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Identification
YMDB IDYMDB00127
NameUridine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionUridine, also known as beta-uridine or allo uridine, belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety. Uridine is an extremely weak basic (essentially neutral) compound (based on its pKa). Uridine exists in all living species, ranging from bacteria to humans.
Structure
Thumb
Synonyms
  • 1-b-D-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione
  • 1-b-D-Ribofuranosyluracil
  • 1-beta-delta-Ribofuranosyl-2,4(1H,3H)-pyrimidinedione
  • 1-beta-delta-Ribofuranosyluracil
  • b-D-Ribofuranoside 2,4(1H,3H)-pyrimidinedione-1
  • b-Uridine
  • beta-delta-Ribofuranoside 2,4(1H,3H)-pyrimidinedione-1
  • beta-Uridine
  • Uridin
  • 1-beta-D-Ribofuranosylpyrimidine-2,4(1H,3H)-dione
  • 1-beta-D-Ribofuranosyluracil
  • u
  • Urd
  • 1-b-D-Ribofuranosylpyrimidine-2,4(1H,3H)-dione
  • 1-Β-D-ribofuranosylpyrimidine-2,4(1H,3H)-dione
  • 1-Β-D-ribofuranosyluracil
  • Β-uridine
  • Allo uridine
  • Allo-uridine
  • Allouridine
CAS number58-96-8
WeightAverage: 244.2014
Monoisotopic: 244.069536126
InChI KeyDRTQHJPVMGBUCF-XVFCMESISA-N
InChIInChI=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
IUPAC Name1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Nameuridine
Chemical FormulaC9H12N2O6
SMILES[H]OC([H])([H])[C@@]1([H])O[C@@]([H])(N2C([H])=C([H])C(=O)N([H])C2=O)[C@]([H])(O[H])[C@]1([H])O[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassNot Available
Direct ParentPyrimidine nucleosides
Alternative Parents
Substituents
  • Pyrimidine nucleoside
  • Glycosyl compound
  • N-glycosyl compound
  • Pentose monosaccharide
  • Pyrimidone
  • Hydropyrimidine
  • Monosaccharide
  • Pyrimidine
  • Vinylogous amide
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Urea
  • Secondary alcohol
  • Lactam
  • Organoheterocyclic compound
  • Oxacycle
  • Azacycle
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Primary alcohol
  • Alcohol
  • Organic oxygen compound
  • Organic oxide
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point163 °C
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogP-1.98 [HANSCH,C ET AL. (1995)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility135 g/LALOGPS
logP-1.8ALOGPS
logP-2.4ChemAxon
logS-0.26ALOGPS
pKa (Strongest Acidic)9.7ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area119.33 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity52.57 m³·mol⁻¹ChemAxon
Polarizability21.81 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • extracellular
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Pyrimidine metabolismPW002469 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Pyrimidine metabolismec00240 Map00240
SMPDB ReactionsNot Available
KEGG Reactions
water + Uridine 5'-monophosphatephosphate + Uridine
water + hydron + CytidineUridine + Ammonium
phosphate + UridineUracil + Ribose 1-phosphate
Adenosine triphosphate + Uridinehydron + ADP + Uridine 5'-monophosphate
GTP + Uridinehydron + Uridine 5'-monophosphate + Guanosine diphosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular Concentrations
Intracellular ConcentrationSubstrateGrowth ConditionsStrainCitation
553 ± 61 µM hops, malted barleyanaerobicBaker's yeastPMID: 16448171
Conversion Details Here
Spectra
Spectra
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Magni, G., Santarelli, I., Natalini, P., Ruggieri, S., Vita, A. (1977). "Catabolite inactivation of bakers'-yeast uridine nucleosidase. Isolation and partial purification of a specific proteolytic inactivase." Eur J Biochem 75:77-82.16754
  • Almeida, C., Duarte, I. F., Barros, A., Rodrigues, J., Spraul, M., Gil, A. M. (2006). "Composition of beer by 1H NMR spectroscopy: effects of brewing site and date of production." J Agric Food Chem 54:700-706.16448171
  • Nakanishi, T., Sekimizu, K. (2002). "SDT1/SSM1, a multicopy suppressor of S-II null mutant, encodes a novel pyrimidine 5'-nucleotidase." J Biol Chem 277:22103-22106.11934891
  • Vickers, M. F., Yao, S. Y., Baldwin, S. A., Young, J. D., Cass, C. E. (2000). "Nucleoside transporter proteins of Saccharomyces cerevisiae. Demonstration of a transporter (FUI1) with high uridine selectivity in plasma membranes and a transporter (FUN26) with broad nucleoside selectivity in intracellular membranes." J Biol Chem 275:25931-25938.10827169
Synthesis Reference:Doi, Muneharu; Asahi, Satoru; Izawa, Motoo. Fermentative production of uridine and cytidine. Baiosaiensu to Indasutori (1993), 51(12), 972-6.
External Links:
ResourceLink
CHEBI ID16704
HMDB IDHMDB00296
Pubchem Compound ID6029
Kegg IDC00299
ChemSpider ID5807
FOODB IDFDB007411
WikipediaUridine
BioCyc IDURIDINE

Enzymes

General function:
Involved in ATP binding
Specific function:
ATP + uridine = ADP + UMP
Gene Name:
Not Available
Uniprot ID:
Q12084
Molecular weight:
26594.80078
Reactions
ATP + uridine → ADP + UMP.
ATP + cytidine → ADP + CMP.
General function:
Involved in catalytic activity
Specific function:
Could be an enzyme that inactivates 6-azauracil by modifying it
Gene Name:
SDT1
Uniprot ID:
P53078
Molecular weight:
31968.40039
Reactions
General function:
Involved in ATP binding
Specific function:
Catalyzes the conversion of uridine into UMP and cytidine into CMP in the pyrimidine salvage pathway
Gene Name:
URK1
Uniprot ID:
P27515
Molecular weight:
56295.5
Reactions
ATP + uridine → ADP + UMP.
ATP + cytidine → ADP + CMP.
General function:
Involved in zinc ion binding
Specific function:
This enzyme scavenge exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis
Gene Name:
CDD1
Uniprot ID:
Q06549
Molecular weight:
15535.90039
Reactions
Cytidine + H(2)O → uridine + NH(3).
General function:
Involved in hydrolase activity, hydrolyzing N-glycosyl compounds
Specific function:
Also acts on cytidine
Gene Name:
URH1
Uniprot ID:
Q04179
Molecular weight:
37960.0
Reactions
Uridine + H(2)O → D-ribose + uracil.

Transporters

General function:
Involved in nucleobase transmembrane transporter activity
Specific function:
High-affinity transport of uridine
Gene Name:
FUI1
Uniprot ID:
P38196
Molecular weight:
72164.39844