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Identification
YMDB IDYMDB00098
NameUracil
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionUracil, also known as U or hybar X, belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Uracil is an extremely weak basic (essentially neutral) compound (based on its pKa). Uracil exists in all living species, ranging from bacteria to humans. Uracil is a potentially toxic compound.
Structure
Thumb
Synonyms
  • 2,4-Dihydroxypyrimidine
  • 2,4-Dioxopyrimidine
  • 2,4-Pyrimidinediol
  • 2,4-Pyrimidinedione
  • Hybar X
  • Pirod
  • Pyrod
  • Uracil
  • 2,4(1H,3H)-Pyrimidinedione
  • U
  • Ura
  • Urazil
CAS number66-22-8
WeightAverage: 112.0868
Monoisotopic: 112.027277382
InChI KeyISAKRJDGNUQOIC-UHFFFAOYSA-N
InChIInChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)
IUPAC Name1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Nameuracil
Chemical FormulaC4H4N2O2
SMILES[H]N1C([H])=C([H])C(=O)N([H])C1=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentPyrimidones
Alternative Parents
Substituents
  • Pyrimidone
  • Hydropyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Urea
  • Lactam
  • Azacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting point330 °C
Experimental Properties
PropertyValueReference
Water Solubility3.6 mg/mL at 25 oC [YALKOWSKY,SH & DANNENFELSER,RM (1992)]PhysProp
LogP-1.07 [HANSCH,C ET AL. (1995)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility26.5 g/LALOGPS
logP-1.2ALOGPS
logP-0.86ChemAxon
logS-0.63ALOGPS
pKa (Strongest Acidic)9.77ChemAxon
pKa (Strongest Basic)-5.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area58.2 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity25.97 m³·mol⁻¹ChemAxon
Polarizability9.37 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • extracellular
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Pantothenate and CoA biosynthesisPW002463 ThumbThumb?image type=greyscaleThumb?image type=simple
Pyrimidine metabolismPW002469 ThumbThumb?image type=greyscaleThumb?image type=simple
beta-Alanine metabolismPW002381 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Pantothenate and CoA biosynthesisec00770 Map00770
Pyrimidine metabolismec00240 Map00240
beta-Alanine metabolismec00410 Map00410
SMPDB ReactionsNot Available
KEGG Reactions
Cytosine + water + hydronUracil + Ammonium
phosphate + 2'-DeoxyuridineUracil + 2-deoxy-D-ribofuranose 1-phosphate
phosphate + UridineUracil + Ribose 1-phosphate
Uracil + Phosphoribosyl pyrophosphatePyrophosphate + Uridine 5'-monophosphate
Uracil + alpha-D-ribose 5-phosphatewater + Pseudouridine 5'-phosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
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
  • Volland, C., Urban-Grimal, D., Geraud, G., Haguenauer-Tsapis, R. (1994). "Endocytosis and degradation of the yeast uracil permease under adverse conditions." J Biol Chem 269:9833-9841.8144575
  • Volland, C., Garnier, C., Haguenauer-Tsapis, R. (1992). "In vivo phosphorylation of the yeast uracil permease." J Biol Chem 267:23767-23771.1429716
  • Kurtz, J. E., Exinger, F., Erbs, P., Jund, R. (1999). "New insights into the pyrimidine salvage pathway of Saccharomyces cerevisiae: requirement of six genes for cytidine metabolism." Curr Genet 36:130-136.10501935
  • Castrillo, J. I., Zeef, L. A., Hoyle, D. C., Zhang, N., Hayes, A., Gardner, D. C., Cornell, M. J., Petty, J., Hakes, L., Wardleworth, L., Rash, B., Brown, M., Dunn, W. B., Broadhurst, D., O'Donoghue, K., Hester, S. S., Dunkley, T. P., Hart, S. R., Swainston, N., Li, P., Gaskell, S. J., Paton, N. W., Lilley, K. S., Kell, D. B., Oliver, S. G. (2007). "Growth control of the eukaryote cell: a systems biology study in yeast." J Biol 6:4.17439666
Synthesis Reference:Burckhalter, J. H.; Scarborough, Homer C. The synthesis of uracils as anticonvulsants. Journal of the American Pharmaceutical Association (1912-1977) (1955), 44 545-50.
External Links:
ResourceLink
CHEBI ID17568
HMDB IDHMDB00300
Pubchem Compound ID1174
Kegg IDC00106
ChemSpider ID1141
FOODB IDFDB006426
WikipediaUracil
BioCyc IDURACIL

Enzymes

General function:
Involved in purine-nucleoside phosphorylase activity
Specific function:
Cleavage of guanosine or inosine to respective bases and sugar-1-phosphate molecules
Gene Name:
PNP1
Uniprot ID:
Q05788
Molecular weight:
33754.60156
Reactions
Purine nucleoside + phosphate → purine + alpha-D-ribose 1-phosphate.
General function:
Involved in zinc ion binding
Specific function:
Converts cytosine to uracil or 5-methylcytosine to thymine by deaminating carbon number 4
Gene Name:
FCY1
Uniprot ID:
Q12178
Molecular weight:
17506.90039
Reactions
Cytosine + H(2)O → uracil + NH(3).
General function:
Involved in RNA binding
Specific function:
Formation of pseudouridine at positions 27 and 28 in the anticodon stem and loop of transfer RNAs; at positions 34 and 36 of intron-containing precursor tRNA(Ile) and at position 35 in the intron-containing tRNA(Tyr)
Gene Name:
PUS1
Uniprot ID:
Q12211
Molecular weight:
62142.0
Reactions
tRNA uridine → tRNA pseudouridine.
General function:
Involved in RNA processing
Specific function:
Responsible for synthesis of pseudouridine from uracil- 55 in the psi GC loop of transfer RNAs
Gene Name:
PUS4
Uniprot ID:
P48567
Molecular weight:
45273.10156
Reactions
tRNA uridine → tRNA pseudouridine.
General function:
Involved in RNA binding
Specific function:
Formation of pseudouridine in the anticodon stem and loop of transfer RNAs
Gene Name:
PUS2
Uniprot ID:
P53167
Molecular weight:
41874.80078
Reactions
tRNA uridine → tRNA pseudouridine.
General function:
Involved in RNA binding
Specific function:
Formation of pseudouridines at positions 38 and 39 in the anticodon stem and loop of transfer RNAs
Gene Name:
PUS3
Uniprot ID:
P31115
Molecular weight:
50888.30078
Reactions
tRNA uridine → tRNA pseudouridine.
General function:
Nucleotide transport and metabolism
Specific function:
Catalyzes the conversion of uracil and 5-phospho-alpha- D-ribose 1-diphosphate (PRPP) to UMP and diphosphate
Gene Name:
FUR1
Uniprot ID:
P18562
Molecular weight:
24594.19922
Reactions
UMP + diphosphate → uracil + 5-phospho-alpha-D-ribose 1-diphosphate.
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:
Transport of uracil
Gene Name:
FUR4
Uniprot ID:
P05316
Molecular weight:
71735.10156