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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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

Pathway: 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. no protein annotated in this organism
  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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei11 – 111SubstrateUniRule annotation
Binding sitei33 – 331SubstrateUniRule annotation
Active sitei62 – 621Proton donorUniRule annotation
Binding sitei120 – 1201SubstrateUniRule annotation
Binding sitei181 – 1811SubstrateUniRule annotation
Binding sitei190 – 1901SubstrateUniRule annotation
Binding sitei210 – 2101Substrate; via amide nitrogenUniRule annotation
Binding sitei211 – 2111SubstrateUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Pyrimidine biosynthesis

Enzyme and pathway databases

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:VC0395_A1501, VC395_2026
OrganismiVibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)
Taxonomic identifieri345073 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000001630 Componenti: Chromosome I

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 231231Orotidine 5'-phosphate decarboxylasePRO_1000073091Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi345073.VC0395_A1501.

Structurei

3D structure databases

ProteinModelPortaliA5F6Y1.
SMRiA5F6Y1. Positions 2-230.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni60 – 6910Substrate bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0284.
HOGENOMiHOG000226071.
KOiK01591.
OMAiNFKIFLD.

Family and domain databases

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

A5F6Y1-1 [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 LRLATLAKNA
160 170 180 190 200
GLDGVVCSAQ EASLLKQHLG REFKLVTPGI RPAGSEQGDQ RRIMTPAQAI
210 220 230
ASGSDYLVIG RPITQAAHPE VVLEEINSSL V
Length:231
Mass (Da):24,973
Last modified:June 12, 2007 - v1
Checksum:iFE3AC11A8211E987
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000627 Genomic DNA. Translation: ABQ21404.1.
CP001235 Genomic DNA. Translation: ACP10019.1.
RefSeqiWP_000999561.1. NC_012582.1.
YP_001217444.1. NC_009457.1.
YP_002820255.1. NC_012582.1.

Genome annotation databases

EnsemblBacteriaiABQ21404; ABQ21404; VC0395_A1501.
ACP10019; ACP10019; VC395_2026.
KEGGivco:VC0395_A1501.
vcr:VC395_2026.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000627 Genomic DNA. Translation: ABQ21404.1.
CP001235 Genomic DNA. Translation: ACP10019.1.
RefSeqiWP_000999561.1. NC_012582.1.
YP_001217444.1. NC_009457.1.
YP_002820255.1. NC_012582.1.

3D structure databases

ProteinModelPortaliA5F6Y1.
SMRiA5F6Y1. Positions 2-230.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi345073.VC0395_A1501.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABQ21404; ABQ21404; VC0395_A1501.
ACP10019; ACP10019; VC395_2026.
KEGGivco:VC0395_A1501.
vcr:VC395_2026.

Phylogenomic databases

eggNOGiCOG0284.
HOGENOMiHOG000226071.
KOiK01591.
OMAiNFKIFLD.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.

Family and domain databases

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

Publicationsi

  1. Heidelberg J.
    Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 39541 / Classical Ogawa 395 / O395.
  2. "A recalibrated molecular clock and independent origins for the cholera pandemic clones."
    Feng L., Reeves P.R., Lan R., Ren Y., Gao C., Zhou Z., Ren Y., Cheng J., Wang W., Wang J., Qian W., Li D., Wang L.
    PLoS ONE 3:E4053-E4053(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 39541 / Classical Ogawa 395 / O395.

Entry informationi

Entry nameiPYRF_VIBC3
AccessioniPrimary (citable) accession number: A5F6Y1
Secondary accession number(s): C3M1W4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 26, 2008
Last sequence update: June 12, 2007
Last modified: June 24, 2015
This is version 53 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

Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.