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P03962 (PYRF_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 151. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Orotidine 5'-phosphate decarboxylase

EC=4.1.1.23
Alternative name(s):
OMP decarboxylase
Short name=OMPDCase
Short name=OMPdecase
Uridine 5'-monophosphate synthase
Short name=UMP synthase
Gene names
Name:URA3
Ordered Locus Names:YEL021W
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length267 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Catalytic activity

Orotidine 5'-phosphate = UMP + CO2.

Pathway

Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 2/2.

Sequence similarities

Belongs to the OMP decarboxylase family.

Sequence caution

The sequence CAA25010.1 differs from that shown. Reason: Erroneous initiation.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.9
Chain2 – 267266Orotidine 5'-phosphate decarboxylase
PRO_0000134692

Regions

Region59 – 613Substrate binding
Region91 – 10010Substrate binding

Sites

Active site931Proton donor
Binding site371Substrate
Binding site2171Substrate
Binding site2351Substrate

Amino acid modifications

Modified residue21N-acetylserine Ref.9
Cross-link93Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.8
Cross-link209Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.8
Cross-link253Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.8

Natural variations

Natural variant1601A → S in strain: +D4.

Experimental info

Mutagenesis591K → A: Reduces Kcat 100-fold. Reduces substrate affinity 900-fold. Ref.7
Mutagenesis911D → A: Reduces activity over 100000-fold. Ref.7
Mutagenesis931K → A: Reduces activity over 100000-fold. Ref.7
Mutagenesis961D → A: Reduces Kcat over 100000-fold. Reduces substrate affinity 11-fold. Ref.7
Mutagenesis2151Q → A: No effect. Ref.7
Sequence conflict71 – 733EGT → RIR in AAA35199. Ref.4

Secondary structure

....................................................... 267
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P03962 [UniParc].

Last modified February 1, 1995. Version 2.
Checksum: D63EF9877BD0F984

FASTA26729,240
        10         20         30         40         50         60 
MSKATYKERA ATHPSPVAAK LFNIMHEKQT NLCASLDVRT TKELLELVEA LGPKICLLKT 

        70         80         90        100        110        120 
HVDILTDFSM EGTVKPLKAL SAKYNFLLFE DRKFADIGNT VKLQYSAGVY RIAEWADITN 

       130        140        150        160        170        180 
AHGVVGPGIV SGLKQAAEEV TKEPRGLLML AELSCKGSLA TGEYTKGTVD IAKSDKDFVI 

       190        200        210        220        230        240 
GFIAQRDMGG RDEGYDWLIM TPGVGLDDKG DALGQQYRTV DDVVSTGSDI IIVGRGLFAK 

       250        260 
GRDAKVEGER YRKAGWEAYL RRCGQQN 

« Hide

References

« Hide 'large scale' references
[1]"Structure and function of the yeast URA3 gene: expression in Escherichia coli."
Rose M., Grisafi P., Botstein D.
Gene 29:113-124(1984) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: +D4 and ATCC 28383 / FL100 / VTT C-80102.
[2]"The nucleotide sequence of Saccharomyces cerevisiae chromosome V."
Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E., Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S., Hyman R.W. expand/collapse author list , Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X., Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y., Botstein D., Davis R.W.
Nature 387:78-81(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]Holtz A., Lou Y.
Submitted (JUN-1997) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[5]"Transcription terminator-like element within a Saccharomyces cerevisiae promoter region."
Yarger J.G., Armilei G., Gorman M.C.
Mol. Cell. Biol. 6:1095-1101(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-73.
[6]"Structure and function of the yeast URA3 gene. Differentially regulated expression of hybrid beta-galactosidase from overlapping coding sequences in yeast."
Rose M., Botstein D.
J. Mol. Biol. 170:883-904(1983) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-11.
[7]"Dissecting a charged network at the active site of orotidine-5'-phosphate decarboxylase."
Miller B.G., Snider M.J., Wolfenden R., Short S.A.
J. Biol. Chem. 276:15174-15176(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF LYS-59; ASP-91; LYS-93; ASP-96 AND GLN-215.
[8]"A proteomics approach to understanding protein ubiquitination."
Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G., Roelofs J., Finley D., Gygi S.P.
Nat. Biotechnol. 21:921-926(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-93; LYS-209 AND LYS-253.
Strain: SUB592.
[9]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
[10]"Anatomy of a proficient enzyme: the structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog."
Miller B.G., Hassell A.M., Wolfenden R., Milburn M.V., Short S.A.
Proc. Natl. Acad. Sci. U.S.A. 97:2011-2016(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH TRANSITION STATE ANALOG.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
K02206 Genomic DNA. Translation: AAA34824.1.
K02207 Genomic DNA. Translation: AAA34825.1.
U18530 Genomic DNA. Translation: AAB64498.1.
U89671 Genomic DNA. Translation: AAB49978.1.
M12926 Genomic DNA. Translation: AAA35199.1.
X00191 Genomic DNA. Translation: CAA25010.1. Different initiation.
U89927 Genomic DNA. Translation: AAB64383.1.
U63018 Genomic DNA. Translation: AAC53678.1.
BK006939 Genomic DNA. Translation: DAA07631.1.
PIRDEBYOP. A01082.
DCBYOF. S05735.
RefSeqNP_010893.3. NM_001178836.3.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1DQWX-ray2.10A/B/C/D1-267[»]
1DQXX-ray2.40A/B/C/D1-267[»]
3GDKX-ray2.00A/B/C/D1-267[»]
3GDLX-ray1.65A/B1-267[»]
3GDMX-ray1.60A/B1-267[»]
3GDRX-ray1.90A/B/C/D1-267[»]
3GDTX-ray1.60A/B/C/D1-267[»]
ProteinModelPortalP03962.
SMRP03962. Positions 3-263.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid36708. 11 interactions.
DIPDIP-6576N.
MINTMINT-410591.
STRING4932.YEL021W.

Chemistry

BindingDBP03962.
ChEMBLCHEMBL4858.

Proteomic databases

PaxDbP03962.
PeptideAtlasP03962.
PRIDEP03962.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYEL021W; YEL021W; YEL021W.
GeneID856692.
KEGGsce:YEL021W.

Organism-specific databases

CYGDYEL021w.
SGDS000000747. URA3.

Phylogenomic databases

eggNOGCOG0284.
GeneTreeENSGT00390000001856.
HOGENOMHOG000213905.
KOK01591.
OMAMGQQYRT.
OrthoDBEOG7CVQ76.

Enzyme and pathway databases

BioCycYEAST:YEL021W-MONOMER.
SABIO-RKP03962.
UniPathwayUPA00070; UER00120.

Gene expression databases

GenevestigatorP03962.

Family and domain databases

Gene3D3.20.20.70. 1 hit.
InterProIPR013785. Aldolase_TIM.
IPR014732. OMPdecase.
IPR018089. OMPdecase_AS.
IPR001754. OMPdeCOase_dom.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]
PfamPF00215. OMPdecase. 1 hit.
[Graphical view]
SMARTSM00934. OMPdecase. 1 hit.
[Graphical view]
SUPFAMSSF51366. SSF51366. 1 hit.
TIGRFAMsTIGR01740. pyrF. 1 hit.
PROSITEPS00156. OMPDECASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP03962.
NextBio982739.

Entry information

Entry namePYRF_YEAST
AccessionPrimary (citable) accession number: P03962
Secondary accession number(s): D3DLM7
Entry history
Integrated into UniProtKB/Swiss-Prot: October 23, 1986
Last sequence update: February 1, 1995
Last modified: July 9, 2014
This is version 151 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome V

Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways