2.02012-05-31 10:25:56 -06002015-09-13 12:56:07 -0600ECMDB00296M2MDB000124UridineUridine is a molecule (known as a nucleoside) that is formed when uracil is attached to a ribose ring (also known as a ribofuranose) via a b-N1-glycosidic bond. (Wikipedia)1-b-D-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione1-b-D-Ribofuranosyluracil1-b-delta-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione1-b-delta-Ribofuranosyluracil1-b-δ-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione1-b-δ-Ribofuranosyluracil1-beta-delta-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione1-beta-delta-Ribofuranosyluracil1-β-δ-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione1-β-δ-RibofuranosyluracilB-D-Ribofuranoside 2,4(1H,3H)-pyrimidinedione-1b-delta-Ribofuranoside 2,4(1H,3H)-pyrimidinedione-1B-Uridineb-δ-Ribofuranoside 2,4(1H,3H)-pyrimidinedione-1Beta-delta-Ribofuranoside 2,4(1H,3H)-pyrimidinedione-1Beta-UridineUridinβ-Uridineβ-δ-Ribofuranoside 2,4(1H,3H)-pyrimidinedione-1C9H12N2O6244.2014244.0695361261-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dioneuridine58-96-8OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(=O)NC1=OInChI=1S/C9H12N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,16)/t4-,6-,7-,8-/m1/s1DRTQHJPVMGBUCF-XVFCMESISA-NSolidCytosolExtra-organismPeriplasmlogp-1.84logs-0.26solubility1.35e+02 g/lmelting_point163 oClogp-2.4pka_strongest_acidic9.7pka_strongest_basic-3iupac1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dioneaverage_mass244.2014mono_mass244.069536126smilesOC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(=O)NC1=OformulaC9H12N2O6inchiInChI=1S/C9H12N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,16)/t4-,6-,7-,8-/m1/s1inchikeyDRTQHJPVMGBUCF-XVFCMESISA-Npolar_surface_area119.33refractivity52.57polarizability21.81rotatable_bond_count2acceptor_count6donor_count4physiological_charge0formal_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.PW000942ec00240MetabolicDrug metabolism - other enzymesec00983Metabolic pathwayseco01100Pyrimidine ribonucleosides degradtionCytidine 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
PW002024Metabolicpyrimidine ribonucleosides degradationThe 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.PW002104Metabolicsalvage pathways of pyrimidine ribonucleotidesPWY0-163pyrimidine ribonucleosides degradation IPWY0-1295Specdb::CMs524Specdb::CMs525Specdb::CMs526Specdb::CMs527Specdb::CMs1976Specdb::CMs1985Specdb::CMs2456Specdb::CMs30409Specdb::CMs30709Specdb::CMs30710Specdb::CMs30764Specdb::CMs31118Specdb::CMs31119Specdb::CMs32283Specdb::CMs32284Specdb::CMs37409Specdb::CMs133686Specdb::CMs141420Specdb::CMs1057331Specdb::CMs1057333Specdb::CMs1057335Specdb::CMs1057337Specdb::CMs1057339Specdb::CMs1057341Specdb::CMs1057342Specdb::EiMs1980Specdb::NmrOneD1228Specdb::NmrOneD1319Specdb::NmrOneD4774Specdb::NmrOneD6482Specdb::NmrOneD6483Specdb::NmrOneD6484Specdb::NmrOneD6485Specdb::NmrOneD6486Specdb::NmrOneD6487Specdb::NmrOneD6488Specdb::NmrOneD6489Specdb::NmrOneD6490Specdb::NmrOneD6491Specdb::NmrOneD6492Specdb::NmrOneD6493Specdb::NmrOneD6494Specdb::NmrOneD6495Specdb::NmrOneD6496Specdb::NmrOneD6497Specdb::NmrOneD6498Specdb::NmrOneD6499Specdb::NmrOneD6500Specdb::NmrOneD6501Specdb::NmrOneD166343Specdb::NmrOneD166506Specdb::MsMs504Specdb::MsMs505Specdb::MsMs506Specdb::MsMs3933Specdb::MsMs3934Specdb::MsMs3935Specdb::MsMs3936Specdb::MsMs3937Specdb::MsMs3938Specdb::MsMs3939Specdb::MsMs3940Specdb::MsMs3941Specdb::MsMs3942Specdb::MsMs3943Specdb::MsMs3944Specdb::MsMs3945Specdb::MsMs3946Specdb::MsMs3947Specdb::MsMs3948Specdb::MsMs3949Specdb::MsMs3950Specdb::MsMs3951Specdb::MsMs3952Specdb::MsMs3953Specdb::MsMs3954Specdb::NmrTwoD1015Specdb::NmrTwoD1261HMDB0029660295807C0029916704URIDINEURIUridineKeseler, 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 80:2939-2948.18331064Bennett, 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 5:593-599.19561621Eells JT, Spector R: Purine and pyrimidine base and nucleoside concentrations in human cerebrospinal fluid and plasma. Neurochem Res. 1983 Nov;8(11):1451-7.6656991Lee SH, Jung BH, Kim SY, Chung BC: A rapid and sensitive method for quantitation of nucleosides in human urine using liquid chromatography/mass spectrometry with direct urine injection. Rapid Commun Mass Spectrom. 2004;18(9):973-7.15116424Doi, Muneharu; Asahi, Satoru; Izawa, Motoo. Fermentative production of uridine and cytidine. Baiosaiensu to Indasutori (1993), 51(12), 972-6. http://hmdb.ca/system/metabolites/msds/000/000/217/original/HMDB00296.pdf?1358463289Protein ushAP07024USHA_ECOLIushAhttp://ecmdb.ca/proteins/P07024.xml2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidaseP08331CPDB_ECOLIcpdBhttp://ecmdb.ca/proteins/P08331.xmlMultifunctional protein surEP0A840SURE_ECOLIsurEhttp://ecmdb.ca/proteins/P0A840.xmlUridine kinaseP0A8F4URK_ECOLIudkhttp://ecmdb.ca/proteins/P0A8F4.xml5'-nucleotidase yjjGP0A8Y1YJJG_ECOLIyjjGhttp://ecmdb.ca/proteins/P0A8Y1.xmlCytidine deaminaseP0ABF6CDD_ECOLIcddhttp://ecmdb.ca/proteins/P0ABF6.xmlClass B acid phosphataseP0AE22APHA_ECOLIaphAhttp://ecmdb.ca/proteins/P0AE22.xmlUridine phosphorylaseP12758UDP_ECOLIudphttp://ecmdb.ca/proteins/P12758.xmlNon-specific ribonucleoside hydrolase rihCP22564RIHC_ECOLIrihChttp://ecmdb.ca/proteins/P22564.xmlPyrimidine-specific ribonucleoside hydrolase rihBP33022RIHB_ECOLIrihBhttp://ecmdb.ca/proteins/P33022.xml5'-nucleotidase yfbRP76491YFBR_ECOLIyfbRhttp://ecmdb.ca/proteins/P76491.xmlPyrimidine-specific ribonucleoside hydrolase rihAP41409RIHA_ECOLIrihAhttp://ecmdb.ca/proteins/P41409.xmlXanthosine permeaseP45562XAPB_ECOLIxapBhttp://ecmdb.ca/proteins/P45562.xmlNucleoside permease nupCP0AFF2NUPC_ECOLInupChttp://ecmdb.ca/proteins/P0AFF2.xmlNucleoside permease nupGP0AFF4NUPG_ECOLInupGhttp://ecmdb.ca/proteins/P0AFF4.xmlNucleoside permease nupXP33021NUPX_ECOLInupXhttp://ecmdb.ca/proteins/P33021.xmlNucleoside-specific channel-forming protein tsxP0A927TSX_ECOLItsxhttp://ecmdb.ca/proteins/P0A927.xmlWater + Uridine 5'-monophosphate > Phosphate + UridineWater + Uridine > Ribose + UracilGuanosine triphosphate + Uridine > Guanosine diphosphate + Hydrogen ion + Uridine 5'-monophosphateR00968URKI-RXNCytidine + Hydrogen ion + Water > Ammonium + UridinePhosphate + Uridine <> Ribose-1-phosphate + UracilURPHOS-RXN3'-UMP + Water > Phosphate + UridineUridine 5'-monophosphate + Water <> Uridine + PhosphateR00963Adenosine triphosphate + Uridine <> ADP + Uridine 5'-monophosphateR00964Uridine triphosphate + Uridine <> Uridine 5'-diphosphate + Uridine 5'-monophosphateR00967Guanosine triphosphate + Uridine <> Guanosine diphosphate + Uridine 5'-monophosphateR00968Inosine triphosphate + Uridine <> IDP + Uridine 5'-monophosphateR00970dATP + Uridine <> dADP + Uridine 5'-monophosphateR01549Uridine + Phosphate <> Uracil + alpha-D-Ribose 1-phosphate + Ribose-1-phosphateR01876Cytidine + Water <> Uridine + AmmoniaR01878dGTP + Uridine <> dGDP + Uridine 5'-monophosphateR01880Thymidine 5'-triphosphate + Uridine <> dTDP + Uridine 5'-monophosphateR02097dCTP + Uridine <> dCDP + Uridine 5'-monophosphateR02327Deoxyuridine triphosphate + Uridine <> dUDP + Uridine 5'-monophosphateR02332Water + Cytidine > Ammonia + UridineR01878CYTIDEAM2-RXNUridine + Water > D-ribose + UracilURIDINE-NUCLEOSIDASE-RXNUridine + Inorganic phosphate > Uracil + Ribose-1-phosphateAdenosine triphosphate + Uridine > ADP + Uridine 5'-monophosphateCytidine + Water + Deoxycytidine <> Uridine + Ammonia + DeoxyuridineR01878 Uridine + Phosphate > Uracil + Ribose-1-phosphatePW_R005898Gutnick 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 glucoseShake flask and filter culture2090.0uM0.037 oCK12 NCM3722Mid-Log Phase83600000Bennett, 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