2.0 2012-05-31 09:57:04 -0600 2015-09-13 12:56:06 -0600 ECMDB00089 M2MDB000033 Cytidine Cytidine is a nucleoside that is composed of the base cytosine linked to the five-carbon sugar D-ribose. Cytidine is a pyrimidine that besides being incorporated into nucleic acids, can serve as substrate for the salvage pathway of pyrimidine nucleotide synthesis; as precursor of the cytidine triphosphate (CTP) needed in the phosphatidylcholine (PC) and phosphatidylethanolamine (PE) biosynthetic pathway. These variations probably reflect the species differences in cytidine deaminase. The biosynthesis of PC via the Kennedy pathway requires phosphocholine and cytidine triphosphate (CTP), a cytidine nucleotide, which is involved in the rate-limiting step. (PMID: 16769123, 15780864, 16720547) 1-(b-D-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine 1-(b-delta-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine 1-(b-δ-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine 1-(beta-D-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine 1-(beta-delta-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine 1-(β-D-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine 1-(β-δ-Ribofuranosyl)-2-oxo-4-amino-1,2-dihydro-1,3-diazine 1-b-D-Ribofuranosyl-cytosine 1-b-D-Ribofuranosylcytosine 1-b-D-ribosyl-Cytosine 1-b-delta-Ribofuranosyl-cytosine 1-b-delta-Ribofuranosylcytosine 1-b-delta-Ribosyl-cytosine 1-b-δ-Ribofuranosyl-cytosine 1-b-δ-Ribofuranosylcytosine 1-b-δ-Ribosyl-cytosine 1-beta-D-Ribofuranosyl-Cytosine 1-beta-D-Ribofuranosylcytosine 1-beta-D-Ribosyl-Cytosine 1-beta-delta-Ribofuranosyl-Cytosine 1-beta-delta-Ribofuranosylcytosine 1-beta-delta-Ribosyl-Cytosine 1-β-D-Ribofuranosyl-cytosine 1-β-D-Ribofuranosylcytosine 1-β-D-Ribosyl-cytosine 1-β-δ-Ribofuranosyl-cytosine 1-β-δ-Ribofuranosylcytosine 1-β-δ-Ribosyl-cytosine 1b-D-Ribofuranosylcytosine 1b-delta-Ribofuranosylcytosine 1b-Ribofuranosylcytosine 1b-δ-Ribofuranosylcytosine 1beta-D-Ribofuranosylcytosine 1beta-delta-Ribofuranosylcytosine 1beta-Ribofuranosylcytosine 1β-D-Ribofuranosylcytosine 1β-Ribofuranosylcytosine 1β-δ-Ribofuranosylcytosine 4-Amino-1-b-D-ribofuranosyl-2(1H)-pyrimidinone 4-amino-1-b-delta-Ribofuranosyl-2(1H)-pyrimidinone 4-amino-1-b-δ-Ribofuranosyl-2(1H)-pyrimidinone 4-Amino-1-beta-delta-ribofuranosyl-2(1H)-pyrimidinone 4-amino-1-β-δ-Ribofuranosyl-2(1H)-pyrimidinone Cytidine Cytosine riboside Cytosine-1b-D-Ribofuranoside Cytosine-1b-delta-Ribofuranoside Cytosine-1b-δ-ribofuranoside Cytosine-1beta-D-Ribofuranoside Cytosine-1beta-delta-Ribofuranoside Cytosine-1β-D-ribofuranoside Cytosine-1β-δ-ribofuranoside C9H13N3O5 243.2166 243.085520541 4-amino-1-[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one cytarabine 65-46-3 NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O InChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)/t4-,6-,7-,8-/m1/s1 UHDGCWIWMRVCDJ-XVFCMESISA-N Solid Cytosol Extra-organism Periplasm logp -2.18 ALOGPS logs -0.74 ALOGPS solubility 4.38e+01 g/l ALOGPS melting_point 230.5 oC logp -2.8 ChemAxon pka_strongest_acidic 12.55 ChemAxon pka_strongest_basic -0.062 ChemAxon iupac 4-amino-1-[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one ChemAxon average_mass 243.2166 ChemAxon mono_mass 243.085520541 ChemAxon smiles NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O ChemAxon formula C9H13N3O5 ChemAxon inchi InChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)/t4-,6-,7-,8-/m1/s1 ChemAxon inchikey UHDGCWIWMRVCDJ-XVFCMESISA-N ChemAxon polar_surface_area 128.61 ChemAxon refractivity 54.54 ChemAxon polarizability 22.53 ChemAxon rotatable_bond_count 2 ChemAxon acceptor_count 7 ChemAxon donor_count 4 ChemAxon physiological_charge 0 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 Drug metabolism - other enzymes ec00983 Metabolic pathways eco01100 Pyrimidine ribonucleosides degradtion Cytidine and Uridine are transported through their corresponding nucleoside hydrogen symporters . Once cytidine is incorporated into the cytosol, it is deaminated through a reaction with water and a hydrogen ion through a cytidine deaminase resulting in the release of ammonium and uridine. Uridine is then lyase by a phosphate through a uridine phosphorylase resulting in the release of a uracil and a alpha-D-ribose-1-phosphate. This compound is then transformed into an isomer D-ribose 5-phosphate through a alpha-D-ribose 1,5-phosphomutase. This cumpound is then incorporated into the pentose phosphate pathway PW002024 Metabolic pyrimidine ribonucleosides degradation The degradation of pyrimidine ribonucleosides starts with either cytidine or uridine being transported into the cytosol. Cytidine is transported into the cytosol through an nupG transporter. Once inside the cytosol, it can be degraded into uridine by reacting with water and ahydrogen ion through a cytidine deaminase resulting in the release of ammonium and uridine. Uridine is transported into the cytosol through a nupG. Once in the cytosol , uridine can be degrade by reacting with phosphate through a uridine phosphorylase resulting in the release of an alpha-D-ribose-1-phosphate and a uracil. The alpha-D-ribose-1-phosphate reacts with an alpha-d-ribose 1,5-phosphomutase resulting in the release of a D-ribose 5-phosphate which can be incorporated into the pentose phosphate pathway. PW002104 Metabolic salvage pathways of pyrimidine ribonucleotides PWY0-163 pyrimidine ribonucleosides degradation I PWY0-1295 Specdb::CMs 16839 Specdb::CMs 40570 Specdb::CMs 102730 Specdb::CMs 102731 Specdb::CMs 102732 Specdb::CMs 102733 Specdb::CMs 155021 Specdb::NmrOneD 5194 Specdb::NmrOneD 103178 Specdb::NmrOneD 103179 Specdb::NmrOneD 103180 Specdb::NmrOneD 103181 Specdb::NmrOneD 103182 Specdb::NmrOneD 103183 Specdb::NmrOneD 103184 Specdb::NmrOneD 103185 Specdb::NmrOneD 103186 Specdb::NmrOneD 103187 Specdb::NmrOneD 103188 Specdb::NmrOneD 103189 Specdb::NmrOneD 103190 Specdb::NmrOneD 103191 Specdb::NmrOneD 103192 Specdb::NmrOneD 103193 Specdb::NmrOneD 103194 Specdb::NmrOneD 103195 Specdb::NmrOneD 103196 Specdb::NmrOneD 103197 Specdb::MsMs 51999 Specdb::MsMs 52000 Specdb::MsMs 52001 Specdb::MsMs 158343 Specdb::MsMs 158344 Specdb::MsMs 158345 Specdb::MsMs 437485 Specdb::MsMs 437486 Specdb::MsMs 437487 Specdb::MsMs 437488 Specdb::MsMs 437489 Specdb::MsMs 445920 Specdb::MsMs 445921 Specdb::MsMs 445922 Specdb::MsMs 445923 Specdb::MsMs 445924 Specdb::MsMs 447206 Specdb::MsMs 2250410 Specdb::MsMs 2251959 Specdb::MsMs 3219907 Specdb::MsMs 3219908 Specdb::MsMs 3219909 Specdb::MsMs 3219910 Specdb::MsMs 3219911 Specdb::MsMs 3219912 Specdb::NmrTwoD 2029 Specdb::NmrTwoD 2030 HMDB00089 6175 5940 C00475 17562 CYTIDINE CTN Cytidine Keseler, 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. 21097882 Kanehisa, 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. 22080510 van 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. 17765195 Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). 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Faming Zhuanli Shenqing Gongkai Shuomingshu (2007), 11pp. http://hmdb.ca/system/metabolites/msds/000/000/063/original/HMDB00089.pdf?1358894016 Protein ushA P07024 USHA_ECOLI ushA http://ecmdb.ca/proteins/P07024.xml 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase P08331 CPDB_ECOLI cpdB http://ecmdb.ca/proteins/P08331.xml Multifunctional protein surE P0A840 SURE_ECOLI surE http://ecmdb.ca/proteins/P0A840.xml Uridine kinase P0A8F4 URK_ECOLI udk http://ecmdb.ca/proteins/P0A8F4.xml 5'-nucleotidase yjjG P0A8Y1 YJJG_ECOLI yjjG http://ecmdb.ca/proteins/P0A8Y1.xml Cytidine deaminase P0ABF6 CDD_ECOLI cdd http://ecmdb.ca/proteins/P0ABF6.xml Class B acid phosphatase P0AE22 APHA_ECOLI aphA http://ecmdb.ca/proteins/P0AE22.xml Non-specific ribonucleoside hydrolase rihC P22564 RIHC_ECOLI rihC http://ecmdb.ca/proteins/P22564.xml Pyrimidine-specific ribonucleoside hydrolase rihB P33022 RIHB_ECOLI rihB http://ecmdb.ca/proteins/P33022.xml 5'-nucleotidase yfbR P76491 YFBR_ECOLI yfbR http://ecmdb.ca/proteins/P76491.xml Pyrimidine-specific ribonucleoside hydrolase rihA P41409 RIHA_ECOLI rihA http://ecmdb.ca/proteins/P41409.xml Xanthosine permease P45562 XAPB_ECOLI xapB http://ecmdb.ca/proteins/P45562.xml Nucleoside permease nupC P0AFF2 NUPC_ECOLI nupC http://ecmdb.ca/proteins/P0AFF2.xml Nucleoside permease nupG P0AFF4 NUPG_ECOLI nupG http://ecmdb.ca/proteins/P0AFF4.xml Nucleoside permease nupX P33021 NUPX_ECOLI nupX http://ecmdb.ca/proteins/P33021.xml Outer membrane protein N P77747 OMPN_ECOLI ompN http://ecmdb.ca/proteins/P77747.xml Outer membrane pore protein E P02932 PHOE_ECOLI phoE http://ecmdb.ca/proteins/P02932.xml Outer membrane protein F P02931 OMPF_ECOLI ompF http://ecmdb.ca/proteins/P02931.xml Outer membrane protein C P06996 OMPC_ECOLI ompC http://ecmdb.ca/proteins/P06996.xml Cytidine monophosphate + Water > Cytidine + Phosphate Cytidine + Water > Cytosine + Ribose R02137 Cytidine + Guanosine triphosphate > Cytidine monophosphate + Guanosine diphosphate + Hydrogen ion R00517 CYTIDINEKIN-RXN Cytidine + Hydrogen ion + Water > Ammonium + Uridine 3'-CMP + Water > Cytidine + Phosphate Cytidine monophosphate + Water <> Cytidine + Phosphate R00511 Adenosine triphosphate + Cytidine <> ADP + Cytidine monophosphate R00513 Uridine triphosphate + Cytidine <> Uridine 5'-diphosphate + Cytidine monophosphate R00516 Guanosine triphosphate + Cytidine <> Guanosine diphosphate + Cytidine monophosphate R00517 Inosine triphosphate + Cytidine <> IDP + Cytidine monophosphate R00962 dATP + Cytidine <> dADP + Cytidine monophosphate R01548 Cytidine + Water <> Uridine + Ammonia R01878 dGTP + Cytidine <> dGDP + Cytidine monophosphate R02091 Thymidine 5'-triphosphate + Cytidine <> dTDP + Cytidine monophosphate R02096 Cytidine + Water <> Cytosine + Ribose R02137 dCTP + Cytidine <> dCDP + Cytidine monophosphate R02371 Deoxyuridine triphosphate + Cytidine <> dUDP + Cytidine monophosphate R02372 Water + Cytidine > Ammonia + Uridine R01878 CYTIDEAM2-RXN Cytidine + Water > D-ribose + Cytosine RXN0-361 Adenosine triphosphate + Cytidine > ADP + Cytidine monophosphate Cytidine + Water + Deoxycytidine <> Uridine + Ammonia + Deoxyuridine R01878 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 2.59 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 10360 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