2.02012-05-31 13:48:09 -06002015-06-03 15:53:52 -0600ECMDB01245M2MDB000307dCDPdCDP or Deoxycytidine 5'-diphosphate (dCDP) is a nucleoside diphosphate. It is related to the common nucleic acid CTP, or cytidine triphosphate, with the -OH (hydroxyl) group on the 2' carbon on the nucleotide's pentose removed (hence the deoxy- part of the name), and with one fewer phosphoryl group than CTP .dCDP is a product and competitive inhibitor of ribonucleoside-diphosphate reductase (EC 1.17.4.1) from Escherichia coli. Structural studies indicate the base is in anti conformation and the sugar in S-type puckering, when bound either to the complete enzyme complex or to the large protein subunit alone. [PMID: 8019775] Ribonucleoside-diphosphate reductase is very tightly controlled by a variety of allosteric effectors. The enzyme has different regions of it that act differently on allosteric regulators. At the activity site, dATP is a general inhibitor for all substrates and ATP is an activator. Binding of nucleotides at the specificity site further controls the activity of the enzyme towards different substrates in order to maintain an appropriate balance of all deoxynucleotides for DNA synthesis. The dNDPs produced by the enzyme are then phosphorylated to dNTPs by kinases.2'-Deoxy-Cytidine 5'-pyrophosphate2'-Deoxy-cytidine 5'-pyrophosphoric acid2'-Deoxy-Cytidine pyrophosphate2'-Deoxy-cytidine pyrophosphoric acid2'-Deoxycytidine 5'-(trihydrogen diphosphate)2'-Deoxycytidine 5'-(trihydrogen diphosphoric acid)2'-Deoxycytidine 5'-diphosphate2'-Deoxycytidine 5'-diphosphoric acid2'-Deoxycytidine diphosphate2'-Deoxycytidine diphosphoric acid2'-Deoxycytidine-5'-diphosphate2'-Deoxycytidine-5'-diphosphoric acid2-Deoxycytidine 5-diphosphate2-Deoxycytidine 5-diphosphoric acid2-Deoxycytidine diphosphate2-Deoxycytidine diphosphoric acid4-amino-1-[2-Deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-b-D-erythro-pentofuranosyl]-2(1H)-pyrimidinone4-amino-1-[2-Deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-b-delta-erythro-pentofuranosyl]-2(1H)-pyrimidinone4-amino-1-[2-Deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-b-δ-erythro-pentofuranosyl]-2(1H)-pyrimidinone4-Amino-1-[2-deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-beta-D-erythro-pentofuranosyl]-2(1H)-pyrimidinone4-Amino-1-[2-deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-beta-delta-erythro-pentofuranosyl]-2(1H)-pyrimidinone4-amino-1-[2-Deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-β-D-erythro-pentofuranosyl]-2(1H)-pyrimidinone4-amino-1-[2-Deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-β-δ-erythro-pentofuranosyl]-2(1H)-pyrimidinoneD-1b-Ribofuranosylcytosine diphosphateD-1b-Ribofuranosylcytosine diphosphoric acidD-1beta-Ribofuranosylcytosine diphosphateD-1beta-Ribofuranosylcytosine diphosphoric acidD-1β-Ribofuranosylcytosine diphosphateD-1β-Ribofuranosylcytosine diphosphoric acidDCDPdelta-1b-Ribofuranosylcytosine diphosphatedelta-1b-Ribofuranosylcytosine diphosphoric acidDelta-1beta-Ribofuranosylcytosine diphosphatedelta-1beta-Ribofuranosylcytosine diphosphoric acidDeoxy-CDPDeoxycytidine 5'-diphosphateDeoxycytidine 5'-diphosphoric acidDeoxycytidine diphosphateDeoxycytidine diphosphoric acidDeoxycytidine-diphosphateDeoxycytidine-diphosphoric acidδ-1b-Ribofuranosylcytosine diphosphateδ-1b-Ribofuranosylcytosine diphosphoric acidδ-1β-Ribofuranosylcytosine diphosphateδ-1β-Ribofuranosylcytosine diphosphoric acidC9H15N3O10P2387.177387.023266739[({[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic aciddCDP800-73-7NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O1InChI=1S/C9H15N3O10P2/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(21-8)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1FTDHDKPUHBLBTL-SHYZEUOFSA-NSolidCytosollogp-1.48logs-1.53solubility1.13e+01 g/llogp-2.6pka_strongest_acidic1.79pka_strongest_basic0.3iupac[({[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acidaverage_mass387.177mono_mass387.023266739smilesNC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O1formulaC9H15N3O10P2inchiInChI=1S/C9H15N3O10P2/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(21-8)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1inchikeyFTDHDKPUHBLBTL-SHYZEUOFSA-Npolar_surface_area201.44refractivity74.78polarizability30.77rotatable_bond_count6acceptor_count10donor_count5physiological_charge-2formal_charge0Pyrimidine metabolismThe 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.PW000942ec00240MetabolicMetabolic pathwayseco01100pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis IPWY0-166Specdb::CMs25964Specdb::CMs37992Specdb::CMs130573Specdb::CMs138307Specdb::NmrOneD8962Specdb::NmrOneD8963Specdb::NmrOneD8964Specdb::NmrOneD8965Specdb::NmrOneD8966Specdb::NmrOneD8967Specdb::NmrOneD8968Specdb::NmrOneD8969Specdb::NmrOneD8970Specdb::NmrOneD8971Specdb::NmrOneD8972Specdb::NmrOneD8973Specdb::NmrOneD8974Specdb::NmrOneD8975Specdb::NmrOneD8976Specdb::NmrOneD8977Specdb::NmrOneD8978Specdb::NmrOneD8979Specdb::NmrOneD8980Specdb::NmrOneD8981Specdb::MsMs27746Specdb::MsMs27747Specdb::MsMs27748Specdb::MsMs34304Specdb::MsMs34305Specdb::MsMs34306Specdb::MsMs439044Specdb::MsMs440125Specdb::MsMs447974Specdb::MsMs447975Specdb::MsMs2236412Specdb::MsMs2236952Specdb::MsMs2238514Specdb::MsMs2239086Specdb::MsMs2241212Specdb::MsMs2304486Specdb::MsMs2304487Specdb::MsMs2304488Specdb::MsMs3061808Specdb::MsMs3061809Specdb::MsMs3061810HMDB01245150855132961C0070528846DCDPYYYDeoxycytidine diphosphateKeseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590.21097882Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114.22080510van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25.17765195Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948.18331064Allard, P., Kuprin, S., Ehrenberg, A. (1994). "Conformation of dCDP bound to protein R1 of Escherichia coli ribonucleotide reductase." J Magn Reson B 103:242-246.8019775Chiu TH, Morimoto H, Baker JJ: Biosynthesis and characterization of phosphatidylglycerophosphoglycerol, a possible intermediate in lipoteichoic acid biosynthesis in Streptococcus sanguis. Biochim Biophys Acta. 1993 Feb 24;1166(2-3):222-8.8443240Nara, Takashi; Misawa, Masanaru. Bacterial phosphorylation of 5'-deoxycytidine monophosphate to di-or triphosphate. Jpn. Tokkyo Koho (1971), 2 pp.Ribonucleoside-diphosphate reductase 1 subunit alphaP00452RIR1_ECOLInrdAhttp://ecmdb.ca/proteins/P00452.xmlCytidylate kinaseP0A6I0KCY_ECOLIcmkhttp://ecmdb.ca/proteins/P0A6I0.xmlNucleoside diphosphate kinaseP0A763NDK_ECOLIndkhttp://ecmdb.ca/proteins/P0A763.xmlUridine kinaseP0A8F4URK_ECOLIudkhttp://ecmdb.ca/proteins/P0A8F4.xmlThioredoxin-2P0AGG4THIO2_ECOLItrxChttp://ecmdb.ca/proteins/P0AGG4.xmlRibonucleoside-diphosphate reductase 2 subunit betaP37146RIR4_ECOLInrdFhttp://ecmdb.ca/proteins/P37146.xmlRibonucleoside-diphosphate reductase 2 subunit alphaP39452RIR3_ECOLInrdEhttp://ecmdb.ca/proteins/P39452.xmlAdenylate kinaseP69441KAD_ECOLIadkhttp://ecmdb.ca/proteins/P69441.xmlRibonucleoside-diphosphate reductase 1 subunit betaP69924RIR2_ECOLInrdBhttp://ecmdb.ca/proteins/P69924.xmlGlutaredoxin-4P0AC69GLRX4_ECOLIgrxDhttp://ecmdb.ca/proteins/P0AC69.xmlGlutaredoxin-3P0AC62GLRX3_ECOLIgrxChttp://ecmdb.ca/proteins/P0AC62.xmlGlutaredoxin-2P0AC59GLRX2_ECOLIgrxBhttp://ecmdb.ca/proteins/P0AC59.xmlGlutaredoxin-1P68688GLRX1_ECOLIgrxAhttp://ecmdb.ca/proteins/P68688.xmlThioredoxin-1P0AA25THIO_ECOLItrxAhttp://ecmdb.ca/proteins/P0AA25.xmlNucleoside diphosphate kinaseP0A763NDK_ECOLIndkhttp://ecmdb.ca/proteins/P0A763.xmlCDP + Reduced Thioredoxin > dCDP + Water + Oxidized ThioredoxinCDP + glutaredoxin > dCDP + glutaredoxin + WaterAdenosine triphosphate + dCDP <> ADP + dCTPR02326DCDPKIN-RXNAdenosine triphosphate + dCMP <> ADP + dCDPR01665RXN-11831dCDP + Thioredoxin disulfide + Water <> Thioredoxin + CDPR02024dCTP + Uridine <> dCDP + Uridine 5'-monophosphateR02327dCTP + Cytidine <> dCDP + Cytidine monophosphateR02371dCDP + Adenosine triphosphate > dCTP + ADPDCDPKIN-RXNAdenosine triphosphate + dCMP ADP + dCDPRXN-11831Adenosine triphosphate + dCMP > ADP + dCDPAdenosine triphosphate + dCMP + Uridine 5'-monophosphate <> ADP + dCDP + Uridine 5'-diphosphateR00512 R01665 dCDP + Adenosine triphosphate > Adenosine diphosphate + dCTP + ADPPW_R003536CDP + a reduced NrdH glutaredoxin-like protein > Water + dCDP + an oxidized NrdH glutaredoxin-like proteinPW_R003544CDP + reduced thioredoxin > Water + oxidized thioredoxin + dCDPPW_R003535