2.02012-05-31 13:54:15 -06002015-06-03 15:54:11 -0600ECMDB01546M2MDB000415CDPCytidine 5'-(trihydrogen diphosphate) is cytosine nucleotide containing two phosphate groups esterified to the sugar (ribose) moiety. CDPCytidine-5'-diphosphateCytidine-5'-diphosphoric acidCytidine-diphosphateCytidine-diphosphoric acidC9H15N3O11P2403.1764403.018181361[({[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acidCDP63-38-7NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]1OInChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1ZWIADYZPOWUWEW-XVFCMESISA-NSolidCytosollogp-1.38logs-1.60solubility1.01e+01 g/llogp-3.3pka_strongest_acidic1.78pka_strongest_basic-0.033iupac[({[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acidaverage_mass403.1764mono_mass403.018181361smilesNC1=NC(=O)N(C=C1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]1OformulaC9H15N3O11P2inchiInChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1inchikeyZWIADYZPOWUWEW-XVFCMESISA-Npolar_surface_area221.67refractivity76.29polarizability31.39rotatable_bond_count6acceptor_count11donor_count6physiological_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.PW000942ec00240Metabolicsalvage pathways of pyrimidine ribonucleotidesPWY0-163pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis IPWY0-166Specdb::CMs25209Specdb::CMs38118Specdb::CMs155671Specdb::NmrOneD4748Specdb::NmrOneD4749Specdb::NmrOneD9562Specdb::NmrOneD9563Specdb::NmrOneD9564Specdb::NmrOneD9565Specdb::NmrOneD9566Specdb::NmrOneD9567Specdb::NmrOneD9568Specdb::NmrOneD9569Specdb::NmrOneD9570Specdb::NmrOneD9571Specdb::NmrOneD9572Specdb::NmrOneD9573Specdb::NmrOneD9574Specdb::NmrOneD9575Specdb::NmrOneD9576Specdb::NmrOneD9577Specdb::NmrOneD9578Specdb::NmrOneD9579Specdb::NmrOneD9580Specdb::NmrOneD9581Specdb::MsMs27626Specdb::MsMs27627Specdb::MsMs27628Specdb::MsMs34184Specdb::MsMs34185Specdb::MsMs34186Specdb::MsMs438897Specdb::MsMs438898Specdb::MsMs438899Specdb::MsMs439054Specdb::MsMs447669Specdb::MsMs447998Specdb::MsMs447999Specdb::MsMs2235957Specdb::MsMs2237445Specdb::MsMs2244328Specdb::MsMs2245760Specdb::MsMs2246497Specdb::MsMs2247795Specdb::MsMs2248458Specdb::MsMs2249903Specdb::MsMs2250462Specdb::MsMs2251939Specdb::MsMs2715139Specdb::MsMs2715140HMDB0154661325902C0011217239CDPCDPCDPKeseler, I. 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"Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948.18331064Ishii, 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 316:593-597.17379776Houtkooper RH, Akbari H, van Lenthe H, Kulik W, Wanders RJ, Frentzen M, Vaz FM: Identification and characterization of human cardiolipin synthase. FEBS Lett. 2006 May 29;580(13):3059-64. Epub 2006 Apr 27.16678169George TP, Cook HW, Byers DM, Palmer FB, Spence MW: Inhibition of phosphatidylcholine and phosphatidylethanolamine biosynthesis by cytochalasin B in cultured glioma cells: potential regulation of biosynthesis by Ca(2+)-dependent mechanisms. Biochim Biophys Acta. 1991 Jul 9;1084(2):185-93.1854804Riekhof WR, Voelker DR: Uptake and utilization of lyso-phosphatidylethanolamine by Saccharomyces cerevisiae. J Biol Chem. 2006 Dec 1;281(48):36588-96. Epub 2006 Oct 2.17015438Tsitolovskii LE, Kraevskii AA: [Possible relation between learning and non-template RNA synthesis in neurons]. Zh Vyssh Nerv Deiat Im I P Pavlova. 1982 Mar-Apr;32(2):284-91.6178232Carstensen S, Pliska-Matyshak G, Bhuvarahamurthy N, Robbins KM, Murthy PP: Biosynthesis and localization of phosphatidyl-scyllo-inositol in barley aleurone cells. Lipids. 1999 Jan;34(1):67-73.10188599Nowicki M, Muller F, Frentzen M: Cardiolipin synthase of Arabidopsis thaliana. 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Journal of the American Chemical Society (1960), 82 970-5.Ribonucleoside-diphosphate reductase 1 subunit alphaP00452RIR1_ECOLInrdAhttp://ecmdb.ca/proteins/P00452.xmlPolyribonucleotide nucleotidyltransferaseP05055PNP_ECOLIpnphttp://ecmdb.ca/proteins/P05055.xml6-phosphofructokinase isozyme 2P06999K6PF2_ECOLIpfkBhttp://ecmdb.ca/proteins/P06999.xmlCytidylate kinaseP0A6I0KCY_ECOLIcmkhttp://ecmdb.ca/proteins/P0A6I0.xmlNucleoside diphosphate kinaseP0A763NDK_ECOLIndkhttp://ecmdb.ca/proteins/P0A763.xml6-phosphofructokinase isozyme 1P0A796K6PF1_ECOLIpfkAhttp://ecmdb.ca/proteins/P0A796.xmlThioredoxin-2P0AGG4THIO2_ECOLItrxChttp://ecmdb.ca/proteins/P0AGG4.xmlRibonucleoside-diphosphate reductase 2 subunit betaP37146RIR4_ECOLInrdFhttp://ecmdb.ca/proteins/P37146.xmlPutative ribosome biogenesis GTPase RsgAP39286RSGA_ECOLIrsgAhttp://ecmdb.ca/proteins/P39286.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 + CDP <> ADP + Cytidine triphosphateR00570CDPKIN-RXNAdenosine triphosphate + Cytidine monophosphate <> ADP + CDPR00512RXN-11832Cytidine triphosphate + Water > CDP + Hydrogen ion + PhosphateRNA + Phosphate <> RNA + CDPR00440dCDP + Thioredoxin disulfide + Water <> Thioredoxin + CDPR02024Cytidine triphosphate + D-Tagatose 6-phosphate <> CDP + D-Tagatose 1,6-bisphosphateR03237CDP + Adenosine triphosphate > Cytidine triphosphate + ADPCDPKIN-RXNCDP + Water > Phosphate + Cytidine monophosphate + Hydrogen ionRXN-12198CDP + a reduced NrdH glutaredoxin-like protein > Water + dCDP + an oxidized NrdH glutaredoxin-like proteinPW_R003544CDP + reduced thioredoxin > Water + oxidized thioredoxin + dCDPPW_R00353548 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 GlucoBioreactor, pH controlled, O2 and CO2 controlled, dilution rate: 0.2/h144.0uM0.037 oCBW25113Stationary Phase, glucose limited5760000Ishii, 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