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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).UniRule annotation

Catalytic activityi

Orotidine 5'-phosphate = UMP + CO2.UniRule annotation

Pathwayi: UMP biosynthesis via de novo pathway

This protein is involved in step 2 of the subpathway that synthesizes UMP from orotate.UniRule annotation
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. Orotate phosphoribosyltransferase (pyrE)
  2. Orotidine 5'-phosphate decarboxylase (pyrF)
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 sitei11SubstrateUniRule annotation1
Binding sitei33SubstrateUniRule annotation1
Active sitei62Proton donorUniRule annotation1
Binding sitei120SubstrateUniRule annotation1
Binding sitei181SubstrateUniRule annotation1
Binding sitei190SubstrateUniRule annotation1
Binding sitei210Substrate; via amide nitrogenUniRule annotation1
Binding sitei211SubstrateUniRule annotation1

GO - Molecular functioni

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

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Pyrimidine biosynthesis

Enzyme and pathway databases

BioCyciVCHO:VC1911-MONOMER.
UniPathwayiUPA00070; UER00120.

Names & Taxonomyi

Protein namesi
Recommended name:
Orotidine 5'-phosphate decarboxylaseUniRule annotation (EC:4.1.1.23UniRule annotation)
Alternative name(s):
OMP decarboxylaseUniRule annotation
Short name:
OMPDCaseUniRule annotation
Short name:
OMPdecaseUniRule annotation
Gene namesi
Name:pyrFUniRule annotation
Ordered Locus Names:VC_1911
OrganismiVibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Taxonomic identifieri243277 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
Proteomesi
  • UP000000584 Componenti: Chromosome 1

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001345961 – 231Orotidine 5'-phosphate decarboxylaseAdd BLAST231

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi243277.VC1911.

Structurei

Secondary structure

1231
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi6 – 10Combined sources5
Helixi15 – 22Combined sources8
Helixi27 – 29Combined sources3
Beta strandi31 – 35Combined sources5
Helixi36 – 52Combined sources17
Beta strandi57 – 63Combined sources7
Helixi67 – 79Combined sources13
Beta strandi83 – 88Combined sources6
Helixi89 – 91Combined sources3
Helixi93 – 103Combined sources11
Helixi104 – 109Combined sources6
Beta strandi112 – 116Combined sources5
Helixi124 – 129Combined sources6
Helixi136 – 149Combined sources14
Beta strandi153 – 156Combined sources4
Helixi159 – 169Combined sources11
Beta strandi173 – 178Combined sources6
Beta strandi191 – 193Combined sources3
Helixi196 – 201Combined sources6
Beta strandi205 – 209Combined sources5
Helixi211 – 214Combined sources4
Helixi219 – 229Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3LDVX-ray1.77A/B1-231[»]
3UWQX-ray1.80A/B1-231[»]
ProteinModelPortaliQ9KQT7.
SMRiQ9KQT7.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9KQT7.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni60 – 69Substrate bindingUniRule annotation10

Sequence similaritiesi

Belongs to the OMP decarboxylase family. Type 1 subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4106EG9. Bacteria.
COG0284. LUCA.
KOiK01591.
OMAiNFKIFLD.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01200_B. OMPdecase_type1_B. 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.

Q9KQT7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNDPKVIVAL DYDNLADALA FVDKIDPSTC RLKVGKEMFT LFGPDFVREL
60 70 80 90 100
HKRGFSVFLD LKFHDIPNTC SKAVKAAAEL GVWMVNVHAS GGERMMAASR
110 120 130 140 150
EILEPYGKER PLLIGVTVLT SMESADLQGI GILSAPQDHV LRLATLTKNA
160 170 180 190 200
GLDGVVCSAQ EASLLKQHLG REFKLVTPGI RPAGSEQGDQ RRIMTPAQAI
210 220 230
ASGSDYLVIG RPITQAAHPE VVLEEINSSL V
Length:231
Mass (Da):25,003
Last modified:October 1, 2000 - v1
Checksum:iEB2E841A990B582C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003852 Genomic DNA. Translation: AAF95059.1.
PIRiA82143.
RefSeqiNP_231545.1. NC_002505.1.
WP_000999562.1. NC_002505.1.

Genome annotation databases

EnsemblBacteriaiAAF95059; AAF95059; VC_1911.
GeneIDi2613540.
KEGGivch:VC1911.
PATRICi20082866. VBIVibCho83274_1828.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003852 Genomic DNA. Translation: AAF95059.1.
PIRiA82143.
RefSeqiNP_231545.1. NC_002505.1.
WP_000999562.1. NC_002505.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3LDVX-ray1.77A/B1-231[»]
3UWQX-ray1.80A/B1-231[»]
ProteinModelPortaliQ9KQT7.
SMRiQ9KQT7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243277.VC1911.

Protocols and materials databases

DNASUi2613540.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF95059; AAF95059; VC_1911.
GeneIDi2613540.
KEGGivch:VC1911.
PATRICi20082866. VBIVibCho83274_1828.

Phylogenomic databases

eggNOGiENOG4106EG9. Bacteria.
COG0284. LUCA.
KOiK01591.
OMAiNFKIFLD.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.
BioCyciVCHO:VC1911-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ9KQT7.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01200_B. OMPdecase_type1_B. 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_VIBCH
AccessioniPrimary (citable) accession number: Q9KQT7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 23, 2002
Last sequence update: October 1, 2000
Last modified: November 2, 2016
This is version 93 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic 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

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.