2.0 2012-05-31 13:03:06 -0600 2015-06-03 15:53:39 -0600 ECMDB00998 M2MDB000219 dCTP Deoxycytidine triphosphate (dCTP) is a cytidine nucleotide triphosphate that is used whenever DNA is synthesized, such as in the polymerase chain reaction. e.g.: 2'-Deoxycytidine-5'-triphosphate 2'-Deoxycytidine-5'-triphosphoric acid DCTP Deoxy-CTP Deoxycytidine-triphosphate Deoxycytidine-triphosphoric acid C9H16N3O13P3 467.1569 466.989597149 ({[({[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acid dCTP 2056-98-6 NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)O1 InChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1 RGWHQCVHVJXOKC-SHYZEUOFSA-N Solid Cytosol logp -0.52 ALOGPS logs -1.60 ALOGPS solubility 1.18e+01 g/l ALOGPS logp -3.3 ChemAxon pka_strongest_acidic 0.99 ChemAxon pka_strongest_basic 0.21 ChemAxon iupac ({[({[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acid ChemAxon average_mass 467.1569 ChemAxon mono_mass 466.989597149 ChemAxon smiles NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)O1 ChemAxon formula C9H16N3O13P3 ChemAxon inchi InChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1 ChemAxon inchikey RGWHQCVHVJXOKC-SHYZEUOFSA-N ChemAxon polar_surface_area 247.97 ChemAxon refractivity 85.65 ChemAxon polarizability 35.21 ChemAxon rotatable_bond_count 8 ChemAxon acceptor_count 12 ChemAxon donor_count 6 ChemAxon physiological_charge -3 ChemAxon formal_charge 0 ChemAxon Pyrimidine metabolism The metabolism of pyrimidines begins with L-glutamine interacting with water molecule and a hydrogen carbonate through an ATP driven carbamoyl phosphate synthetase resulting in a hydrogen ion, an ADP, a phosphate, an L-glutamic acid and a carbamoyl phosphate. The latter compound interacts with an L-aspartic acid through a aspartate transcarbamylase resulting in a phosphate, a hydrogen ion and a N-carbamoyl-L-aspartate. The latter compound interacts with a hydrogen ion through a dihydroorotase resulting in the release of a water molecule and a 4,5-dihydroorotic acid. This compound interacts with an ubiquinone-1 through a dihydroorotate dehydrogenase, type 2 resulting in a release of an ubiquinol-1 and an orotic acid. The orotic acid then interacts with a phosphoribosyl pyrophosphate through a orotate phosphoribosyltransferase resulting in a pyrophosphate and an orotidylic acid. The latter compound then interacts with a hydrogen ion through an orotidine-5 '-phosphate decarboxylase, resulting in an release of carbon dioxide and an Uridine 5' monophosphate. The Uridine 5' monophosphate process to get phosphorylated by an ATP driven UMP kinase resulting in the release of an ADP and an Uridine 5--diphosphate. Uridine 5-diphosphate can be metabolized in multiple ways in order to produce a Deoxyuridine triphosphate. 1.-Uridine 5-diphosphate interacts with a reduced thioredoxin through a ribonucleoside diphosphate reductase 1 resulting in the release of a water molecule and an oxidized thioredoxin and an dUDP. The dUDP is then phosphorylated by an ATP through a nucleoside diphosphate kinase resulting in the release of an ADP and a DeoxyUridine triphosphate. 2.-Uridine 5-diphosphate interacts with a reduced NrdH glutaredoxin-like protein through a Ribonucleoside-diphosphate reductase 1 resulting in a release of a water molecule, an oxidized NrdH glutaredoxin-like protein and a dUDP. The dUDP is then phosphorylated by an ATP through a nucleoside diphosphate kinase resulting in the release of an ADP and a DeoxyUridine triphosphate. 3.-Uridine 5-diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and an Uridinetriphosphate. The latter compound interacts with a reduced flavodoxin through ribonucleoside-triphosphate reductase resulting in the release of an oxidized flavodoxin, a water molecule and a Deoxyuridine triphosphate 4.-Uridine 5-diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and an Uridinetriphosphate The uridine triphosphate interacts with a L-glutamine and a water molecule through an ATP driven CTP synthase resulting in an ADP, a phosphate, a hydrogen ion, an L-glutamic acid and a cytidine triphosphate. The cytidine triphosphate interacts with a reduced flavodoxin through a ribonucleoside-triphosphate reductase resulting in the release of a water molecule, an oxidized flavodoxin and a dCTP. The dCTP interacts with a water molecule and a hydrogen ion through a dCTP deaminase resulting in a release of an ammonium molecule and a Deoxyuridine triphosphate. 5.-Uridine 5-diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and an Uridinetriphosphate The uridine triphosphate interacts with a L-glutamine and a water molecule through an ATP driven CTP synthase resulting in an ADP, a phosphate, a hydrogen ion, an L-glutamic acid and a cytidine triphosphate. The cytidine triphosphate then interacts spontaneously with a water molecule resulting in the release of a phosphate, a hydrogen ion and a CDP. The CDP then interacts with a reduced NrdH glutaredoxin-like protein through a ribonucleoside-diphosphate reductase 2 resulting in the release of a water molecule, an oxidized NrdH glutaredoxin-like protein and a dCDP. The dCDP is then phosphorylated through an ATP driven nucleoside diphosphate kinase resulting in an ADP and a dCTP. The dCTP interacts with a water molecule and a hydrogen ion through a dCTP deaminase resulting in a release of an ammonium molecule and a Deoxyuridine triphosphate. 6.-Uridine 5-diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and an Uridinetriphosphate The uridine triphosphate interacts with a L-glutamine and a water molecule through an ATP driven CTP synthase resulting in an ADP, a phosphate, a hydrogen ion, an L-glutamic acid and a cytidine triphosphate. The cytidine triphosphate then interacts spontaneously with a water molecule resulting in the release of a phosphate, a hydrogen ion and a CDP. The CDP interacts with a reduced thioredoxin through a ribonucleoside diphosphate reductase 1 resulting in a release of a water molecule, an oxidized thioredoxin and a dCDP. The dCDP is then phosphorylated through an ATP driven nucleoside diphosphate kinase resulting in an ADP and a dCTP. The dCTP interacts with a water molecule and a hydrogen ion through a dCTP deaminase resulting in a release of an ammonium molecule and a Deoxyuridine triphosphate. The deoxyuridine triphosphate then interacts with a water molecule through a nucleoside triphosphate pyrophosphohydrolase resulting in a release of a hydrogen ion, a phosphate and a dUMP. The dUMP then interacts with a methenyltetrahydrofolate through a thymidylate synthase resulting in a dihydrofolic acid and a 5-thymidylic acid. Then 5-thymidylic acid is then phosphorylated through a nucleoside diphosphate kinase resulting in the release of an ADP and thymidine 5'-triphosphate. PW000942 ec00240 Metabolic Metabolic pathways eco01100 salvage pathways of pyrimidine deoxyribonucleotides The pathway begins with the introduction of deoxycytidine into the cytosol, either through a nupG symporter or a nupC symporter. Once inside it is deaminated when reacting with a water molecule, a hydrogen ion and a deoxycytidine deaminase resulting in the release of an ammonium and a deoxyuridine. Deoxyuridine can also be imported through a nupG symporter or a nupC symporter. Deoxyuridine can react with an ATP through a deoxyuridine kinase resulting in the release of a ADP , a hydrogen ion and a dUMP. Deoxyuridine can also react with a phosphate through a uracil phosphorylase resulting in the release of a uracil and a deoxy-alpha-D-ribose 1-phosphate. This compound in turn reacts with a thymine through a thymidine phosphorylase resulting in the release of a phosphate and a thymidine. Thymidine in turn reacts with an ATP through a thymidine kinase resulting in a release of an ADP, a hydrogen ion and a dTMP PW002061 Metabolic pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis I PWY0-166 Specdb::CMs 25420 Specdb::CMs 32115 Specdb::CMs 37883 Specdb::CMs 99639 Specdb::CMs 164201 Specdb::CMs 1083213 Specdb::CMs 1083214 Specdb::CMs 1083215 Specdb::CMs 1083216 Specdb::CMs 1083217 Specdb::CMs 1083218 Specdb::CMs 1083219 Specdb::CMs 1083220 Specdb::CMs 1083221 Specdb::NmrOneD 8202 Specdb::NmrOneD 8203 Specdb::NmrOneD 8204 Specdb::NmrOneD 8205 Specdb::NmrOneD 8206 Specdb::NmrOneD 8207 Specdb::NmrOneD 8208 Specdb::NmrOneD 8209 Specdb::NmrOneD 8210 Specdb::NmrOneD 8211 Specdb::NmrOneD 8212 Specdb::NmrOneD 8213 Specdb::NmrOneD 8214 Specdb::NmrOneD 8215 Specdb::NmrOneD 8216 Specdb::NmrOneD 8217 Specdb::NmrOneD 8218 Specdb::NmrOneD 8219 Specdb::NmrOneD 8220 Specdb::NmrOneD 8221 Specdb::MsMs 26102 Specdb::MsMs 26103 Specdb::MsMs 26104 Specdb::MsMs 32660 Specdb::MsMs 32661 Specdb::MsMs 32662 Specdb::MsMs 1471668 Specdb::MsMs 1471669 Specdb::MsMs 1471670 Specdb::MsMs 1471671 Specdb::MsMs 1471672 Specdb::MsMs 1471673 Specdb::MsMs 1471674 Specdb::MsMs 1471675 Specdb::MsMs 1471676 Specdb::MsMs 1471677 Specdb::MsMs 1471678 Specdb::MsMs 1471679 Specdb::MsMs 1471680 Specdb::MsMs 1471681 Specdb::MsMs 1471682 Specdb::MsMs 1473423 Specdb::MsMs 1473424 Specdb::MsMs 1475467 Specdb::MsMs 1475468 HMDB00998 625 58601 C00458 DCTP DCP dCTP Keseler, I. 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DNA polymerase I P00582 DPO1_ECOLI polA http://ecmdb.ca/proteins/P00582.xml DNA polymerase III subunit epsilon P03007 DPO3E_ECOLI dnaQ http://ecmdb.ca/proteins/P03007.xml DNA polymerase III subunit tau P06710 DPO3X_ECOLI dnaX http://ecmdb.ca/proteins/P06710.xml Nucleoside diphosphate kinase P0A763 NDK_ECOLI ndk http://ecmdb.ca/proteins/P0A763.xml Uridine kinase P0A8F4 URK_ECOLI udk http://ecmdb.ca/proteins/P0A8F4.xml DNA polymerase III subunit beta P0A988 DPO3B_ECOLI dnaN http://ecmdb.ca/proteins/P0A988.xml Anaerobic ribonucleoside-triphosphate reductase-activating protein P0A9N8 NRDG_ECOLI nrdG http://ecmdb.ca/proteins/P0A9N8.xml DNA polymerase III subunit theta P0ABS8 HOLE_ECOLI holE http://ecmdb.ca/proteins/P0ABS8.xml Protein mazG P0AEY3 MAZG_ECOLI mazG http://ecmdb.ca/proteins/P0AEY3.xml DNA polymerase III subunit alpha P10443 DPO3A_ECOLI dnaE http://ecmdb.ca/proteins/P10443.xml Deoxycytidine triphosphate deaminase P28248 DCD_ECOLI dcd http://ecmdb.ca/proteins/P28248.xml DNA polymerase III subunit delta P28630 HOLA_ECOLI holA http://ecmdb.ca/proteins/P28630.xml DNA polymerase III subunit delta' P28631 HOLB_ECOLI holB http://ecmdb.ca/proteins/P28631.xml DNA polymerase III subunit psi P28632 HOLD_ECOLI holD http://ecmdb.ca/proteins/P28632.xml Ferredoxin--NADP reductase P28861 FENR_ECOLI fpr http://ecmdb.ca/proteins/P28861.xml Anaerobic ribonucleoside-triphosphate reductase P28903 NRDD_ECOLI nrdD http://ecmdb.ca/proteins/P28903.xml DNA polymerase III subunit chi P28905 HOLC_ECOLI holC http://ecmdb.ca/proteins/P28905.xml Nucleoside triphosphatase nudI P52006 NUDI_ECOLI nudI http://ecmdb.ca/proteins/P52006.xml Adenylate kinase P69441 KAD_ECOLI adk http://ecmdb.ca/proteins/P69441.xml CTP pyrophosphohydrolase P77788 NUDG_ECOLI nudG http://ecmdb.ca/proteins/P77788.xml Flavodoxin-2 P0ABY4 FLAW_ECOLI fldB http://ecmdb.ca/proteins/P0ABY4.xml Flavodoxin-1 P61949 FLAV_ECOLI fldA http://ecmdb.ca/proteins/P61949.xml Nucleoside diphosphate kinase P0A763 NDK_ECOLI ndk http://ecmdb.ca/proteins/P0A763.xml Cytidine triphosphate + 2 Flavodoxin reduced + 2 Hydrogen ion > dCTP +2 flavodoxin semi oxidized + Water Adenosine triphosphate + dCDP <> ADP + dCTP R02326 DCDPKIN-RXN dCTP + Water > dCMP + Hydrogen ion + Pyrophosphate DCTP-PYROPHOSPHATASE-RXN dCTP + Hydrogen ion + Water > Deoxyuridine triphosphate + Ammonium dCTP + DNA <> Pyrophosphate + DNA R00377 dCTP + Thioredoxin disulfide + Water <> Cytidine triphosphate + Thioredoxin R02022 dCTP + Water <> Deoxyuridine triphosphate + Ammonia R02325 dCTP + Uridine <> dCDP + Uridine 5'-monophosphate R02327 dCTP + Cytidine <> dCDP + Cytidine monophosphate R02371 dCDP + Adenosine triphosphate > dCTP + ADP DCDPKIN-RXN Water + dCTP > Ammonia + Deoxyuridine triphosphate R02325 DCTP-DEAM-RXN Cytidine triphosphate + Water + dCTP <> Cytidine monophosphate + Pyrophosphate + dCMP R00515 dCDP + Adenosine triphosphate > Adenosine diphosphate + dCTP + ADP PW_R003536 Cytidine triphosphate + a reduced flavodoxin > Water + an oxidized flavodoxin + dCTP PW_R003542 Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glucose Shake flask and filter culture 34.5 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 138000 0 Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. 19561621 48 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, 45 mM (NH4)2SO4, supplemented with 1 mM MgSO4, 1 mg/l thiamine·HCl, 5.6 mg/l CaCl2, 8 mg/l FeCl3, 1 mg/l MnCl2·4H2O, 1.7 mg/l ZnCl2, 0.43 mg/l CuCl2·2H2O, 0.6 mg/l CoCl2·2H2O and 0.6 mg/l Na2MoO4·2H2O. 4 g/L Gluco Bioreactor, pH controlled, O2 and CO2 controlled, dilution rate: 0.2/h 17.0 uM 0.0 37 oC BW25113 Stationary Phase, glucose limited 68000 0 Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Ho, P. Y., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, Y., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H., Tomita, M. (2007). "Multiple high-throughput analyses monitor the response of E. coli to perturbations." Science 316:593-597. 17379776