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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: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

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

Pathwayi: UMP biosynthesis via de novo pathway

This protein is involved in step 2 of the subpathway that synthesizes UMP from orotate.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. Orotate phosphoribosyltransferase 1 (URA5), Orotate phosphoribosyltransferase 2 (URA10)
  2. Orotidine 5'-phosphate decarboxylase (URA3)
This subpathway is part of the pathway UMP biosynthesis via de novo pathway, which is itself part of Pyrimidine metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes UMP from orotate, the pathway UMP biosynthesis via de novo pathway and in Pyrimidine metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei37Substrate1
Active sitei93Proton donor1
Binding sitei217Substrate1
Binding sitei235Substrate1

GO - Molecular functioni

  • orotidine-5'-phosphate decarboxylase activity Source: SGD

GO - Biological processi

  • 'de novo' pyrimidine nucleobase biosynthetic process Source: SGD
  • 'de novo' UMP biosynthetic process Source: UniProtKB-UniPathway
  • 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.
BRENDAi4.1.1.23. 984.
ReactomeiR-SCE-500753. Pyrimidine biosynthesis.
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
Proteomesi
  • UP000002311 Componenti: Chromosome V

Organism-specific databases

EuPathDBiFungiDB:YEL021W.
SGDiS000000747. URA3.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: SGD
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi59K → A: Reduces Kcat 100-fold. Reduces substrate affinity 900-fold. 1 Publication1
Mutagenesisi91D → A: Reduces activity over 100000-fold. 1 Publication1
Mutagenesisi93K → A: Reduces activity over 100000-fold. 1 Publication1
Mutagenesisi96D → A: Reduces Kcat over 100000-fold. Reduces substrate affinity 11-fold. 1 Publication1
Mutagenesisi215Q → A: No effect. 1 Publication1

Chemistry databases

ChEMBLiCHEMBL4858.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00001346922 – 267Orotidine 5'-phosphate decarboxylaseAdd BLAST266

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1
Cross-linki93Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki209Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki253Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication

Keywords - PTMi

Acetylation, Isopeptide bond, Ubl conjugation

Proteomic databases

PRIDEiP03962.

Interactioni

Protein-protein interaction databases

BioGridi36708. 11 interactors.
DIPiDIP-6576N.
MINTiMINT-410591.

Chemistry databases

BindingDBiP03962.

Structurei

Secondary structure

1267
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 12Combined sources7
Helixi16 – 28Combined sources13
Beta strandi32 – 35Combined sources4
Helixi41 – 51Combined sources11
Helixi52 – 54Combined sources3
Beta strandi56 – 60Combined sources5
Helixi62 – 64Combined sources3
Turni70 – 73Combined sources4
Helixi74 – 84Combined sources11
Beta strandi87 – 94Combined sources8
Helixi98 – 106Combined sources9
Turni108 – 110Combined sources3
Helixi112 – 115Combined sources4
Beta strandi117 – 122Combined sources6
Helixi123 – 125Combined sources3
Helixi128 – 140Combined sources13
Beta strandi146 – 150Combined sources5
Helixi162 – 172Combined sources11
Turni176 – 178Combined sources3
Beta strandi179 – 183Combined sources5
Helixi191 – 193Combined sources3
Beta strandi198 – 201Combined sources4
Beta strandi203 – 205Combined sources3
Turni208 – 210Combined sources3
Helixi214 – 216Combined sources3
Beta strandi217 – 219Combined sources3
Helixi220 – 225Combined sources6
Beta strandi229 – 233Combined sources5
Helixi235 – 237Combined sources3
Helixi244 – 262Combined sources19

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03962.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni59 – 61Substrate binding3
Regioni91 – 100Substrate binding10

Sequence similaritiesi

Belongs to the OMP decarboxylase family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000001856.
HOGENOMiHOG000213905.
KOiK01591.
OMAiMGQQYRT.
OrthoDBiEOG092C3SZ1.

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 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti71 – 73EGT → RIR in AAA35199 (Ref. 4) Curated3

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti160A → S in strain: +D4. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36708. 11 interactors.
DIPiDIP-6576N.
MINTiMINT-410591.

Chemistry databases

BindingDBiP03962.
ChEMBLiCHEMBL4858.

Proteomic databases

PRIDEiP03962.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YEL021W.
SGDiS000000747. URA3.

Phylogenomic databases

GeneTreeiENSGT00390000001856.
HOGENOMiHOG000213905.
KOiK01591.
OMAiMGQQYRT.
OrthoDBiEOG092C3SZ1.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.
BioCyciYEAST:YEL021W-MONOMER.
BRENDAi4.1.1.23. 984.
ReactomeiR-SCE-500753. Pyrimidine biosynthesis.
SABIO-RKP03962.

Miscellaneous databases

EvolutionaryTraceiP03962.
PROiP03962.

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]
ProtoNetiSearch...

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: November 2, 2016
This is version 168 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.