2.0 2012-05-31 10:25:56 -0600 2015-09-13 12:56:07 -0600 ECMDB00296 M2MDB000124 Uridine Uridine 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)-pyrimidinedione 1-b-D-Ribofuranosyluracil 1-b-delta-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione 1-b-delta-Ribofuranosyluracil 1-b-δ-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione 1-b-δ-Ribofuranosyluracil 1-beta-delta-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione 1-beta-delta-Ribofuranosyluracil 1-β-δ-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione 1-β-δ-Ribofuranosyluracil B-D-Ribofuranoside 2,4(1H,3H)-pyrimidinedione-1 b-delta-Ribofuranoside 2,4(1H,3H)-pyrimidinedione-1 B-Uridine b-δ-Ribofuranoside 2,4(1H,3H)-pyrimidinedione-1 Beta-delta-Ribofuranoside 2,4(1H,3H)-pyrimidinedione-1 Beta-Uridine Uridin β-Uridine β-δ-Ribofuranoside 2,4(1H,3H)-pyrimidinedione-1 C9H12N2O6 244.2014 244.069536126 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione uridine 58-96-8 OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(=O)NC1=O InChI=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/s1 DRTQHJPVMGBUCF-XVFCMESISA-N Solid Cytosol Extra-organism Periplasm logp -1.84 ALOGPS logs -0.26 ALOGPS solubility 1.35e+02 g/l ALOGPS melting_point 163 oC logp -2.4 ChemAxon pka_strongest_acidic 9.7 ChemAxon pka_strongest_basic -3 ChemAxon iupac 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione ChemAxon average_mass 244.2014 ChemAxon mono_mass 244.069536126 ChemAxon smiles OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(=O)NC1=O ChemAxon formula C9H12N2O6 ChemAxon inchi InChI=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/s1 ChemAxon inchikey DRTQHJPVMGBUCF-XVFCMESISA-N ChemAxon polar_surface_area 119.33 ChemAxon refractivity 52.57 ChemAxon polarizability 21.81 ChemAxon rotatable_bond_count 2 ChemAxon acceptor_count 6 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 524 Specdb::CMs 525 Specdb::CMs 526 Specdb::CMs 527 Specdb::CMs 1976 Specdb::CMs 1985 Specdb::CMs 2456 Specdb::CMs 30409 Specdb::CMs 30709 Specdb::CMs 30710 Specdb::CMs 30764 Specdb::CMs 31118 Specdb::CMs 31119 Specdb::CMs 32283 Specdb::CMs 32284 Specdb::CMs 37409 Specdb::CMs 133686 Specdb::CMs 141420 Specdb::CMs 1057331 Specdb::CMs 1057333 Specdb::CMs 1057335 Specdb::CMs 1057337 Specdb::CMs 1057339 Specdb::CMs 1057341 Specdb::CMs 1057342 Specdb::EiMs 1980 Specdb::NmrOneD 1228 Specdb::NmrOneD 1319 Specdb::NmrOneD 4774 Specdb::NmrOneD 6482 Specdb::NmrOneD 6483 Specdb::NmrOneD 6484 Specdb::NmrOneD 6485 Specdb::NmrOneD 6486 Specdb::NmrOneD 6487 Specdb::NmrOneD 6488 Specdb::NmrOneD 6489 Specdb::NmrOneD 6490 Specdb::NmrOneD 6491 Specdb::NmrOneD 6492 Specdb::NmrOneD 6493 Specdb::NmrOneD 6494 Specdb::NmrOneD 6495 Specdb::NmrOneD 6496 Specdb::NmrOneD 6497 Specdb::NmrOneD 6498 Specdb::NmrOneD 6499 Specdb::NmrOneD 6500 Specdb::NmrOneD 6501 Specdb::NmrOneD 166343 Specdb::NmrOneD 166506 Specdb::MsMs 504 Specdb::MsMs 505 Specdb::MsMs 506 Specdb::MsMs 3933 Specdb::MsMs 3934 Specdb::MsMs 3935 Specdb::MsMs 3936 Specdb::MsMs 3937 Specdb::MsMs 3938 Specdb::MsMs 3939 Specdb::MsMs 3940 Specdb::MsMs 3941 Specdb::MsMs 3942 Specdb::MsMs 3943 Specdb::MsMs 3944 Specdb::MsMs 3945 Specdb::MsMs 3946 Specdb::MsMs 3947 Specdb::MsMs 3948 Specdb::MsMs 3949 Specdb::MsMs 3950 Specdb::MsMs 3951 Specdb::MsMs 3952 Specdb::MsMs 3953 Specdb::MsMs 3954 Specdb::NmrTwoD 1015 Specdb::NmrTwoD 1261 HMDB00296 6029 5807 C00299 16704 URIDINE URI Uridine 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). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. 18331064 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 Eells JT, Spector R: Purine and pyrimidine base and nucleoside concentrations in human cerebrospinal fluid and plasma. Neurochem Res. 1983 Nov;8(11):1451-7. 6656991 Lee 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. 15116424 Doi, 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?1358463289 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 Uridine phosphorylase P12758 UDP_ECOLI udp http://ecmdb.ca/proteins/P12758.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 Nucleoside-specific channel-forming protein tsx P0A927 TSX_ECOLI tsx http://ecmdb.ca/proteins/P0A927.xml Water + Uridine 5'-monophosphate > Phosphate + Uridine Water + Uridine > Ribose + Uracil Guanosine triphosphate + Uridine > Guanosine diphosphate + Hydrogen ion + Uridine 5'-monophosphate R00968 URKI-RXN Cytidine + Hydrogen ion + Water > Ammonium + Uridine Phosphate + Uridine <> Ribose-1-phosphate + Uracil URPHOS-RXN 3'-UMP + Water > Phosphate + Uridine Uridine 5'-monophosphate + Water <> Uridine + Phosphate R00963 Adenosine triphosphate + Uridine <> ADP + Uridine 5'-monophosphate R00964 Uridine triphosphate + Uridine <> Uridine 5'-diphosphate + Uridine 5'-monophosphate R00967 Guanosine triphosphate + Uridine <> Guanosine diphosphate + Uridine 5'-monophosphate R00968 Inosine triphosphate + Uridine <> IDP + Uridine 5'-monophosphate R00970 dATP + Uridine <> dADP + Uridine 5'-monophosphate R01549 Uridine + Phosphate <> Uracil + alpha-D-Ribose 1-phosphate + Ribose-1-phosphate R01876 Cytidine + Water <> Uridine + Ammonia R01878 dGTP + Uridine <> dGDP + Uridine 5'-monophosphate R01880 Thymidine 5'-triphosphate + Uridine <> dTDP + Uridine 5'-monophosphate R02097 dCTP + Uridine <> dCDP + Uridine 5'-monophosphate R02327 Deoxyuridine triphosphate + Uridine <> dUDP + Uridine 5'-monophosphate R02332 Water + Cytidine > Ammonia + Uridine R01878 CYTIDEAM2-RXN Uridine + Water > D-ribose + Uracil URIDINE-NUCLEOSIDASE-RXN Uridine + Inorganic phosphate > Uracil + Ribose-1-phosphate Adenosine triphosphate + Uridine > ADP + Uridine 5'-monophosphate Cytidine + Water + Deoxycytidine <> Uridine + Ammonia + Deoxyuridine R01878 Uridine + Phosphate > Uracil + Ribose-1-phosphate PW_R005898 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 2090.0 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 8360000 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