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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei9 – 91SubstrateUniRule annotation
Binding sitei31 – 311SubstrateUniRule annotation
Active sitei60 – 601Proton donorUniRule annotation
Binding sitei121 – 1211SubstrateUniRule annotation
Binding sitei180 – 1801SubstrateUniRule annotation
Binding sitei190 – 1901SubstrateUniRule annotation
Binding sitei210 – 2101Substrate; via amide nitrogenUniRule annotation
Binding sitei211 – 2111SubstrateUniRule annotation

GO - Molecular functioni

  1. orotidine-5'-phosphate decarboxylase activity Source: UniProtKB-HAMAP

GO - Biological processi

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

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Pyrimidine biosynthesis

Enzyme and pathway databases

BioCyciDVUL882:GJIL-925-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:DVU_0901
OrganismiDesulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Taxonomic identifieri882 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
ProteomesiUP000002194: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 235235Orotidine 5'-phosphate decarboxylasePRO_0000241855Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi882.DVU0901.

Structurei

3D structure databases

ProteinModelPortaliQ72DM8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni58 – 6710Substrate bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0284.
KOiK01591.
OMAiNFKIFLD.
OrthoDBiEOG6N6815.
PhylomeDBiQ72DM8.

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.

Q72DM8-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAELVVALDF PAADVAVDMA GRLRGTAPWM KVGLELFCAA GPDVVRAVAD
60 70 80 90 100
LGFRVFLDLK FHDIPNTVRG AVRSAVRSGA DMVNIHLMGG ERMARAAVEG
110 120 130 140 150
LHEGAQTTGS VPLLFGVTVL TSTAQGELPG ISTDIGEYAA SLAASGAAWG
160 170 180 190 200
LNGVVCSGYE VESIKKRCGA SFLCLTPGIR PGGGAGGDDQ RRVMTPAQAV
210 220 230
SAGSDYLVVG RPVTGAADPA AAARAIMAEM AAVRR
Length:235
Mass (Da):24,025
Last modified:July 5, 2004 - v1
Checksum:i892DC580E9D51098
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE017285 Genomic DNA. Translation: AAS95381.1.
RefSeqiYP_010122.1. NC_002937.3.

Genome annotation databases

EnsemblBacteriaiAAS95381; AAS95381; DVU_0901.
GeneIDi2795411.
KEGGidvu:DVU0901.
PATRICi32061716. VBIDesVul119526_0845.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE017285 Genomic DNA. Translation: AAS95381.1.
RefSeqiYP_010122.1. NC_002937.3.

3D structure databases

ProteinModelPortaliQ72DM8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi882.DVU0901.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAS95381; AAS95381; DVU_0901.
GeneIDi2795411.
KEGGidvu:DVU0901.
PATRICi32061716. VBIDesVul119526_0845.

Phylogenomic databases

eggNOGiCOG0284.
KOiK01591.
OMAiNFKIFLD.
OrthoDBiEOG6N6815.
PhylomeDBiQ72DM8.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.
BioCyciDVUL882:GJIL-925-MONOMER.

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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Hildenborough / ATCC 29579 / NCIMB 8303.

Entry informationi

Entry nameiPYRF_DESVH
AccessioniPrimary (citable) accession number: Q72DM8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 27, 2006
Last sequence update: July 5, 2004
Last modified: January 7, 2015
This is version 73 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, Reference 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.