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MetaCyc Compound: uridine

Superclasses: a nucleic acid component a nucleoside a pyrimidine nucleoside a pyrimidine ribonucleoside
a nucleic acid component a nucleoside a ribonucleoside a pyrimidine ribonucleoside
an organic heterocyclic compound an organonitrogen heterocyclic compound a diazine a pyrimidine a pyrimidine nucleoside a pyrimidine ribonucleoside

Chemical Formula: C9H12N2O6

Molecular Weight: 244.2 Daltons

Monoisotopic Molecular Weight: 244.0695361282 Daltons

uridine compound structure

SMILES: C(O)C1(OC(C(O)C(O)1)N2(C=CC(=O)NC(=O)2))

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

InChIKey: InChIKey=DRTQHJPVMGBUCF-XVFCMESISA-N

Unification Links: CAS:58-96-8 , ChEBI:16704 , ChemSpider:5807 , DrugBank:DB02745 , HMDB:HMDB00296 , IAF1260:34541 , KEGG:C00299 , MetaboLights:MTBLC16704 , PubChem:6029

Standard Gibbs Free Energy of Change Formation (ΔfG in kcal/mol): -71.02655 Inferred by computational analysis [Latendresse13]

Reactions known to consume the compound:

pyrimidine ribonucleosides salvage I :
uridine + ATP → UMP + ADP + H+

pyrimidine ribonucleosides salvage II :
uridine + H2O → D-ribofuranose + uracil

Not in pathways:
a pyrimidine nucleoside + H2O + H+ → a pyrimidine base + D-ribofuranose

Reactions known to produce the compound:

pyrimidine ribonucleosides degradation , pyrimidine ribonucleosides salvage I , pyrimidine ribonucleosides salvage II :
cytidine + H+ + H2O → uridine + ammonium

UTP and CTP dephosphorylation I :
UMP + H2O → uridine + phosphate

Not in pathways:
2'-deoxyuridine + 2-oxoglutarate + oxygen → uridine + succinate + CO2
uridine 3'-monophosphate + H2O → uridine + phosphate
uridine 2'-monophosphate[periplasmic space] + H2O[periplasmic space]uridine[periplasmic space] + phosphate[periplasmic space]

Not in pathways:
a ribonucleoside 5'-monophosphate + H2O → a ribonucleoside + phosphate
a ribonucleoside 3'-phosphate + H2O → a ribonucleoside + phosphate

Not in pathways:
a nucleoside 5'-monophosphate[periplasmic space] + H2O[periplasmic space]a nucleoside[periplasmic space] + phosphate[periplasmic space]
a nucleotide + H2O → a nucleoside + phosphate

Reactions known to both consume and produce the compound:

pyrimidine ribonucleosides degradation :
uridine + phosphate ↔ α-D-ribose-1-phosphate + uracil

In Reactions of unknown directionality:

Not in pathways:
uridine + GTP = UMP + GDP + H+

Not in pathways:
a nucleotide + a 2'-deoxynucleoside = a nucleoside + a 2'-deoxyribonucleoside 5'-monophosphate

In Transport reactions:
uridine[periplasmic space] + H+[periplasmic space]uridine[cytosol] + H+[cytosol] ,
a nucleoside[periplasmic space] + H+[periplasmic space]a nucleoside[cytosol] + H+[cytosol] ,
a nucleoside[extracellular space]a nucleoside[periplasmic space]

Enzymes inhibited by uridine, sorted by the type of inhibition, are:

Inhibitor (Competitive) of: uridine phosphorylase [Budman67, Comment 1] , deoxycytidine deaminase [FaivreNitschke99] , cytidine deaminase [FaivreNitschke99]

Inhibitor (Mechanism unknown) of: acid phosphatase / phosphotransferase [Thaller97]

This compound has been characterized as an alternative substrate of the following enzymes: nucleoside oxidase


References

Budman67: Budman DR, Pardee AB (1967). "Thymidine and thymine incorporation into deoxyribonucleic acid: inhibition and repression by uridine of thymidine phosphorylase of Escherichia coli." J Bacteriol 94(5);1546-50. PMID: 4862197

FaivreNitschke99: Faivre-Nitschke SE, Grienenberger JM, Gualberto JM (1999). "A prokaryotic-type cytidine deaminase from Arabidopsis thaliana gene expression and functional characterization." Eur J Biochem 263(3);896-903. PMID: 10469156

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Thaller97: Thaller MC, Schippa S, Bonci A, Cresti S, Rossolini GM (1997). "Identification of the gene (aphA) encoding the class B acid phosphatase/phosphotransferase of Escherichia coli MG1655 and characterization of its product." FEMS Microbiol Lett 1997;146(2);191-8. PMID: 9011040

Vita83: Vita A, Huang CY, Magni G (1983). "Uridine phosphorylase from Escherichia coli B.: kinetic studies on the mechanism of catalysis." Arch Biochem Biophys 1983;226(2);687-92. PMID: 6357095


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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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