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Uracil (YMDB00098)

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
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
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)8.8ChemAxon
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 + hydron → Uracil + Ammonium
phosphate + 2'-Deoxyuridine ↔ Uracil + 2-deoxy-D-ribofuranose 1-phosphate
phosphate + Uridine ↔ Uracil + Ribose 1-phosphate
Uracil + Phosphoribosyl pyrophosphate → Pyrophosphate + Uridine 5'-monophosphate
Uracil + alpha-D-ribose 5-phosphate ↔ water + Pseudouridine 5'-phosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-0002-5950000000-18425875415ad150c4fcJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (2 TMS)splash10-006t-9740000000-e884a4b98e7e9dc75e5fJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (2 TMS)splash10-052e-7790000000-026cb6beb5cde6a61b80JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-02tc-9200000000-4a57c4e06fd552d6a9bfJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-03xu-9400000000-1c29f070a8135b06f88bJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0002-5950000000-18425875415ad150c4fcJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-006t-9740000000-e884a4b98e7e9dc75e5fJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-052e-7790000000-026cb6beb5cde6a61b80JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0002-6940000000-a726178341f6443e60ccJSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-03xu-9300000000-6a96f6ce1ef731689107JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-03di-3900000000-e422eda255a4b6414f86JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-006y-9000000000-130eb5f4414426e03667JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0006-9100000000-c096d08ca715d97cd732JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - EI-B (HITACHI M-60) , Positivesplash10-02tc-9200000000-83a0a6ad4fc1b407e570JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - EI-B (HITACHI M-80) , Positivesplash10-03xu-9400000000-acd0cfd54af7d6a55283JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-03di-0900000000-309fe212c929f3c6a930JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-03di-6900000000-55a7de75a40eab61da8bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-0006-9000000000-1c3caab26eb7e359db92JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0006-9000000000-7494d4e611a73ecb79eaJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0006-9000000000-ed4046b040337db620d8JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-03di-0900000000-ff54f3083ce4ccccfd95JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-03di-0900000000-6728c1eb6f68b40c09f8JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-03di-0900000000-309fe212c929f3c6a930JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-03di-6900000000-55a7de75a40eab61da8bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-9000000000-1c3caab26eb7e359db92JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-9000000000-7494d4e611a73ecb79eaJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-9000000000-ed4046b040337db620d8JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-03di-0900000000-6728c1eb6f68b40c09f8JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - , negativesplash10-03di-0900000000-a21102c708f8d5eaf262JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-1900000000-0029cbdcaa1377a4d03eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0229-9400000000-c227e1deb392170cb323JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-9000000000-3cf6f9fc3ab6890266acJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-4900000000-67a3d94ab649e28bda13JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-9100000000-bbf50de54fc413b6588eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-98042b91f1087b0c2563JSpectraViewer
MSMass Spectrum (Electron Ionization)splash10-03xu-9400000000-d7ffe72f606f1af3349bJSpectraViewer | MoNA
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
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

Protein Details
1. Purine nucleoside phosphorylase
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.
Protein Details
2. Cytosine deaminase
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).
Protein Details
3. tRNA pseudouridine synthase 1
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.
Protein Details
4. tRNA pseudouridine synthase 4
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.
Protein Details
5. tRNA pseudouridine synthase 2
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.
Protein Details
6. tRNA pseudouridine synthase 3
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.
Protein Details
7. Uracil phosphoribosyltransferase
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.
Protein Details
8. Uridine nucleosidase
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

Protein Details
1. Uracil permease
General function:
Involved in nucleobase transmembrane transporter activity
Specific function:
Transport of uracil
Gene Name:
FUR4
Uniprot ID:
P05316
Molecular weight:
71735.10156