamide ribonucleotide synthetase from Escherichia coli: cloning, sequencing, overproduction, isolation, and characterization. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2659070 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration). Parameters were evaluated basing on [Schendel et al., 1989] experimental data. can be calculated from the whole model basing on the flow rate magnitude.","Parameter set links":" ID: Schendel et al., 1989 Formylglycinamide ribonucleotide synthetase from Escherichia coli: cloning, sequencing, overproduction, isolation, and characterization. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2659070 ;","Structural model information":" In enzymology, a phosphoribosylformylglycinamidine synthase (EC 6.3.5.3) is an enzyme that catalyzes the chemical reaction\nATP + N-formyl-N-(5-phospho-D-ribosyl)glycinamide + L-glutamine + H2O &lt;-&gt;  ADP + phosphate + 2-(formamido)-N-(5-phospho-D-ribosyl)acetamidine + L-glutamate. The 4 substrates of this enzyme are ATP, N2-formyl-N-(5-phospho-D-ribosyl)glycinamide, L-glutamine, and H2O, whereas its 4 products are ADP, phosphate, 2-(formamido)-N-(5-phospho-D-ribosyl)acetamidine, and L-glutamate. This enzyme belongs to the family of ligases, specifically those forming carbon-nitrogen bonds carbon-nitrogen ligases with glutamine as amido-N-donor. The systematic name of this enzyme class is N-formyl-N-(5-phospho-D-ribosyl)glycinamide:L-glutamine amido-ligase (ADP-forming). This enzyme participates in purine metabolism.\n ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=FGAMSYN-RXN ;"},"mmid":"MM0000209","psid":"PS0000201","gnid":"GN0000200","reversible":false,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Schendel et al., 1989 Formylglycinamide ribonucleotide synthetase from Escherichia coli: cloning, sequencing, overproduction, isolation, and characterization. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2659070 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration). Parameters were evaluated basing on [Schendel et al., 1989] experimental data. can be calculated from the whole model basing on the flow rate magnitude.","Parameter set links":" ID: Schendel et al., 1989 Formylglycinamide ribonucleotide synthetase from Escherichia coli: cloning, sequencing, overproduction, isolation, and characterization. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2659070 ;","Structural model information":" In enzymology, a phosphoribosylformylglycinamidine synthase (EC 6.3.5.3) is an enzyme that catalyzes the chemical reaction\nATP + N-formyl-N-(5-phospho-D-ribosyl)glycinamide + L-glutamine + H2O &lt;-&gt;  ADP + phosphate + 2-(formamido)-N-(5-phospho-D-ribosyl)acetamidine + L-glutamate. The 4 substrates of this enzyme are ATP, N2-formyl-N-(5-phospho-D-ribosyl)glycinamide, L-glutamine, and H2O, whereas its 4 products are ADP, phosphate, 2-(formamido)-N-(5-phospho-D-ribosyl)acetamidine, and L-glutamate. This enzyme belongs to the family of ligases, specifically those forming carbon-nitrogen bonds carbon-nitrogen ligases with glutamine as amido-N-donor. The systematic name of this enzyme class is N-formyl-N-(5-phospho-D-ribosyl)glycinamide:L-glutamine amido-ligase (ADP-forming). This enzyme participates in purine metabolism.\n ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=FGAMSYN-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmATP","value":"0.051"},{"units":"mM","information":"","name":"KmFGAR","value":"0.0468"},{"units":"1/sec","information":"","name":"kcat","value":"1"}]},{"scheme":"GMP + ATP <=> GDP + ADP + H+","substrates":{"s1":{"theSubstance":{"name":"GMP","type":"substance","synonyms":["GMP","Guanosine 5'-monophosphate","Guanosine 5'-phosphate","Guanosine monophosphate","Guanylic acid"],"links":[],"id":"SS0000112"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"GDP","type":"substance","synonyms":["GDP","Guanosine 5'-diphosphate","Guanosine diphosphate"],"links":[],"id":"SS0000087"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Gmk","type":"protein","synonyms":["deoxyguanylate kinase / guanylate kinase","EC:2.7.4.8","Gmk","GMP kinase","SpoR"],"links":[],"id":"SS0000185"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"dGMP","type":"substance","synonyms":["2'-Deoxyguanosine 5'-monophosphate","2'-Deoxyguanosine 5'-phosphate","Deoxyguanosine monophosphate","Deoxyguanylic acid","dGMP"],"links":[],"id":"SS0000118"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"(kcat*r1*((s1/KmGMP)^hGMP)*s2)/((1+((s1/KmGMP)^hGMP))*(KmATP+s2))","theSubMathModel":null,"theInformation":{"Mathematical model information":"To construct a model used by Hill's function proposed in [Gentry et al., 1993], describing the dependence of reaction rate on substrate concentration GMP.For ATP observed Michaelis-Menten kinetics [Oeschger et al., 1966].\n","Mathematical model links":" ID: Gentry D., 1993 Guanylate kinase of Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8390989 ; ID: Oeschger M.P., Bessman M.J., 1966 Purification and properties of guanylate kinase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5333666 ;","Parameter set information":"Parametrs KmGMP and hGMP were taken from [Gentry et al., 1993] article. Parametr KmATP was taken from [Oeschger et al., 1966] article. kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude.","Parameter set links":" ID: Gentry D., 1993 Guanylate kinase of Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8390989 ; ID: Oeschger M.P., Bessman M.J., 1966 Purification and properties of guanylate kinase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5333666 ;","Structural model information":" Guanylate kinase is highly specific for ribo- and deoxyriboguanylate. The E. coli enzyme is multimeric, and its protomeric state is dictated by ionic conditions. Under high ionic conditions the enzyme is a dimer and under low ionic conditions the enzyme is a tetramer. The effect of the tetramerization is to lower the level of interaction between binding sites and to decrease the total activity. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=GUANYL-KIN-RXN ;"},"mmid":"MM0000178","psid":"PS0000174","gnid":"GN0000126","reversible":true,"information":{"Mathematical model information":"To construct a model used by Hill's function proposed in [Gentry et al., 1993], describing the dependence of reaction rate on substrate concentration GMP.For ATP observed Michaelis-Menten kinetics [Oeschger et al., 1966].\n","Mathematical model links":" ID: Gentry D., 1993 Guanylate kinase of Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8390989 ; ID: Oeschger M.P., Bessman M.J., 1966 Purification and properties of guanylate kinase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5333666 ;","Parameter set information":"Parametrs KmGMP and hGMP were taken from [Gentry et al., 1993] article. Parametr KmATP was taken from [Oeschger et al., 1966] article. kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude.","Parameter set links":" ID: Gentry D., 1993 Guanylate kinase of Escherichia coli K-12. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8390989 ; ID: Oeschger M.P., Bessman M.J., 1966 Purification and properties of guanylate kinase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/5333666 ;","Structural model information":" Guanylate kinase is highly specific for ribo- and deoxyriboguanylate. The E. coli enzyme is multimeric, and its protomeric state is dictated by ionic conditions. Under high ionic conditions the enzyme is a dimer and under low ionic conditions the enzyme is a tetramer. The effect of the tetramerization is to lower the level of interaction between binding sites and to decrease the total activity. ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=GUANYL-KIN-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmATP","value":"0.333"},{"units":"mM","information":"","name":"KmGMP","value":"0.015"},{"units":"","information":"","name":"hGMP","value":"2"},{"units":"1/sec","information":"","name":"kcat","value":"1"}]},{"scheme":"IMP + H2O + NAD+ <=> XMP + NADH + H+","substrates":{"s1":{"theSubstance":{"name":"IMP","type":"substance","synonyms":["5'-IMP","5'-Inosinate","5'-Inosine monophosphate","5'-Inosinic acid","IMP","Inosine 5'-monophosphate","Inosine 5'-phosphate","Inosine monophosphate","Inosinic acid"],"links":[],"id":"SS0000104"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""},"s3":{"theSubstance":{"name":"NAD+","type":"substance","synonyms":["NAD+"],"links":[],"id":"SS0000188"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"XMP","type":"substance","synonyms":["(9-D-Ribosylxanthine)-5'-phosphate","Xanthosine 5'-phosphate","Xanthylic acid","XMP"],"links":[],"id":"SS0000109"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"NADH","type":"substance","synonyms":["DPNH","NADH","Nicotinamide adenine dinucleotide"],"links":[],"id":"SS0000064"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"GuaB","type":"protein","synonyms":["GuaB"],"links":[],"id":"SS0000384"},"theState":null,"compartment":"","theInfluence":"activator"},"r2":{"theSubstance":{"name":"GMP","type":"substance","synonyms":["GMP","Guanosine 5'-monophosphate","Guanosine 5'-phosphate","Guanosine monophosphate","Guanylic acid"],"links":[],"id":"SS0000112"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"(((r1^4)/((kdis^3)+4*r1^3))*kcat*(s1/KmIMP))/(1+(s1/KmIMP)+(r2/kGMP))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Gilbert et al., 1979 Inosine 5-monophosphate dehydrogenase of Escherichia coli. Purification by affinity chromatography, subunit structure and inhibition by guanosine 5-monophosphate. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/44191 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. Parametrs KmIMP and kGMP were taken from [Gilbert et al., 1979] article.","Parameter set links":" ID: Gilbert et al., 1979 Inosine 5-monophosphate dehydrogenase of Escherichia coli. Purification by affinity chromatography, subunit structure and inhibition by guanosine 5-monophosphate. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/44191 ;","Structural model information":"This is the first reaction unique to GMP biosynthesis.Subunit composition of enzyme of IMP dehydrogenase  = [GuaB]4.","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=IMP-DEHYDROG-RXN ;"},"mmid":"MM0000218","psid":"PS0000210","gnid":"GN0000211","reversible":true,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Gilbert et al., 1979 Inosine 5-monophosphate dehydrogenase of Escherichia coli. Purification by affinity chromatography, subunit structure and inhibition by guanosine 5-monophosphate. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/44191 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. Parametrs KmIMP and kGMP were taken from [Gilbert et al., 1979] article.","Parameter set links":" ID: Gilbert et al., 1979 Inosine 5-monophosphate dehydrogenase of Escherichia coli. Purification by affinity chromatography, subunit structure and inhibition by guanosine 5-monophosphate. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/44191 ;","Structural model information":"This is the first reaction unique to GMP biosynthesis.Subunit composition of enzyme of IMP dehydrogenase  = [GuaB]4.","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=IMP-DEHYDROG-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmIMP","value":"0.08"},{"units":"mM","information":"","name":"kGMP","value":"0.0115"},{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kdis","value":"0.001"}]},{"scheme":"FAICAR <=> IMP + H2O","substrates":{"s1":{"theSubstance":{"name":"FAICAR","type":"substance","synonyms":["1-(5'-Phosphoribosyl)-5-formamido-4-imidazolecarboxamide","5-Formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide","5-Formamido-1-(5-phosphoribosyl)imidazole-4-carboxamide","5'-Phosphoribosyl-5-formamido-4-imidazolecarboxamide","FAICAR"],"links":[],"id":"SS0000103"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"IMP","type":"substance","synonyms":["5'-IMP","5'-Inosinate","5'-Inosine monophosphate","5'-Inosinic acid","IMP","Inosine 5'-monophosphate","Inosine 5'-phosphate","Inosine monophosphate","Inosinic acid"],"links":[],"id":"SS0000104"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PurH","type":"protein","synonyms":["PurH"],"links":[],"id":"SS0000382"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"r1*kcat*s1/(KmFAICAR+s1)","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Vergis et al., 2001 Human 5-aminoimidazole-4-carboxamide ribonucleotide transformylase/inosine 5-monophosphate cyclohydrolase. A bifunctional protein requiring dimerization for transformylase activity but not for cyclohydrolase activity. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11096114 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. Michaelis constant (kmfaicar) with respect to faicar of Homo sapiens [Vergis et al., 2001].","Parameter set links":" ID: Vergis et al., 2001 Human 5-aminoimidazole-4-carboxamide ribonucleotide transformylase/inosine 5-monophosphate cyclohydrolase. A bifunctional protein requiring dimerization for transformylase activity but not for cyclohydrolase activity. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11096114 ;","Structural model information":"The ninth and tenth reactions of the de novo purine biosynthetic pathway for IMP biosynthesis are sequentially catalysed by AICAR transformylase and IMP cyclohydrolase. Recent studies have concluded that AICAR transformylase and IMP cyclohydrolase form a bifunctional enzyme with both activities residing on a single polypeptide. The two activities reside in two distinct domains of a single polypeptide which requires dimerization for maximum activity of both reactions [Flannigan et al., 1990]. EC 2.1.2.3 (AICAR transformylase), EC 3.5.4.10 (IMP cyclohydrolase). Subunit composition of enzyme of AICAR transformylase / IMP cyclohydrolase = [PurH].","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=IMPCYCLOHYDROLASE-RXN ; ID: Flannigan et al., 1990 Purine biosynthesis in Escherichia coli K12: structure and DNA sequence studies of the purHD locus. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2192230 ;"},"mmid":"MM0000216","psid":"PS0000208","gnid":"GN0000208","reversible":true,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Vergis et al., 2001 Human 5-aminoimidazole-4-carboxamide ribonucleotide transformylase/inosine 5-monophosphate cyclohydrolase. A bifunctional protein requiring dimerization for transformylase activity but not for cyclohydrolase activity. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11096114 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. Michaelis constant (kmfaicar) with respect to faicar of Homo sapiens [Vergis et al., 2001].","Parameter set links":" ID: Vergis et al., 2001 Human 5-aminoimidazole-4-carboxamide ribonucleotide transformylase/inosine 5-monophosphate cyclohydrolase. A bifunctional protein requiring dimerization for transformylase activity but not for cyclohydrolase activity. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11096114 ;","Structural model information":"The ninth and tenth reactions of the de novo purine biosynthetic pathway for IMP biosynthesis are sequentially catalysed by AICAR transformylase and IMP cyclohydrolase. Recent studies have concluded that AICAR transformylase and IMP cyclohydrolase form a bifunctional enzyme with both activities residing on a single polypeptide. The two activities reside in two distinct domains of a single polypeptide which requires dimerization for maximum activity of both reactions [Flannigan et al., 1990]. EC 2.1.2.3 (AICAR transformylase), EC 3.5.4.10 (IMP cyclohydrolase). Subunit composition of enzyme of AICAR transformylase / IMP cyclohydrolase = [PurH].","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=IMPCYCLOHYDROLASE-RXN ; ID: Flannigan et al., 1990 Purine biosynthesis in Escherichia coli K12: structure and DNA sequence studies of the purHD locus. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2192230 ;"},"parameters":[{"units":"mM","information":"","name":"KmFAICAR","value":"0.0009"},{"units":"1/sec","information":"","name":"kcat","value":"1"}]},{"scheme":"IMP + asp + GTP -> ADS + GDP + Pi + H+","substrates":{"s1":{"theSubstance":{"name":"IMP","type":"substance","synonyms":["5'-IMP","5'-Inosinate","5'-Inosine monophosphate","5'-Inosinic acid","IMP","Inosine 5'-monophosphate","Inosine 5'-phosphate","Inosine monophosphate","Inosinic acid"],"links":[],"id":"SS0000104"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"asp","type":"substance","synonyms":["2-Aminosuccinic acid","asp","L-Asp","L-Aspartate","L-Aspartic acid"],"links":[],"id":"SS0000059"},"theState":null,"compartment":""},"s3":{"theSubstance":{"name":"GTP","type":"substance","synonyms":["GTP","Guanosine 5'-triphosphate"],"links":[],"id":"SS0000140"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"ADS","type":"substance","synonyms":["Adenylosuccinate","Adenylosuccinic acid","ADS","N6-(1,2-Dicarboxyethyl)AMP","N6-(1,2-Dicarboxyethyl)-AMP"],"links":[],"id":"SS0000083"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"GDP","type":"substance","synonyms":["GDP","Guanosine 5'-diphosphate","Guanosine diphosphate"],"links":[],"id":"SS0000087"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"Pi","type":"substance","synonyms":["H3PO4","Orthophosphate","Orthophosphoric acid","Phosphate","Phosphoric acid","Pi"],"links":[],"id":"SS0000070"},"theState":null,"compartment":""},"p4":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PurA","type":"protein","synonyms":["PurA"],"links":[],"id":"SS0000383"},"theState":null,"compartment":"","theInfluence":"activator"},"r2":{"theSubstance":{"name":"GMP","type":"substance","synonyms":["GMP","Guanosine 5'-monophosphate","Guanosine 5'-phosphate","Guanosine monophosphate","Guanylic acid"],"links":[],"id":"SS0000112"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"AMP","type":"substance","synonyms":["5'-Adenosine monophosphate","5'-Adenylic acid","5'-AMP","Adenosine 5'-monophosphate","Adenosine 5'-phosphate","Adenylate","Adenylic acid","AMP"],"links":[],"id":"SS0000073"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"(((r1^2)/(kdis+2*r1))*kcat*(s1/KmIMP)*(s3/KmGTP))/((1+(s1/KmIMP)+(p1/kADS)+(r3/kAMP))*(1+(s3/KmGTP)+(r2/kGMP)+(p2/kGDP)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics. As GMP, GDP and GTP are known to be noncompetetive inhibitors[Oshchepkova-Nedosekina et al., 2007] of this reaction the equasion can be written as a sum of inhibitors influenses. As IMP, AMP and ADS are known to be noncompetetive inhibitors[Oshchepkova-Nedosekina et al., 2007] of this reaction the equasion can be written as a sum of inhibitors influenses.","Mathematical model links":" ID: Oshchepkova-Nedosekina et al., 2007 A mathematical model for the adenylosuccinate synthetase reaction involved in purine biosynthesis ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17326829 ;","Parameter set information":"kcat equals to 1 as there is different publications use different values of the rate constant of enzyme: 15600 1/sec [Dong et al., 1991], 1.47 1/sec [Kang et al., 1995], 1.0 1/sec [Wang et al., 1998]. However, since most publications do not indicate the enzyme concentrations used. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. Parametrs were taken from [Oshchepkova Nedosekina et al., 2007] article.","Parameter set links":" ID: Dong et al., 1991 Evidence for an arginine residue at the substrate binding site of Escherichia coli adenylosuccinate synthetase as studied by chemical modification and site-directed mutagenesis. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2061308 ; ID: Kang et al., 1995 Identification of an essential second metal ion in the reaction mechanism of Escherichia coli adenylosuccinate synthetase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7797548 ; ID: Oshchepkova-Nedosekina et al., 2007 A mathematical model for the adenylosuccinate synthetase reaction involved in purine biosynthesis. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17326829 ; ID: Wang et al., 1998 Ambiguities in mapping the active site of a conformationally dynamic enzyme by directed mutation. Role of dynamics in structure-function correlations in Escherichia coli adenylosuccinate synthetase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9632649 ;","Structural model information":"This is the first committed step in AMP biosynthesis, converting IMP to AMP. Subunit composition of enzyme of adenylosuccinate synthetase  = [PurA].","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=ADENYLOSUCCINATE-SYNTHASE-RXN ;"},"mmid":"MM0000217","psid":"PS0000209","gnid":"GN0000210","reversible":false,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics. As GMP, GDP and GTP are known to be noncompetetive inhibitors[Oshchepkova-Nedosekina et al., 2007] of this reaction the equasion can be written as a sum of inhibitors influenses. As IMP, AMP and ADS are known to be noncompetetive inhibitors[Oshchepkova-Nedosekina et al., 2007] of this reaction the equasion can be written as a sum of inhibitors influenses.","Mathematical model links":" ID: Oshchepkova-Nedosekina et al., 2007 A mathematical model for the adenylosuccinate synthetase reaction involved in purine biosynthesis ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17326829 ;","Parameter set information":"kcat equals to 1 as there is different publications use different values of the rate constant of enzyme: 15600 1/sec [Dong et al., 1991], 1.47 1/sec [Kang et al., 1995], 1.0 1/sec [Wang et al., 1998]. However, since most publications do not indicate the enzyme concentrations used. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. Parametrs were taken from [Oshchepkova Nedosekina et al., 2007] article.","Parameter set links":" ID: Dong et al., 1991 Evidence for an arginine residue at the substrate binding site of Escherichia coli adenylosuccinate synthetase as studied by chemical modification and site-directed mutagenesis. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/2061308 ; ID: Kang et al., 1995 Identification of an essential second metal ion in the reaction mechanism of Escherichia coli adenylosuccinate synthetase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/7797548 ; ID: Oshchepkova-Nedosekina et al., 2007 A mathematical model for the adenylosuccinate synthetase reaction involved in purine biosynthesis. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17326829 ; ID: Wang et al., 1998 Ambiguities in mapping the active site of a conformationally dynamic enzyme by directed mutation. Role of dynamics in structure-function correlations in Escherichia coli adenylosuccinate synthetase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9632649 ;","Structural model information":"This is the first committed step in AMP biosynthesis, converting IMP to AMP. Subunit composition of enzyme of adenylosuccinate synthetase  = [PurA].","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=ADENYLOSUCCINATE-SYNTHASE-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmGTP","value":"0.023"},{"units":"mM","information":"","name":"KmIMP","value":"0.02"},{"units":"mM","information":"","name":"kADS","value":"0.0075"},{"units":"mM","information":"","name":"kAMP","value":"0.01"},{"units":"mM","information":"","name":"kGDP","value":"0.008"},{"units":"mM","information":"","name":"kGMP","value":"0.024"},{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kdis","value":"0.001"}]},{"scheme":"-> NrdA","substrates":null,"products":{"p1":{"theSubstance":{"name":"NrdA","type":"protein","synonyms":["NrdA","ribonucleoside diphosphate reductase 1, a subunit dimer"],"links":[],"id":"SS0000370"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"nrdA","type":"gene","synonyms":["nrdA"],"links":[],"id":"SS0000394"},"theState":null,"compartment":"","theInfluence":""},"r10":{"theSubstance":{"name":"RutR","type":"protein","synonyms":["RutR","RutR DNA-binding transcriptional dual regulator"],"links":[],"id":"SS0000357"},"theState":null,"compartment":"","theInfluence":"activator"},"r11":{"theSubstance":{"name":"Ura","type":"substance","synonyms":["Ura","Uracil"],"links":[],"id":"SS0000040"},"theState":null,"compartment":"","theInfluence":"activator"},"r12":{"theSubstance":{"name":"Thy","type":"substance","synonyms":["5-Methyluracil","Thy","Thymine"],"links":[],"id":"SS0000056"},"theState":null,"compartment":"","theInfluence":"activator"},"r2":{"theSubstance":{"name":"DnaA","type":"protein","synonyms":["DnaA"],"links":[],"id":"SS0000390"},"theState":null,"compartment":"","theInfluence":"complex regulator"},"r3":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":"","theInfluence":"activator"},"r4":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":"","theInfluence":"activator"},"r5":{"theSubstance":{"name":"NrdR","type":"protein","synonyms":["NrdR"],"links":[],"id":"SS0000391"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r6":{"theSubstance":{"name":"dATP","type":"substance","synonyms":["2'-Deoxyadenosine 5'-triphosphate","dATP","Deoxyadenosine 5'-triphosphate","Deoxyadenosine triphosphate"],"links":[],"id":"SS0000079"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r7":{"theSubstance":{"name":"Fis","type":"protein","synonyms":["Fis"],"links":[],"id":"SS0000389"},"theState":null,"compartment":"","theInfluence":"activator"},"r8":{"theSubstance":{"name":"ArgP","type":"protein","synonyms":["ArgP"],"links":[],"id":"SS0000392"},"theState":null,"compartment":"","theInfluence":"activator"},"r9":{"theSubstance":{"name":"arg","type":"substance","synonyms":["2-amino-5-guanidinovaleric acid","arg","arginine","L-arginine","R"],"links":[],"id":"SS0000387"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"ks*((1+(k1DnaA*(((k0*(((r2*r3)/kdisDnaAATP)/(1+((r2*r3)/kdisDnaAATP)+((r2*r4)/kdisDnaAADP))))/k2DnaA)^hDnaA)))/(1+(((k0*(((r2*r3)/kdisDnaAATP)/(1+((r2*r3)/kdisDnaAATP)+((r2*r4)/kdisDnaAADP))))/k2DnaA)^hDnaA)))*(1/(1+((((k0*(((r2*r3)/kdisDnaAATP)/(1+((r2*r3)/kdisDnaAATP)+((r2*r4)/kdisDnaAADP))))^3)/((kdisDnaA^2)+3*((k0*(((r2*r3)/kdisDnaAATP)/(1+((r2*r3)/kdisDnaAATP)+((r2*r4)/kdisDnaAADP))))^2)))/k3Dna)))*((1+k1NrdR*(((((r5*r3)/kdisNrdRATP)/(1+((r5*r3)/kdisNrdRATP)+((r5*r6)/kdisNrdRdATP)))/k2NrdR)+((((r5*r6)/kdisNrdRdATP)/(1+((r5*r3)/kdisNrdRATP)+((r5*r6)/kdisNrdRdATP)))/k3NrdR)))/(1+((((r5*r3)/kdisNrdRATP)/(1+((r5*r3)/kdisNrdRATP)+((r5*r6)/kdisNrdRdATP)))/k2NrdR)+((((r5*r6)/kdisNrdRdATP)/(1+((r5*r3)/kdisNrdRATP)+((r5*r6)/kdisNrdRdATP)))/k3NrdR)))*((1+k1Fis*(r7/k2Fis))/(1+(r7/k2Fis)))*((1+k3Fis*(r7/k4Fis))/(1+(r7/k4Fis)))*((1+k1ArgP*(((((r8*(r9^2))/(kdisArgParg^2))/(1+((2*r8*r9+(r9^2))/(kdisArgParg^2))))/k2ArgP)^hArgP))/(1+(((((r8*(r9^2))/(kdisArgParg^2))/(1+((2*r8*r9+(r9^2))/(kdisArgParg^2))))/k2ArgP)^hArgP)))*((1+k1RutR*((((r10*(r11^2))/(kdisRutRura^2))/(1+((r10*(r11^2))/(kdisRutRura^2))+((r10*(r12^2))/(kdisRutRthy^2))))/k2RutR))/(1+((((r10*(r12^2))/(kdisRutRthy^2))/(1+((r10*(r11^2))/(kdisRutRura^2))+((r10*(r12^2))/(kdisRutRthy^2))))/k2RutR)))","theSubMathModel":null,"theInformation":{"Mathematical model information":" To describe the model we have used the generalized Hill function. The efficiency of transcription of the operon nrdAB is regulated positively transcription factors Fis, ArgP and negatively NrdR [Augustin et al., 1994, Torrents et al., 2007, Han et al., 1998]. Active nrdAB operon and controls factor DnaA, but the direction of its impact depends on the concentration of its ATP-bound form [Olliver et al., 2010]. ","Mathematical model links":" ID: Augustin L.B., 1994 Jacobson B.A., Fuchs J.A., Escherichia coli Fis and DnaA proteins bind specifically to the nrd promoter region and affect expression of an nrd-lac fusion. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8288532 ; ID: Han J.S. et al., 1998 Effect of IciA protein on the expression of the nrd gene encoding ribonucleoside diphosphate reductase in E. coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9819053 ; ID: Olliver A. et al., 2010 DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/20487274 ; ID: Torrents E. et al., 2007 NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17496099 ;","Parameter set information":" Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*NrdA = 0, where NrdA - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter nrdAp. ks - protein synthesis generalized constant from the promoter nrdAp. kd = 0.002 [1/sec],NrdA = 0.002544 [mM]. Parameters k1DnaA, k2DnaA, k3DnaA and hDnaA were evaluated basing on [Olliver A. et al., 2010] experimental data. Parameters k1Fis, k2Fis, k3Fis and k4Fis were evaluated basing on [Augustin L.B., 1994] experimental data. Parameters k1NrdR, k2NrdR and k3NrdR were evaluated basing on [Torrents E. et al., 2007] experimental data.Parameters k1ArgP, k2ArgP, hArgP were evaluated basing on [Han J.S. et al., 1998 ] experimental data. Parameters kdisDnaAATP, and kdisDnaAADP are taken from article [Kaguni, 2006]. Parameter kdisDnaA was evaluated basing on [Olliver et al., 2010] experimental data. ","Parameter set links":" ID: Augustin L.B., 1994 Jacobson B.A., Fuchs J.A., Escherichia coli Fis and DnaA proteins bind specifically to the nrd promoter region and affect expression of an nrd-lac fusion. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8288532 ; ID: Han J.S. et al., 1998 Effect of IciA protein on the expression of the nrd gene encoding ribonucleoside diphosphate reductase in E. coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9819053 ; ID: Kaguni J.M., 2006 DnaA: controlling the initiation of bacterial DNA replication and more. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16753031 ; ID: Olliver A. et al., 2010 DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/20487274 ; ID: Torrents E. et al., 2007 NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17496099 ;","Structural model information":" Genes nrdA and nrdB are part of an operon nrdAB and encode structure of the subunits of the enzyme ribonucleoside diphosphate reductase. Here we consider the process of synthesis protein NrdA with the promoter nrdAp. The efficiency of transcription of the operon nrdAB is regulated positively transcription factors Fis, ArgP and negatively NrdR [Augustin et al., 1994, Torrents et al., 2007, Han et al., 1998]. Active nrdAB operon and controls factor DnaA, but the direction of its impact depends on the concentration of its ATP-bound form [Olliver et al., 2010].\n ","Structural model links":" ID: Augustin L.B., 1994 Jacobson B.A., Fuchs J.A.,  Escherichia coli Fis and DnaA proteins bind specifically to the nrd promoter region and affect expression of an nrd-lac fusion. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8288532 ; ID: Han J.S. et al., 1998 Effect of IciA protein on the expression of the nrd gene encoding ribonucleoside diphosphate reductase in E. coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9819053 ; ID: Olliver A. et al., 2010 DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/20487274 ; ID: Torrents E. et al., 2007  NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17496099 ;"},"mmid":"MM0000231","psid":"PS0000221","gnid":"GN0000222","reversible":false,"information":{"Mathematical model information":" To describe the model we have used the generalized Hill function. The efficiency of transcription of the operon nrdAB is regulated positively transcription factors Fis, ArgP and negatively NrdR [Augustin et al., 1994, Torrents et al., 2007, Han et al., 1998]. Active nrdAB operon and controls factor DnaA, but the direction of its impact depends on the concentration of its ATP-bound form [Olliver et al., 2010]. ","Mathematical model links":" ID: Augustin L.B., 1994 Jacobson B.A., Fuchs J.A., Escherichia coli Fis and DnaA proteins bind specifically to the nrd promoter region and affect expression of an nrd-lac fusion. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8288532 ; ID: Han J.S. et al., 1998 Effect of IciA protein on the expression of the nrd gene encoding ribonucleoside diphosphate reductase in E. coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9819053 ; ID: Olliver A. et al., 2010 DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/20487274 ; ID: Torrents E. et al., 2007 NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17496099 ;","Parameter set information":" Parameter ks was obtained from the algebraic equation of the form: ks*f-kd*NrdA = 0, where NrdA - concentration of the protein, kd - the constant of degradation, f - the proportion of transcripts from the promoter nrdAp. ks - protein synthesis generalized constant from the promoter nrdAp. kd = 0.002 [1/sec],NrdA = 0.002544 [mM]. Parameters k1DnaA, k2DnaA, k3DnaA and hDnaA were evaluated basing on [Olliver A. et al., 2010] experimental data. Parameters k1Fis, k2Fis, k3Fis and k4Fis were evaluated basing on [Augustin L.B., 1994] experimental data. Parameters k1NrdR, k2NrdR and k3NrdR were evaluated basing on [Torrents E. et al., 2007] experimental data.Parameters k1ArgP, k2ArgP, hArgP were evaluated basing on [Han J.S. et al., 1998 ] experimental data. Parameters kdisDnaAATP, and kdisDnaAADP are taken from article [Kaguni, 2006]. Parameter kdisDnaA was evaluated basing on [Olliver et al., 2010] experimental data. ","Parameter set links":" ID: Augustin L.B., 1994 Jacobson B.A., Fuchs J.A., Escherichia coli Fis and DnaA proteins bind specifically to the nrd promoter region and affect expression of an nrd-lac fusion. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8288532 ; ID: Han J.S. et al., 1998 Effect of IciA protein on the expression of the nrd gene encoding ribonucleoside diphosphate reductase in E. coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9819053 ; ID: Kaguni J.M., 2006 DnaA: controlling the initiation of bacterial DNA replication and more. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/16753031 ; ID: Olliver A. et al., 2010 DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/20487274 ; ID: Torrents E. et al., 2007 NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17496099 ;","Structural model information":" Genes nrdA and nrdB are part of an operon nrdAB and encode structure of the subunits of the enzyme ribonucleoside diphosphate reductase. Here we consider the process of synthesis protein NrdA with the promoter nrdAp. The efficiency of transcription of the operon nrdAB is regulated positively transcription factors Fis, ArgP and negatively NrdR [Augustin et al., 1994, Torrents et al., 2007, Han et al., 1998]. Active nrdAB operon and controls factor DnaA, but the direction of its impact depends on the concentration of its ATP-bound form [Olliver et al., 2010].\n ","Structural model links":" ID: Augustin L.B., 1994 Jacobson B.A., Fuchs J.A.,  Escherichia coli Fis and DnaA proteins bind specifically to the nrd promoter region and affect expression of an nrd-lac fusion. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/8288532 ; ID: Han J.S. et al., 1998 Effect of IciA protein on the expression of the nrd gene encoding ribonucleoside diphosphate reductase in E. coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/9819053 ; ID: Olliver A. et al., 2010 DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/20487274 ; ID: Torrents E. et al., 2007  NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/17496099 ;"},"parameters":[{"units":"","information":"","name":"hArgP","value":"2"},{"units":"","information":"","name":"hDnaA","value":"2"},{"units":"","information":"","name":"k0","value":"0.12"},{"units":"","information":"","name":"k1ArgP","value":"5"},{"units":"","information":"","name":"k1DnaA","value":"2.07"},{"units":"","information":"","name":"k1Fis","value":"2.53"},{"units":"","information":"","name":"k1NrdR","value":"0.228"},{"units":"","information":"","name":"k1RutR","value":"2"},{"units":"mM","information":"","name":"k2ArgP","value":"0.000167"},{"units":"mM","information":"","name":"k2DnaA","value":"0.00002"},{"units":"mM","information":"","name":"k2Fis","value":"0.001"},{"units":"mM","information":"","name":"k2NrdR","value":"0.0003"},{"units":"mM","information":"","name":"k2RutR","value":"0.0001"},{"units":"mM","information":"","name":"k3Dna","value":"0.0001"},{"units":"","information":"","name":"k3Fis","value":"6.4"},{"units":"mM","information":"","name":"k3NrdR","value":"0.0003"},{"units":"mM","information":"","name":"k4Fis","value":"0.004"},{"units":"mM","information":"","name":"kdisArgParg","value":"0.001"},{"units":"mM","information":"","name":"kdisDnaA","value":"0.00134"},{"units":"mM","information":"","name":"kdisDnaAADP","value":"0.0001"},{"units":"mM","information":"","name":"kdisDnaAATP","value":"0.00003"},{"units":"mM","information":"","name":"kdisNrdRATP","value":"0.001"},{"units":"mM","information":"","name":"kdisNrdRdATP","value":"0.001"},{"units":"mM","information":"","name":"kdisRutRthy","value":"0.001"},{"units":"mM","information":"","name":"kdisRutRura","value":"0.001"},{"units":"mM/sec","information":"","name":"ks","value":"0.000007"}]},{"scheme":"FGAM + ATP -> AIR + ADP + Pi + H+","substrates":{"s1":{"theSubstance":{"name":"FGAM","type":"substance","synonyms":["1-(5'-Phosphoribosyl)-N-formylglycinamidine","2-(Formamido)-N1-(5-phospho-D-ribosyl)acetamidine","2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine","5'-Phosphoribosylformylglycinamidine","5'-Phosphoribosyl-N-formylglycinamidine","FGAM"],"links":[],"id":"SS0000097"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"AIR","type":"substance","synonyms":["1-(5-Phospho-D-ribosyl)-5-aminoimidazole","1-(5'-Phosphoribosyl)-5-aminoimidazole","5-Amino-1-(5-phospho-D-ribosyl)imidazole","5'-Phosphoribosyl-5-aminoimidazole","AIR","Aminoimidazole ribotide"],"links":[],"id":"SS0000098"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"Pi","type":"substance","synonyms":["H3PO4","Orthophosphate","Orthophosphoric acid","Phosphate","Phosphoric acid","Pi"],"links":[],"id":"SS0000070"},"theState":null,"compartment":""},"p4":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PurM","type":"protein","synonyms":["PurM"],"links":[],"id":"SS0000377"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"(((r1^2)/(kdis+2*r1))*kcat*(s1/KmFGAM)*(s2/KmATP))/((1+(s1/KmFGAM))*(1+(s2/KmATP)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Schrimsher et al., 1986 Purification and characterization of aminoimidazole ribonucleotide synthetase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3530323 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration). Parameters were evaluated basing on [Schrimsher et al., 1986] experimental data. can be calculated from the whole model basing on the flow rate magnitude. can be calculated from the whole model basing on the flow rate magnitude.","Parameter set links":" ID: Schrimsher et al., 1986 Purification and characterization of aminoimidazole ribonucleotide synthetase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3530323 ;","Structural model information":" AIR synthetase from E. coli, as in the case of the chicken liver protein, catalyzes transfer of the oxygen of the formyl group to inorganic phosphate. Both K and Mg ions were found to be absolutely required for catalytic activity. Kinetic studies are available.  ","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=AIRS-RXN ;"},"mmid":"MM0000210","psid":"PS0000202","gnid":"GN0000201","reversible":false,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Schrimsher et al., 1986 Purification and characterization of aminoimidazole ribonucleotide synthetase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3530323 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration). Parameters were evaluated basing on [Schrimsher et al., 1986] experimental data. can be calculated from the whole model basing on the flow rate magnitude. can be calculated from the whole model basing on the flow rate magnitude.","Parameter set links":" ID: Schrimsher et al., 1986 Purification and characterization of aminoimidazole ribonucleotide synthetase from Escherichia coli. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/3530323 ;","Structural model information":" AIR synthetase from E. coli, as in the case of the chicken liver protein, catalyzes transfer of the oxygen of the formyl group to inorganic phosphate. Both K and Mg ions were found to be absolutely required for catalytic activity. Kinetic studies are available.  ","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=AIRS-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmATP","value":"0.065"},{"units":"mM","information":"","name":"KmFGAM","value":"0.027"},{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kdis","value":"0.001"}]},{"scheme":"AIR + ATP + CO2 -> N-CAIR + ADP + Pi + H+","substrates":{"s1":{"theSubstance":{"name":"AIR","type":"substance","synonyms":["1-(5-Phospho-D-ribosyl)-5-aminoimidazole","1-(5'-Phosphoribosyl)-5-aminoimidazole","5-Amino-1-(5-phospho-D-ribosyl)imidazole","5'-Phosphoribosyl-5-aminoimidazole","AIR","Aminoimidazole ribotide"],"links":[],"id":"SS0000098"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":""},"s3":{"theSubstance":{"name":"CO2","type":"substance","synonyms":["Carbon dioxide","CO2"],"links":[],"id":"SS0000071"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"N-CAIR","type":"substance","synonyms":["5-phosphoribosyl-5-carboxyaminoimidazole","N-CAIR"],"links":[],"id":"SS0000196"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"Pi","type":"substance","synonyms":["H3PO4","Orthophosphate","Orthophosphoric acid","Phosphate","Phosphoric acid","Pi"],"links":[],"id":"SS0000070"},"theState":null,"compartment":""},"p4":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"PurK","type":"protein","synonyms":["PurK"],"links":[],"id":"SS0000378"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"(((r1^2)/(kdis+2*r1))*kcat*(s1/KmAIR)*(s2/KmATP))/((1+(s1/KmAIR))*(1+(s2/KmATP)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Li et al., 2009 Structural and functional modularity of proteins in the de novo purine biosynthetic pathway. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/19384989 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. Parameters were evaluated basing on [Li et al., 2009] experimental data.","Parameter set links":" ID: Li et al., 2009 Structural and functional modularity of proteins in the de novo purine biosynthetic pathway. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/19384989 ;","Structural model information":" In enzymology, a 5-(carboxyamino)imidazole ribonucleotide synthase (EC 6.3.4.18) is an enzyme that catalyzes the chemical reaction\nATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3- &lt;-&gt;  ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole. The 3 substrates of this enzyme are ATP, 5-amino-1-(5-phospho-D-ribosyl)imidazole (&quot;AIR&quot;), and HCO3-, whereas its 3 products are ADP, phosphate, and 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole. This enzyme belongs to the family of ligases, specifically those forming generic carbon-nitrogen bonds. The systematic name of this enzyme class is 5-amino-1-(5-phospho-D-ribosyl)imidazole:carbon-dioxide ligase (ADP-forming).  ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=RXN0-742 ;"},"mmid":"MM0000211","psid":"PS0000203","gnid":"GN0000202","reversible":false,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Li et al., 2009 Structural and functional modularity of proteins in the de novo purine biosynthetic pathway. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/19384989 ;","Parameter set information":"kcat equals to 1 as there is no experimental data for this subsystem. In spite of this fact Vmax=kcat*r1 (where r1 is enzyme concentration) can be calculated from the whole model basing on the flow rate magnitude. Parameters were evaluated basing on [Li et al., 2009] experimental data.","Parameter set links":" ID: Li et al., 2009 Structural and functional modularity of proteins in the de novo purine biosynthetic pathway. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/19384989 ;","Structural model information":" In enzymology, a 5-(carboxyamino)imidazole ribonucleotide synthase (EC 6.3.4.18) is an enzyme that catalyzes the chemical reaction\nATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3- &lt;-&gt;  ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole. The 3 substrates of this enzyme are ATP, 5-amino-1-(5-phospho-D-ribosyl)imidazole (&quot;AIR&quot;), and HCO3-, whereas its 3 products are ADP, phosphate, and 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole. This enzyme belongs to the family of ligases, specifically those forming generic carbon-nitrogen bonds. The systematic name of this enzyme class is 5-amino-1-(5-phospho-D-ribosyl)imidazole:carbon-dioxide ligase (ADP-forming).  ","Structural model links":" ID: EcoCyc ; Value:http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&object=RXN0-742 ;"},"parameters":[{"units":"mM","information":"","name":"KmAIR","value":"0.026"},{"units":"mM","information":"","name":"KmATP","value":"0.09"},{"units":"1/sec","information":"","name":"kcat","value":"1"},{"units":"mM","information":"","name":"kdis","value":"0.001"}]},{"scheme":"A + prpp -> AMP + ppi","substrates":{"s1":{"theSubstance":{"name":"A","type":"substance","synonyms":["6-Aminopurine","A","Adenine"],"links":[],"id":"SS0000080"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"prpp","type":"substance","synonyms":["5-Phospho-alpha-D-ribose 1-diphosphate","5-Phosphoribosyl 1-pyrophosphate","5-Phosphoribosyl diphosphate","prpp"],"links":[],"id":"SS0000021"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"AMP","type":"substance","synonyms":["5'-Adenosine monophosphate","5'-Adenylic acid","5'-AMP","Adenosine 5'-monophosphate","Adenosine 5'-phosphate","Adenylate","Adenylic acid","AMP"],"links":[],"id":"SS0000073"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ppi","type":"substance","synonyms":["Diphosphate","PP","ppi","pyrophosphate"],"links":[],"id":"SS0000023"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Apt","type":"protein","synonyms":["adenine phosphoribosyltransferase","Apt","ec:2.4.2.7"],"links":[],"id":"SS0000248"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"ADP","type":"substance","synonyms":["Adenosine 5'-diphosphate","ADP"],"links":[],"id":"SS0000069"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"GDP","type":"substance","synonyms":["GDP","Guanosine 5'-diphosphate","Guanosine diphosphate"],"links":[],"id":"SS0000087"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"GTP","type":"substance","synonyms":["GTP","Guanosine 5'-triphosphate"],"links":[],"id":"SS0000140"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"ATP","type":"substance","synonyms":["Adenosine 5'-triphosphate","ATP"],"links":[],"id":"SS0000065"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"(kcat*r1*s1*(s2/KmPRPP))/((KmAde+s1)*(1+(s2/KmPRPP)+(r2/kADP)+(r3/kGDP)+(r4/kGTP)+(r5/kATP)))","theSubMathModel":null,"theInformation":{"Mathematical model information":" Reaction follows Michaelis-Menten kinetics. As ADP, GDP, ATP and GTP are known to be noncompetetive inhibitors [Hochstadt-Ozer and Stadtman, 1971] of this reaction the equasion can be written as a sum of inhibitors influenses.  ","Mathematical model links":" ID: Hochstadt-Ozer J., Stadtman E.R., 1971 The regulation of purine utilization in bacteria. I. Purification of adenine phosphoribosyltransferase from Escherichia coli K12 and control of activity by nucleotides. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4328693 ;","Parameter set information":"Parameters kcat, KmPRPP and KmAde are taken from article [Hochstadt-Ozer J., Stadtman E.R., 1971].\nParameters kADP, kGDP, kATP and kGTP were evaluated basing on [Hochstadt-Ozer J., Stadtman E.R., 1971] experimental data.","Parameter set links":" ID: Hochstadt-Ozer J., Stadtman E.R., 1971 The regulation of purine utilization in bacteria. I. Purification of adenine phosphoribosyltransferase from Escherichia coli K12 and control of activity by nucleotides. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4328693 ;","Structural model information":" Adenine phosphoribosyltransferase (EC 2.4.2.7) from Escherichia coli catalyzes the reaction adenine and PRPP.  ","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=ADENPRIBOSYLTRAN-RXN ; ID: Hochstadt-Ozer and Stadtman, 1971 The regulation of purine utilization in bacteria. I. Purification of adenine phosphoribosyltransferase from Escherichia coli K12 and control of activity by nucleotides. ; Value:hhttp://www.ncbi.nlm.nih.gov/pubmed/4328693 ;"},"mmid":"MM0000249","psid":"PS0000239","gnid":"GN0000239","reversible":false,"information":{"Mathematical model information":" Reaction follows Michaelis-Menten kinetics. As ADP, GDP, ATP and GTP are known to be noncompetetive inhibitors [Hochstadt-Ozer and Stadtman, 1971] of this reaction the equasion can be written as a sum of inhibitors influenses.  ","Mathematical model links":" ID: Hochstadt-Ozer J., Stadtman E.R., 1971 The regulation of purine utilization in bacteria. I. Purification of adenine phosphoribosyltransferase from Escherichia coli K12 and control of activity by nucleotides. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4328693 ;","Parameter set information":"Parameters kcat, KmPRPP and KmAde are taken from article [Hochstadt-Ozer J., Stadtman E.R., 1971].\nParameters kADP, kGDP, kATP and kGTP were evaluated basing on [Hochstadt-Ozer J., Stadtman E.R., 1971] experimental data.","Parameter set links":" ID: Hochstadt-Ozer J., Stadtman E.R., 1971 The regulation of purine utilization in bacteria. I. Purification of adenine phosphoribosyltransferase from Escherichia coli K12 and control of activity by nucleotides. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4328693 ;","Structural model information":" Adenine phosphoribosyltransferase (EC 2.4.2.7) from Escherichia coli catalyzes the reaction adenine and PRPP.  ","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=ADENPRIBOSYLTRAN-RXN ; ID: Hochstadt-Ozer and Stadtman, 1971 The regulation of purine utilization in bacteria. I. Purification of adenine phosphoribosyltransferase from Escherichia coli K12 and control of activity by nucleotides. ; Value:hhttp://www.ncbi.nlm.nih.gov/pubmed/4328693 ;"},"parameters":[{"units":"mM","information":"","name":"KmAde","value":"0.011"},{"units":"mM","information":"","name":"KmPRPP","value":"0.142"},{"units":"mM","information":"","name":"kADP","value":"0.23"},{"units":"mM","information":"","name":"kATP","value":"0.27"},{"units":"mM","information":"","name":"kGDP","value":"0.9"},{"units":"mM","information":"","name":"kGTP","value":"0.5"},{"units":"1/sec","information":"","name":"kcat","value":"9.3"}]},{"scheme":"Hypoxanthine + H2O + NAD+ -> Xanthine + NADH + H+","substrates":{"s1":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""},"s3":{"theSubstance":{"name":"NAD+","type":"substance","synonyms":["NAD+"],"links":[],"id":"SS0000188"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"Xanthine","type":"substance","synonyms":["Xanthine"],"links":[],"id":"SS0000116"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"NADH","type":"substance","synonyms":["DPNH","NADH","Nicotinamide adenine dinucleotide"],"links":[],"id":"SS0000064"},"theState":null,"compartment":""},"p3":{"theSubstance":{"name":"H+","type":"substance","synonyms":["H","H+","hydrogen ion","proton"],"links":[],"id":"SS0000063"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"XdhABC","type":"protein","synonyms":["ec:1.17.1.4","xanthine dehydrogenase","XdhABC"],"links":[],"id":"SS0000410"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"(kcat*r1*s1)/(KmHyp+s1)","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics. ","Parameter set information":"Michaelis constant (KmHyp) with respect to hypoxanthine of Eubacterium barkeri  [Schrader et al., 1999].\nCatalytic constant (kcat) with respect to hypoxanthine of Veillonella atypica [Smith et al., 1967].","Parameter set links":" ID: Schrader et al., 1999 Selenium-containing xanthine dehydrogenase from Eubacterium barkeri. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10491134 ; ID: Smith et al., 1967 Purification and properties of xanthine dehydroganase from Micrococcus lactilyticus. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6061702 ;","Structural model information":"Xanthine dehydrogenase catalyzes the conversion of hypoxanthine to xanthine.","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=RXN-7682 ;"},"mmid":"MM0000250","psid":"PS0000240","gnid":"GN0000240","reversible":false,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics. ","Parameter set information":"Michaelis constant (KmHyp) with respect to hypoxanthine of Eubacterium barkeri  [Schrader et al., 1999].\nCatalytic constant (kcat) with respect to hypoxanthine of Veillonella atypica [Smith et al., 1967].","Parameter set links":" ID: Schrader et al., 1999 Selenium-containing xanthine dehydrogenase from Eubacterium barkeri. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10491134 ; ID: Smith et al., 1967 Purification and properties of xanthine dehydroganase from Micrococcus lactilyticus. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6061702 ;","Structural model information":"Xanthine dehydrogenase catalyzes the conversion of hypoxanthine to xanthine.","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=RXN-7682 ;"},"parameters":[{"units":"mM","information":"","name":"KmHyp","value":"0.21"},{"units":"1/sec","information":"","name":"kcat","value":"0.75"}]},{"scheme":"G + H2O -> Xanthine + NH3","substrates":{"s1":{"theSubstance":{"name":"G","type":"substance","synonyms":["2-Amino-6-hydroxypurine","G","Guanine"],"links":[],"id":"SS0000114"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"H2O","type":"substance","synonyms":["H2O","Water"],"links":[],"id":"SS0000062"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"Xanthine","type":"substance","synonyms":["Xanthine"],"links":[],"id":"SS0000116"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"NH3","type":"substance","synonyms":["Ammonia","NH3"],"links":[],"id":"SS0000060"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"GuaD","type":"protein","synonyms":["ec:3.5.4.3","GuaD","guanine deaminase","YgfP"],"links":[],"id":"SS0000411"},"theState":null,"compartment":"","theInfluence":"enzyme"}},"theMathModel":"(kcat*r1*s1)/(KmGua+s1)","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Maynes et al., 2000 Identification, Expression, and Characterization of Escherichia coli Guanine Deaminase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10913105 ;","Parameter set information":"Parameters kcat and KmGua are taken from article [Maynes et al., 2000]. ","Parameter set links":" ID: Maynes et al., 2000 Identification, Expression, and Characterization of Escherichia coli Guanine Deaminase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10913105 ;","Structural model information":"Guanine deaminase catalyzes the conversion of guanine to xanthine.","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=GUANINE-DEAMINASE-RXN ;"},"mmid":"MM0000251","psid":"PS0000241","gnid":"GN0000241","reversible":false,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics.","Mathematical model links":" ID: Maynes et al., 2000 Identification, Expression, and Characterization of Escherichia coli Guanine Deaminase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10913105 ;","Parameter set information":"Parameters kcat and KmGua are taken from article [Maynes et al., 2000]. ","Parameter set links":" ID: Maynes et al., 2000 Identification, Expression, and Characterization of Escherichia coli Guanine Deaminase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/10913105 ;","Structural model information":"Guanine deaminase catalyzes the conversion of guanine to xanthine.","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=GUANINE-DEAMINASE-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmGua","value":"0.015"},{"units":"1/sec","information":"","name":"kcat","value":"3.2"}]},{"scheme":"G + prpp <=> GMP + ppi","substrates":{"s1":{"theSubstance":{"name":"G","type":"substance","synonyms":["2-Amino-6-hydroxypurine","G","Guanine"],"links":[],"id":"SS0000114"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"prpp","type":"substance","synonyms":["5-Phospho-alpha-D-ribose 1-diphosphate","5-Phosphoribosyl 1-pyrophosphate","5-Phosphoribosyl diphosphate","prpp"],"links":[],"id":"SS0000021"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"GMP","type":"substance","synonyms":["GMP","Guanosine 5'-monophosphate","Guanosine 5'-phosphate","Guanosine monophosphate","Guanylic acid"],"links":[],"id":"SS0000112"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ppi","type":"substance","synonyms":["Diphosphate","PP","ppi","pyrophosphate"],"links":[],"id":"SS0000023"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Hpt","type":"protein","synonyms":["ec:2.4.2.8","Hpt","Hypoxanthine phosphoribosyltransferase"],"links":[],"id":"SS0000412"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"Xanthine","type":"substance","synonyms":["Xanthine"],"links":[],"id":"SS0000116"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"IMP","type":"substance","synonyms":["5'-IMP","5'-Inosinate","5'-Inosine monophosphate","5'-Inosinic acid","IMP","Inosine 5'-monophosphate","Inosine 5'-phosphate","Inosine monophosphate","Inosinic acid"],"links":[],"id":"SS0000104"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"GMP","type":"substance","synonyms":["GMP","Guanosine 5'-monophosphate","Guanosine 5'-phosphate","Guanosine monophosphate","Guanylic acid"],"links":[],"id":"SS0000112"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"(kcat*r1*(s1/KmGua)*s2)/((KmPRPP+s2)*(1+(s1/KmGua)+(r2/kHyp)+(r3/kXan)+(r4/kIMP)+(r5/kGMP)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics. As hypoxanthine, xanthine, IMP and GMP are known to be noncompetetive inhibitors [Guddat et al., 2002] of this reaction the equasion can be written as a sum of inhibitors influenses.","Mathematical model links":" ID: Guddat et al., 2002 Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12070315 ;","Parameter set information":" Parameters kcat, KmPRPP and KmGua are taken from article [Guddat et al., 2002]. Parameters kHyp, kXan, kIMP and kGMP were evaluated basing on [Guddat et al., 2002] experimental data. ","Parameter set links":" ID: Guddat et al., 2002 Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12070315 ;","Structural model information":"Hypoxanthine phosphoribosyltransferase catalyzes the reaction guanine and PRPP.","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=GUANPRIBOSYLTRAN-RXN ;"},"mmid":"MM0000252","psid":"PS0000242","gnid":"GN0000243","reversible":true,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics. As hypoxanthine, xanthine, IMP and GMP are known to be noncompetetive inhibitors [Guddat et al., 2002] of this reaction the equasion can be written as a sum of inhibitors influenses.","Mathematical model links":" ID: Guddat et al., 2002 Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12070315 ;","Parameter set information":" Parameters kcat, KmPRPP and KmGua are taken from article [Guddat et al., 2002]. Parameters kHyp, kXan, kIMP and kGMP were evaluated basing on [Guddat et al., 2002] experimental data. ","Parameter set links":" ID: Guddat et al., 2002 Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12070315 ;","Structural model information":"Hypoxanthine phosphoribosyltransferase catalyzes the reaction guanine and PRPP.","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=GUANPRIBOSYLTRAN-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmGua","value":"0.294"},{"units":"mM","information":"","name":"KmPRPP","value":"0.192"},{"units":"mM","information":"","name":"kGMP","value":"0.526"},{"units":"mM","information":"","name":"kHyp","value":"0.0125"},{"units":"mM","information":"","name":"kIMP","value":"0.247"},{"units":"mM","information":"","name":"kXan","value":"0.025"},{"units":"1/sec","information":"","name":"kcat","value":"10.2"}]},{"scheme":"Hypoxanthine + prpp -> IMP + ppi","substrates":{"s1":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"prpp","type":"substance","synonyms":["5-Phospho-alpha-D-ribose 1-diphosphate","5-Phosphoribosyl 1-pyrophosphate","5-Phosphoribosyl diphosphate","prpp"],"links":[],"id":"SS0000021"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"IMP","type":"substance","synonyms":["5'-IMP","5'-Inosinate","5'-Inosine monophosphate","5'-Inosinic acid","IMP","Inosine 5'-monophosphate","Inosine 5'-phosphate","Inosine monophosphate","Inosinic acid"],"links":[],"id":"SS0000104"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ppi","type":"substance","synonyms":["Diphosphate","PP","ppi","pyrophosphate"],"links":[],"id":"SS0000023"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Hpt","type":"protein","synonyms":["ec:2.4.2.8","Hpt","Hypoxanthine phosphoribosyltransferase"],"links":[],"id":"SS0000412"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"Gua","type":"substance","synonyms":["Gua","Guanosine"],"links":[],"id":"SS0000113"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"Xanthine","type":"substance","synonyms":["Xanthine"],"links":[],"id":"SS0000116"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"IMP","type":"substance","synonyms":["5'-IMP","5'-Inosinate","5'-Inosine monophosphate","5'-Inosinic acid","IMP","Inosine 5'-monophosphate","Inosine 5'-phosphate","Inosine monophosphate","Inosinic acid"],"links":[],"id":"SS0000104"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"GMP","type":"substance","synonyms":["GMP","Guanosine 5'-monophosphate","Guanosine 5'-phosphate","Guanosine monophosphate","Guanylic acid"],"links":[],"id":"SS0000112"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"(kcat*r1*(s1/KmHyp)*s2)/((KmPRPP+s2)*(1+(s1/KmHyp)+(r2/kGua)+(r3/kXan)+(r4/kIMP)+(r5/kGMP)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics. As guanine, xanthine, IMP and GMP are known to be noncompetetive inhibitors [Guddat et al., 2002] of this reaction the equasion can be written as a sum of inhibitors influenses.","Mathematical model links":" ID: Guddat et al., 2002 Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12070315 ;","Parameter set information":" Parameters kcat, KmPRPP and KmHyp are taken from article [Guddat et al., 2002]. Parameters kGua, kXan, kIMP and kGMP were evaluated basing on [Guddat et al., 2002] experimental data. ","Parameter set links":" ID: Guddat et al., 2002 Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12070315 ;","Structural model information":"Hypoxanthine phosphoribosyltransferase catalyzes the reaction hypoxanthine and PRPP.","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=HYPOXANPRIBOSYLTRAN-RXN ;"},"mmid":"MM0000253","psid":"PS0000243","gnid":"GN0000244","reversible":false,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics. As guanine, xanthine, IMP and GMP are known to be noncompetetive inhibitors [Guddat et al., 2002] of this reaction the equasion can be written as a sum of inhibitors influenses.","Mathematical model links":" ID: Guddat et al., 2002 Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12070315 ;","Parameter set information":" Parameters kcat, KmPRPP and KmHyp are taken from article [Guddat et al., 2002]. Parameters kGua, kXan, kIMP and kGMP were evaluated basing on [Guddat et al., 2002] experimental data. ","Parameter set links":" ID: Guddat et al., 2002 Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12070315 ;","Structural model information":"Hypoxanthine phosphoribosyltransferase catalyzes the reaction hypoxanthine and PRPP.","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=HYPOXANPRIBOSYLTRAN-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmHyp","value":"0.0125"},{"units":"mM","information":"","name":"KmPRPP","value":"0.192"},{"units":"mM","information":"","name":"kGMP","value":"0.526"},{"units":"mM","information":"","name":"kGua","value":"0.294"},{"units":"mM","information":"","name":"kIMP","value":"0.247"},{"units":"mM","information":"","name":"kXan","value":"0.025"},{"units":"1/sec","information":"","name":"kcat","value":"59"}]},{"scheme":"Xanthine + prpp -> XMP + ppi","substrates":{"s1":{"theSubstance":{"name":"Xanthine","type":"substance","synonyms":["Xanthine"],"links":[],"id":"SS0000116"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"prpp","type":"substance","synonyms":["5-Phospho-alpha-D-ribose 1-diphosphate","5-Phosphoribosyl 1-pyrophosphate","5-Phosphoribosyl diphosphate","prpp"],"links":[],"id":"SS0000021"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"XMP","type":"substance","synonyms":["(9-D-Ribosylxanthine)-5'-phosphate","Xanthosine 5'-phosphate","Xanthylic acid","XMP"],"links":[],"id":"SS0000109"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ppi","type":"substance","synonyms":["Diphosphate","PP","ppi","pyrophosphate"],"links":[],"id":"SS0000023"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Hpt","type":"protein","synonyms":["ec:2.4.2.8","Hpt","Hypoxanthine phosphoribosyltransferase"],"links":[],"id":"SS0000412"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"G","type":"substance","synonyms":["2-Amino-6-hydroxypurine","G","Guanine"],"links":[],"id":"SS0000114"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"IMP","type":"substance","synonyms":["5'-IMP","5'-Inosinate","5'-Inosine monophosphate","5'-Inosinic acid","IMP","Inosine 5'-monophosphate","Inosine 5'-phosphate","Inosine monophosphate","Inosinic acid"],"links":[],"id":"SS0000104"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"GMP","type":"substance","synonyms":["GMP","Guanosine 5'-monophosphate","Guanosine 5'-phosphate","Guanosine monophosphate","Guanylic acid"],"links":[],"id":"SS0000112"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"(kcat*r1*(s1/KmXan)*s2)/((KmPRPP+s2)*(1+(s1/KmXan)+(r2/kHyp)+(r3/kGua)+(r4/kIMP)+(r5/kGMP)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics. As hypoxanthine, guanine, IMP and GMP are known to be noncompetetive inhibitors [Guddat et al., 2002] of this reaction the equasion can be written as a sum of inhibitors influenses.","Mathematical model links":" ID: Guddat et al., 2002 Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12070315 ;","Parameter set information":" Parameters kcat, KmPRPP and KmXan are taken from article [Guddat et al., 2002]. Parameters kHyp, kGua, kIMP and kGMP were evaluated basing on [Guddat et al., 2002] experimental data. ","Parameter set links":" ID: Guddat et al., 2002 Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12070315 ;","Structural model information":"Hypoxanthine phosphoribosyltransferase catalyzes the reaction xanthine and PRPP.","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=XANPRIBOSYLTRAN-RXN ;"},"mmid":"MM0000254","psid":"PS0000244","gnid":"GN0000245","reversible":false,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics. As hypoxanthine, guanine, IMP and GMP are known to be noncompetetive inhibitors [Guddat et al., 2002] of this reaction the equasion can be written as a sum of inhibitors influenses.","Mathematical model links":" ID: Guddat et al., 2002 Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12070315 ;","Parameter set information":" Parameters kcat, KmPRPP and KmXan are taken from article [Guddat et al., 2002]. Parameters kHyp, kGua, kIMP and kGMP were evaluated basing on [Guddat et al., 2002] experimental data. ","Parameter set links":" ID: Guddat et al., 2002 Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12070315 ;","Structural model information":"Hypoxanthine phosphoribosyltransferase catalyzes the reaction xanthine and PRPP.","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=XANPRIBOSYLTRAN-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmPRPP","value":"0.192"},{"units":"mM","information":"","name":"KmXan","value":"0.025"},{"units":"mM","information":"","name":"kGMP","value":"0.526"},{"units":"mM","information":"","name":"kGua","value":"0.294"},{"units":"mM","information":"","name":"kHyp","value":"0.0125"},{"units":"mM","information":"","name":"kIMP","value":"0.247"},{"units":"1/sec","information":"","name":"kcat","value":"0.008"}]},{"scheme":"Gua + prpp <=> GMP + ppi","substrates":{"s1":{"theSubstance":{"name":"Gua","type":"substance","synonyms":["Gua","Guanosine"],"links":[],"id":"SS0000113"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"prpp","type":"substance","synonyms":["5-Phospho-alpha-D-ribose 1-diphosphate","5-Phosphoribosyl 1-pyrophosphate","5-Phosphoribosyl diphosphate","prpp"],"links":[],"id":"SS0000021"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"GMP","type":"substance","synonyms":["GMP","Guanosine 5'-monophosphate","Guanosine 5'-phosphate","Guanosine monophosphate","Guanylic acid"],"links":[],"id":"SS0000112"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ppi","type":"substance","synonyms":["Diphosphate","PP","ppi","pyrophosphate"],"links":[],"id":"SS0000023"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Gpt","type":"protein","synonyms":["ec:2.4.2.22","GlyD","Gpp","Gpt","Gxu","xanthine-guanine phosphoribosyltransferase"],"links":[],"id":"SS0000268"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"Xanthine","type":"substance","synonyms":["Xanthine"],"links":[],"id":"SS0000116"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"Ura","type":"substance","synonyms":["Ura","Uracil"],"links":[],"id":"SS0000040"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"A","type":"substance","synonyms":["6-Aminopurine","A","Adenine"],"links":[],"id":"SS0000080"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r6":{"theSubstance":{"name":"Thy","type":"substance","synonyms":["5-Methyluracil","Thy","Thymine"],"links":[],"id":"SS0000056"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r7":{"theSubstance":{"name":"IMP","type":"substance","synonyms":["5'-IMP","5'-Inosinate","5'-Inosine monophosphate","5'-Inosinic acid","IMP","Inosine 5'-monophosphate","Inosine 5'-phosphate","Inosine monophosphate","Inosinic acid"],"links":[],"id":"SS0000104"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r8":{"theSubstance":{"name":"XMP","type":"substance","synonyms":["(9-D-Ribosylxanthine)-5'-phosphate","Xanthosine 5'-phosphate","Xanthylic acid","XMP"],"links":[],"id":"SS0000109"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r9":{"theSubstance":{"name":"GMP","type":"substance","synonyms":["GMP","Guanosine 5'-monophosphate","Guanosine 5'-phosphate","Guanosine monophosphate","Guanylic acid"],"links":[],"id":"SS0000112"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"(kcat*r1*(s1/KmGua)*s2)/((KmPRPP+s2)*(1+(s1/KmGua)+(r2/kHyp)+(r3/kXan)+(r4/kUra)+(r5/kAde)+(r6/kThy)+(r7/kIMP)+(r8/kXMP)+(r9/kGMP)))","theSubMathModel":null,"theInformation":{"Mathematical model information":" Reaction follows Michaelis-Menten kinetics. As hypoxanthine, xanthine, uracil, adenine, thymine, IMP, XMP and GMP are known to be noncompetetive inhibitors [Miller et al., 1972; Liu S.W. and Milman G., 1983; Guddat et al., 2002] of this reaction the equasion can be written as a sum of inhibitors influenses. ","Mathematical model links":" ID: Guddat et al., 2002 Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12070315 ; ID: Liu S.W., Milman G., 1983 Purification and characterization of Escherichia coli guanine-xanthine phosphoribosyltransferase produced by a high efficiency expression plasmid utilizing a lambda PL promoter and CI857 temperature-sensitive repressor. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6305942 ; ID: Miller et al., 1972 Guanine phosphoribosyltransferase from Escherichia coli, specificity and properties. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4347700 ;","Parameter set information":"Parameters kcat, KmPRPP and KmGua are taken from article [Guddat et al., 2002]. Parameters kHyp, kXan, kUra, kAde and kThy are taken from article [Miller et al., 1972].Parameters kIMP, kXMP and kGMP were evaluated basing on [Liu S.W. and Milman G., 1983] experimental data.","Parameter set links":" ID: Guddat et al., 2002 Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12070315 ; ID: Liu S.W., Milman G., 1983 Purification and characterization of Escherichia coli guanine-xanthine phosphoribosyltransferase produced by a high efficiency expression plasmid utilizing a lambda PL promoter and CI857 temperature-sensitive repressor. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6305942 ; ID: Miller et al., 1972 Guanine phosphoribosyltransferase from Escherichia coli, specificity and properties. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4347700 ;","Structural model information":"Xanthine-guanine phosphoribosyltransferase catalyzes the reaction guanine and PRPP.","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=GUANPRIBOSYLTRAN-RXN ;"},"mmid":"MM0000255","psid":"PS0000245","gnid":"GN0000246","reversible":true,"information":{"Mathematical model information":" Reaction follows Michaelis-Menten kinetics. As hypoxanthine, xanthine, uracil, adenine, thymine, IMP, XMP and GMP are known to be noncompetetive inhibitors [Miller et al., 1972; Liu S.W. and Milman G., 1983; Guddat et al., 2002] of this reaction the equasion can be written as a sum of inhibitors influenses. ","Mathematical model links":" ID: Guddat et al., 2002 Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12070315 ; ID: Liu S.W., Milman G., 1983 Purification and characterization of Escherichia coli guanine-xanthine phosphoribosyltransferase produced by a high efficiency expression plasmid utilizing a lambda PL promoter and CI857 temperature-sensitive repressor. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6305942 ; ID: Miller et al., 1972 Guanine phosphoribosyltransferase from Escherichia coli, specificity and properties. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4347700 ;","Parameter set information":"Parameters kcat, KmPRPP and KmGua are taken from article [Guddat et al., 2002]. Parameters kHyp, kXan, kUra, kAde and kThy are taken from article [Miller et al., 1972].Parameters kIMP, kXMP and kGMP were evaluated basing on [Liu S.W. and Milman G., 1983] experimental data.","Parameter set links":" ID: Guddat et al., 2002 Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12070315 ; ID: Liu S.W., Milman G., 1983 Purification and characterization of Escherichia coli guanine-xanthine phosphoribosyltransferase produced by a high efficiency expression plasmid utilizing a lambda PL promoter and CI857 temperature-sensitive repressor. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6305942 ; ID: Miller et al., 1972 Guanine phosphoribosyltransferase from Escherichia coli, specificity and properties. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4347700 ;","Structural model information":"Xanthine-guanine phosphoribosyltransferase catalyzes the reaction guanine and PRPP.","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=GUANPRIBOSYLTRAN-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmGua","value":"0.0043"},{"units":"mM","information":"","name":"KmPRPP","value":"0.139"},{"units":"mM","information":"","name":"kAde","value":"1"},{"units":"mM","information":"","name":"kGMP","value":"0.03037"},{"units":"mM","information":"","name":"kHyp","value":"0.18"},{"units":"mM","information":"","name":"kIMP","value":"0.598"},{"units":"mM","information":"","name":"kThy","value":"1"},{"units":"mM","information":"","name":"kUra","value":"1"},{"units":"mM","information":"","name":"kXMP","value":"0.224"},{"units":"mM","information":"","name":"kXan","value":"0.048"},{"units":"1/sec","information":"","name":"kcat","value":"28"}]},{"scheme":"Hypoxanthine + prpp -> IMP + ppi","substrates":{"s1":{"theSubstance":{"name":"Hypoxanthine","type":"substance","synonyms":["Hypoxanthine","Purine-6-ol"],"links":[],"id":"SS0000106"},"theState":null,"compartment":""},"s2":{"theSubstance":{"name":"prpp","type":"substance","synonyms":["5-Phospho-alpha-D-ribose 1-diphosphate","5-Phosphoribosyl 1-pyrophosphate","5-Phosphoribosyl diphosphate","prpp"],"links":[],"id":"SS0000021"},"theState":null,"compartment":""}},"products":{"p1":{"theSubstance":{"name":"IMP","type":"substance","synonyms":["5'-IMP","5'-Inosinate","5'-Inosine monophosphate","5'-Inosinic acid","IMP","Inosine 5'-monophosphate","Inosine 5'-phosphate","Inosine monophosphate","Inosinic acid"],"links":[],"id":"SS0000104"},"theState":null,"compartment":""},"p2":{"theSubstance":{"name":"ppi","type":"substance","synonyms":["Diphosphate","PP","ppi","pyrophosphate"],"links":[],"id":"SS0000023"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"Gpt","type":"protein","synonyms":["ec:2.4.2.22","GlyD","Gpp","Gpt","Gxu","xanthine-guanine phosphoribosyltransferase"],"links":[],"id":"SS0000268"},"theState":null,"compartment":"","theInfluence":"enzyme"},"r2":{"theSubstance":{"name":"Gua","type":"substance","synonyms":["Gua","Guanosine"],"links":[],"id":"SS0000113"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r3":{"theSubstance":{"name":"Xanthine","type":"substance","synonyms":["Xanthine"],"links":[],"id":"SS0000116"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r4":{"theSubstance":{"name":"Ura","type":"substance","synonyms":["Ura","Uracil"],"links":[],"id":"SS0000040"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r5":{"theSubstance":{"name":"A","type":"substance","synonyms":["6-Aminopurine","A","Adenine"],"links":[],"id":"SS0000080"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r6":{"theSubstance":{"name":"Thy","type":"substance","synonyms":["5-Methyluracil","Thy","Thymine"],"links":[],"id":"SS0000056"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r7":{"theSubstance":{"name":"IMP","type":"substance","synonyms":["5'-IMP","5'-Inosinate","5'-Inosine monophosphate","5'-Inosinic acid","IMP","Inosine 5'-monophosphate","Inosine 5'-phosphate","Inosine monophosphate","Inosinic acid"],"links":[],"id":"SS0000104"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r8":{"theSubstance":{"name":"XMP","type":"substance","synonyms":["(9-D-Ribosylxanthine)-5'-phosphate","Xanthosine 5'-phosphate","Xanthylic acid","XMP"],"links":[],"id":"SS0000109"},"theState":null,"compartment":"","theInfluence":"inhibitor"},"r9":{"theSubstance":{"name":"GMP","type":"substance","synonyms":["GMP","Guanosine 5'-monophosphate","Guanosine 5'-phosphate","Guanosine monophosphate","Guanylic acid"],"links":[],"id":"SS0000112"},"theState":null,"compartment":"","theInfluence":"inhibitor"}},"theMathModel":"(kcat*r1*(s1/KmHyp)*s2)/((KmPRPP+s2)*(1+(s1/KmHyp)+(r2/kGua)+(r3/kXan)+(r4/kUra)+(r5/kAde)+(r6/kThy)+(r7/kIMP)+(r8/kXMP)+(r9/kGMP)))","theSubMathModel":null,"theInformation":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics. As guanine, xanthine, uracil, adenine, thymine, IMP, XMP and GMP are known to be noncompetetive inhibitors [Miller et al., 1972; Liu S.W. and Milman G., 1983; Guddat et al., 2002] of this reaction the equasion can be written as a sum of inhibitors influenses.","Mathematical model links":" ID: Guddat et al., 2002 Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12070315 ; ID: Liu S.W., Milman G., 1983 Purification and characterization of Escherichia coli guanine-xanthine phosphoribosyltransferase produced by a high efficiency expression plasmid utilizing a lambda PL promoter and CI857 temperature-sensitive repressor. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6305942 ; ID: Miller et al., 1972 Guanine phosphoribosyltransferase from Escherichia coli, specificity and properties. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4347700 ;","Parameter set information":"Parameters kcat, KmPRPP and KmHyp are taken from article [Guddat et al., 2002]. Parameters kGua, kXan, kUra, kAde and kThy are taken from article [Miller et al., 1972].Parameters kIMP, kXMP and kGMP were evaluated basing on [Liu S.W. and Milman G., 1983] experimental data.","Parameter set links":" ID: Guddat et al., 2002 Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12070315 ; ID: Liu S.W., Milman G., 1983 Purification and characterization of Escherichia coli guanine-xanthine phosphoribosyltransferase produced by a high efficiency expression plasmid utilizing a lambda PL promoter and CI857 temperature-sensitive repressor. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6305942 ; ID: Miller et al., 1972 Guanine phosphoribosyltransferase from Escherichia coli, specificity and properties. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4347700 ;","Structural model information":"Xanthine-guanine phosphoribosyltransferase catalyzes the reaction hypoxanthine and PRPP.","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=HYPOXANPRIBOSYLTRAN-RXN ;"},"mmid":"MM0000256","psid":"PS0000246","gnid":"GN0000247","reversible":false,"information":{"Mathematical model information":"Reaction follows Michaelis-Menten kinetics. As guanine, xanthine, uracil, adenine, thymine, IMP, XMP and GMP are known to be noncompetetive inhibitors [Miller et al., 1972; Liu S.W. and Milman G., 1983; Guddat et al., 2002] of this reaction the equasion can be written as a sum of inhibitors influenses.","Mathematical model links":" ID: Guddat et al., 2002 Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12070315 ; ID: Liu S.W., Milman G., 1983 Purification and characterization of Escherichia coli guanine-xanthine phosphoribosyltransferase produced by a high efficiency expression plasmid utilizing a lambda PL promoter and CI857 temperature-sensitive repressor. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6305942 ; ID: Miller et al., 1972 Guanine phosphoribosyltransferase from Escherichia coli, specificity and properties. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4347700 ;","Parameter set information":"Parameters kcat, KmPRPP and KmHyp are taken from article [Guddat et al., 2002]. Parameters kGua, kXan, kUra, kAde and kThy are taken from article [Miller et al., 1972].Parameters kIMP, kXMP and kGMP were evaluated basing on [Liu S.W. and Milman G., 1983] experimental data.","Parameter set links":" ID: Guddat et al., 2002 Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/12070315 ; ID: Liu S.W., Milman G., 1983 Purification and characterization of Escherichia coli guanine-xanthine phosphoribosyltransferase produced by a high efficiency expression plasmid utilizing a lambda PL promoter and CI857 temperature-sensitive repressor. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/6305942 ; ID: Miller et al., 1972 Guanine phosphoribosyltransferase from Escherichia coli, specificity and properties. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/4347700 ;","Structural model information":"Xanthine-guanine phosphoribosyltransferase catalyzes the reaction hypoxanthine and PRPP.","Structural model links":" ID: EcoCyc ; Value:http://ecocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=HYPOXANPRIBOSYLTRAN-RXN ;"},"parameters":[{"units":"mM","information":"","name":"KmHyp","value":"0.0908"},{"units":"mM","information":"","name":"KmPRPP","value":"0.139"},{"units":"mM","information":"","name":"kAde","value":"1"},{"units":"mM","information":"","name":"kGMP","value":"0.03037"},{"units":"mM","information":"","name":"kGua","value":"0.0027"},{"units":"mM","information":"","name":"kIMP","value":"0.598"},{"units":"mM","information":"","name":"kThy","value":"1"},{"units":"mM","information":"","name":"kUra","value":"1"},{"units":"mM","information":"","name":"kXMP","value":"0.224"},{"units":"mM","information":"","name":"kXan","value":"0.048"},{"units":"1/sec","information":"","name":"kcat","value":"13.7"}]},{"scheme":"-> NrfA","substrates":null,"products":{"p1":{"theSubstance":{"name":"NrfA","type":"protein","synonyms":["aeg-93","EC:1.7.2.2","NrfA","periplasmic cytochrome c nitrite reductase"],"links":[],"id":"SS0000150"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"nrfA","type":"gene","synonyms":["b4070","b4071","b4072","b4073","nrfA","nrfB","nrfC","nrfD"],"links":[],"id":"SS0000149"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"NO3","type":"substance","synonyms":["nitrate","NO3","NO3-"],"links":[],"id":"SS0000016"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"NO2","type":"substance","synonyms":["nitrite","NO2","NO2-"],"links":[],"id":"SS0000017"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"k1*( (((k2+(r3/k3)^k4)*(1+k5*(r3/k6)^k7+k8*(r3/k9)^k10)+k14*(r2/k15)^k16+k17*(r2/k18)^k19)/ ((1+(r3/k3)^k4)*(1+(r3/k6)^k7+(r3/k9)^k10+(r2/k15)^k16+(r2/k18)^k19)))*((1+k11*(r3/k12)^k13)/(1+(r3/k12)^k13))*((1+k20*(r2/k21)^k22)/(1+(r2/k21)^k22))) ","theSubMathModel":null,"theInformation":{"Mathematical model information":"Expression of nrf operon is increased if nitrite and/or nitrate are presented in environment. Both nitrate and nitrite act via NarP and NarL transcription factors. As nitrite cause changing in nrf expression in NarPL double mutant the formula includes the first term of nitrite influence on nrf expression characterizing basal response of protein production on nitrite. NarP and NarL compete for activation sites (appropriate terms in the formula are summing up) while NarL inhibition site is located far from activation sites. NarP and NarL transcriptional factors induced by nitrate and nitrite  compete with each other. The detailed description of enzyme formation submodel was given in the article [Khlebodarova et al., 2016].","Mathematical model links":" ID: Khlebodarova T.M. et al., 2016 On the control mechanisms of the nitrite level in Escherichia coli cells: the mathematical model. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/26823079 ;","Parameter set information":"There is no experimental data for k1. Other parameters were adaptated for nrf expression data with NarP and NarL mutants and wild type when nitrate or nitrite are added in the environment [Wang et al., 2000].","Parameter set links":" ID: Wang et al., 2000 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11004182 ;","Structural model information":"NrfA expression is activated by nitrate and more slightly by nitrite.","Structural model links":" ID: Wang et al., 2000. The nrfA and nirB nitrite reductase operons in Escherichia coli are expressed differently in response to nitrate than to nitrite. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11004182 ;"},"mmid":"MM0000257","psid":"PS0000247","gnid":"GN0000142","reversible":false,"information":{"Mathematical model information":"Expression of nrf operon is increased if nitrite and/or nitrate are presented in environment. Both nitrate and nitrite act via NarP and NarL transcription factors. As nitrite cause changing in nrf expression in NarPL double mutant the formula includes the first term of nitrite influence on nrf expression characterizing basal response of protein production on nitrite. NarP and NarL compete for activation sites (appropriate terms in the formula are summing up) while NarL inhibition site is located far from activation sites. NarP and NarL transcriptional factors induced by nitrate and nitrite  compete with each other. The detailed description of enzyme formation submodel was given in the article [Khlebodarova et al., 2016].","Mathematical model links":" ID: Khlebodarova T.M. et al., 2016 On the control mechanisms of the nitrite level in Escherichia coli cells: the mathematical model. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/26823079 ;","Parameter set information":"There is no experimental data for k1. Other parameters were adaptated for nrf expression data with NarP and NarL mutants and wild type when nitrate or nitrite are added in the environment [Wang et al., 2000].","Parameter set links":" ID: Wang et al., 2000 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11004182 ;","Structural model information":"NrfA expression is activated by nitrate and more slightly by nitrite.","Structural model links":" ID: Wang et al., 2000. The nrfA and nirB nitrite reductase operons in Escherichia coli are expressed differently in response to nitrate than to nitrite. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11004182 ;"},"parameters":[{"units":"mM/s","information":"","name":"k1","value":"1"},{"units":"","information":"","name":"k10","value":"4"},{"units":"","information":"","name":"k11","value":"0.15"},{"units":"mM","information":"","name":"k12","value":"2.5"},{"units":"","information":"","name":"k13","value":"4"},{"units":"","information":"","name":"k14","value":"5.3"},{"units":"mM","information":"","name":"k15","value":"0.4"},{"units":"","information":"","name":"k16","value":"2"},{"units":"","information":"","name":"k17","value":"9"},{"units":"mM","information":"","name":"k18","value":"0.5"},{"units":"","information":"","name":"k19","value":"1.3"},{"units":"","information":"","name":"k2","value":"0.182"},{"units":"","information":"","name":"k20","value":"0.08"},{"units":"mM","information":"","name":"k21","value":"1.2"},{"units":"","information":"","name":"k22","value":"1.7"},{"units":"mM","information":"","name":"k3","value":"0.35"},{"units":"","information":"","name":"k4","value":"2"},{"units":"","information":"","name":"k5","value":"5.5"},{"units":"mM","information":"","name":"k6","value":"1"},{"units":"","information":"","name":"k7","value":"2"},{"units":"","information":"","name":"k8","value":"12"},{"units":"mM","information":"","name":"k9","value":"1.5"}]},{"scheme":"-> NirB","substrates":null,"products":{"p1":{"theSubstance":{"name":"NirB","type":"protein","synonyms":["EC:1.7.1.4","NADH:nitrite oxidoreductase","NirB","nitrite reductase NADH"],"links":[],"id":"SS0000151"},"theState":null,"compartment":""}},"regulators":{"r1":{"theSubstance":{"name":"nirB","type":"gene","synonyms":["b3365","b3366","nirB","nirD"],"links":[],"id":"SS0000205"},"theState":null,"compartment":"","theInfluence":""},"r2":{"theSubstance":{"name":"NO3","type":"substance","synonyms":["nitrate","NO3","NO3-"],"links":[],"id":"SS0000016"},"theState":null,"compartment":"","theInfluence":"activator"},"r3":{"theSubstance":{"name":"NO2","type":"substance","synonyms":["nitrite","NO2","NO2-"],"links":[],"id":"SS0000017"},"theState":null,"compartment":"","theInfluence":"activator"}},"theMathModel":"ks*((k0+ omP_no2*(r3/KmsP_no2)^nP_no2 + omL_no2*(r3/KmsL_no2)^nL_no2 +     omL_no3*(r2/(( (1 + omi*(r2/kmi))/((1 + r2/kmi)))*KmsL_no3))^nL_no3 +     omP_no3*(r2/KmsP_no3)^nP_no3)/(1 + (r3/KmsP_no2)^nP_no2 +     (r3/KmsL_no2)^nL_no2 + (r2/((1 + omi*(r2/kmi))/((1 + r2/kmi))*KmsL_no3))^nL_no3 +     (r2/KmsP_no3)^nP_no3)) ","theSubMathModel":null,"theInformation":{"Mathematical model information":"The maximum nirB expression is achieved at high nitrate concentrations through the proteins NarL and NarP, which function independently of each other (therefore summing was used for appropriate terms describing activation by NarP and NarL factors), but NarL appears to be the main activator. The nitrite is a less effective inductor of nirB expression. NarP antagonized NarL activation of nir expression when nitrate was present [Wang et al., 2000], thus in the model KmsL_no3 is multiplied by twiddle factor of inhibition. The detailed description of enzyme formation submodel was given in the article [Khlebodarova et al., 2016].","Mathematical model links":" ID: Khlebodarova T.M. et al., 2016 On the control mechanisms of the nitrite level in Escherichia coli cells: the mathematical model. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/26823079 ;","Parameter set information":"There is no experimental data for k1. Other parameters were adaptated for nir expression data for NarP and NarL mutants and wild type strain when nitrate or nitrite are added in the environment [Wang et al., 2000].","Parameter set links":" ID: Wang et al., 2000 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11004182 ;","Structural model information":"NirB operon expression is induced only by high nitrate conditions and more slightly by nitrite.","Structural model links":" ID: Wang et al., 2000. The nrfA and nirB nitrite reductase operons in Escherichia coli are expressed differently in response to nitrate than to nitrite. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11004182 ;"},"mmid":"MM0000258","psid":"PS0000248","gnid":"GN0000118","reversible":false,"information":{"Mathematical model information":"The maximum nirB expression is achieved at high nitrate concentrations through the proteins NarL and NarP, which function independently of each other (therefore summing was used for appropriate terms describing activation by NarP and NarL factors), but NarL appears to be the main activator. The nitrite is a less effective inductor of nirB expression. NarP antagonized NarL activation of nir expression when nitrate was present [Wang et al., 2000], thus in the model KmsL_no3 is multiplied by twiddle factor of inhibition. The detailed description of enzyme formation submodel was given in the article [Khlebodarova et al., 2016].","Mathematical model links":" ID: Khlebodarova T.M. et al., 2016 On the control mechanisms of the nitrite level in Escherichia coli cells: the mathematical model. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/26823079 ;","Parameter set information":"There is no experimental data for k1. Other parameters were adaptated for nir expression data for NarP and NarL mutants and wild type strain when nitrate or nitrite are added in the environment [Wang et al., 2000].","Parameter set links":" ID: Wang et al., 2000 ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11004182 ;","Structural model information":"NirB operon expression is induced only by high nitrate conditions and more slightly by nitrite.","Structural model links":" ID: Wang et al., 2000. The nrfA and nirB nitrite reductase operons in Escherichia coli are expressed differently in response to nitrate than to nitrite. ; Value:http://www.ncbi.nlm.nih.gov/pubmed/11004182 ;"},"parameters":[{"units":"mM","information":"","name":"KmsL_no2","value":"1.5"},{"units":"mM","information":"","name":"KmsL_no3","value":"0.3"},{"units":"mM","information":"","name":"KmsP_no2","value":"1.3"},{"units":"mM","information":"","name":"KmsP_no3","value":"1.6"},{"units":"","information":"","name":"k0","value":"0.041"},{"units":"mM","information":"","name":"kmi","value":"0.4"},{"units":"mM/s","information":"","name":"ks","value":"1"},{"units":"","information":"","name":"nL_no2","value":"4.7"},{"units":"","information":"","name":"nL_no3","value":"3.7"},{"units":"","information":"","name":"nP_no2","value":"2"},{"units":"","information":"","name":"nP_no3","value":"2.8"},{"units":"","information":"","name":"omL_no2","value":"0.8"},{"units":"","information":"","name":"omL_no3","value":"1.05"},{"units":"","information":"","name":"omP_no2","value":"0.45"},{"units":"","information":"","name":"omP_no3","value":"0.78"},{"units":"","information":"","name":"omi","value":"3.5"}]}]