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P03962

- PYRF_YEAST

UniProt

P03962 - PYRF_YEAST

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Protein

Orotidine 5'-phosphate decarboxylase

Gene

URA3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Catalytic activityi

Orotidine 5'-phosphate = UMP + CO2.PROSITE-ProRule annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei37 – 371Substrate
Active sitei93 – 931Proton donor
Binding sitei217 – 2171Substrate
Binding sitei235 – 2351Substrate

GO - Molecular functioni

  1. orotidine-5'-phosphate decarboxylase activity Source: SGD

GO - Biological processi

  1. 'de novo' pyrimidine nucleobase biosynthetic process Source: SGD
  2. 'de novo' UMP biosynthetic process Source: UniProtKB-UniPathway
  3. UMP biosynthetic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Pyrimidine biosynthesis

Enzyme and pathway databases

BioCyciYEAST:YEL021W-MONOMER.
SABIO-RKP03962.
UniPathwayiUPA00070; UER00120.

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:URA3
Ordered Locus Names:YEL021W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome V

Organism-specific databases

CYGDiYEL021w.
SGDiS000000747. URA3.

Subcellular locationi

GO - Cellular componenti

  1. cytosol Source: SGD
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi59 – 591K → A: Reduces Kcat 100-fold. Reduces substrate affinity 900-fold. 1 Publication
Mutagenesisi91 – 911D → A: Reduces activity over 100000-fold. 1 Publication
Mutagenesisi93 – 931K → A: Reduces activity over 100000-fold. 1 Publication
Mutagenesisi96 – 961D → A: Reduces Kcat over 100000-fold. Reduces substrate affinity 11-fold. 1 Publication
Mutagenesisi215 – 2151Q → A: No effect. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 267266Orotidine 5'-phosphate decarboxylasePRO_0000134692Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserine1 Publication
Cross-linki93 – 93Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki209 – 209Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki253 – 253Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication

Keywords - PTMi

Acetylation, Isopeptide bond, Ubl conjugation

Proteomic databases

PaxDbiP03962.
PeptideAtlasiP03962.
PRIDEiP03962.

Expressioni

Gene expression databases

GenevestigatoriP03962.

Interactioni

Protein-protein interaction databases

BioGridi36708. 11 interactions.
DIPiDIP-6576N.
MINTiMINT-410591.
STRINGi4932.YEL021W.

Structurei

Secondary structure

1
267
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi6 – 127
Helixi16 – 2813
Beta strandi32 – 354
Helixi41 – 5111
Helixi52 – 543
Beta strandi56 – 605
Helixi62 – 643
Turni70 – 734
Helixi74 – 8411
Beta strandi87 – 948
Helixi98 – 1069
Turni108 – 1103
Helixi112 – 1154
Beta strandi117 – 1226
Helixi123 – 1253
Helixi128 – 14013
Beta strandi146 – 1505
Helixi162 – 17211
Turni176 – 1783
Beta strandi179 – 1835
Helixi191 – 1933
Beta strandi198 – 2014
Beta strandi203 – 2053
Turni208 – 2103
Helixi214 – 2163
Beta strandi217 – 2193
Helixi220 – 2256
Beta strandi229 – 2335
Helixi235 – 2373
Helixi244 – 26219

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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[»]
ProteinModelPortaliP03962.
SMRiP03962. Positions 3-263.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03962.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni59 – 613Substrate binding
Regioni91 – 10010Substrate binding

Sequence similaritiesi

Belongs to the OMP decarboxylase family.Curated

Phylogenomic databases

eggNOGiCOG0284.
GeneTreeiENSGT00390000001856.
HOGENOMiHOG000213905.
KOiK01591.
OMAiMGQQYRT.
OrthoDBiEOG7CVQ76.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR014732. OMPdecase.
IPR018089. OMPdecase_AS.
IPR001754. OMPdeCOase_dom.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]
PfamiPF00215. OMPdecase. 1 hit.
[Graphical view]
SMARTiSM00934. OMPdecase. 1 hit.
[Graphical view]
SUPFAMiSSF51366. SSF51366. 1 hit.
TIGRFAMsiTIGR01740. pyrF. 1 hit.
PROSITEiPS00156. OMPDECASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P03962-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSKATYKERA ATHPSPVAAK LFNIMHEKQT NLCASLDVRT TKELLELVEA
60 70 80 90 100
LGPKICLLKT HVDILTDFSM EGTVKPLKAL SAKYNFLLFE DRKFADIGNT
110 120 130 140 150
VKLQYSAGVY RIAEWADITN AHGVVGPGIV SGLKQAAEEV TKEPRGLLML
160 170 180 190 200
AELSCKGSLA TGEYTKGTVD IAKSDKDFVI GFIAQRDMGG RDEGYDWLIM
210 220 230 240 250
TPGVGLDDKG DALGQQYRTV DDVVSTGSDI IIVGRGLFAK GRDAKVEGER
260
YRKAGWEAYL RRCGQQN
Length:267
Mass (Da):29,240
Last modified:February 1, 1995 - v2
Checksum:iD63EF9877BD0F984
GO

Sequence cautioni

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

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti71 – 733EGT → RIR in AAA35199. 1 PublicationCurated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti160 – 1601A → S in strain: +D4.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
PIRiA01082. DEBYOP.
S05735. DCBYOF.
RefSeqiNP_010893.3. NM_001178836.3.

Genome annotation databases

EnsemblFungiiYEL021W; YEL021W; YEL021W.
GeneIDi856692.
KEGGisce:YEL021W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
PIRi A01082. DEBYOP.
S05735. DCBYOF.
RefSeqi NP_010893.3. NM_001178836.3.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1DQW X-ray 2.10 A/B/C/D 1-267 [» ]
1DQX X-ray 2.40 A/B/C/D 1-267 [» ]
3GDK X-ray 2.00 A/B/C/D 1-267 [» ]
3GDL X-ray 1.65 A/B 1-267 [» ]
3GDM X-ray 1.60 A/B 1-267 [» ]
3GDR X-ray 1.90 A/B/C/D 1-267 [» ]
3GDT X-ray 1.60 A/B/C/D 1-267 [» ]
ProteinModelPortali P03962.
SMRi P03962. Positions 3-263.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 36708. 11 interactions.
DIPi DIP-6576N.
MINTi MINT-410591.
STRINGi 4932.YEL021W.

Chemistry

BindingDBi P03962.
ChEMBLi CHEMBL4858.

Proteomic databases

PaxDbi P03962.
PeptideAtlasi P03962.
PRIDEi P03962.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YEL021W ; YEL021W ; YEL021W .
GeneIDi 856692.
KEGGi sce:YEL021W.

Organism-specific databases

CYGDi YEL021w.
SGDi S000000747. URA3.

Phylogenomic databases

eggNOGi COG0284.
GeneTreei ENSGT00390000001856.
HOGENOMi HOG000213905.
KOi K01591.
OMAi MGQQYRT.
OrthoDBi EOG7CVQ76.

Enzyme and pathway databases

UniPathwayi UPA00070 ; UER00120 .
BioCyci YEAST:YEL021W-MONOMER.
SABIO-RK P03962.

Miscellaneous databases

EvolutionaryTracei P03962.
NextBioi 982739.

Gene expression databases

Genevestigatori P03962.

Family and domain databases

Gene3Di 3.20.20.70. 1 hit.
InterProi IPR013785. Aldolase_TIM.
IPR014732. OMPdecase.
IPR018089. OMPdecase_AS.
IPR001754. OMPdeCOase_dom.
IPR011060. RibuloseP-bd_barrel.
[Graphical view ]
Pfami PF00215. OMPdecase. 1 hit.
[Graphical view ]
SMARTi SM00934. OMPdecase. 1 hit.
[Graphical view ]
SUPFAMi SSF51366. SSF51366. 1 hit.
TIGRFAMsi TIGR01740. pyrF. 1 hit.
PROSITEi PS00156. OMPDECASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. 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. Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-93; LYS-209 AND LYS-253.
    Strain: SUB592.
  9. 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.

Entry informationi

Entry nameiPYRF_YEAST
AccessioniPrimary (citable) accession number: P03962
Secondary accession number(s): D3DLM7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 23, 1986
Last sequence update: February 1, 1995
Last modified: October 1, 2014
This is version 152 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome V
    Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

External Data

Dasty 3