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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Geobacter daltonii (strain DSM 22248 / JCM 15807 / FRC-32)
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 sitei15 – 151SubstrateUniRule annotation
Binding sitei37 – 371SubstrateUniRule annotation
Active sitei66 – 661Proton donorUniRule annotation
Binding sitei126 – 1261SubstrateUniRule annotation
Binding sitei187 – 1871SubstrateUniRule annotation
Binding sitei196 – 1961SubstrateUniRule annotation
Binding sitei216 – 2161Substrate; via amide nitrogenUniRule annotation
Binding sitei217 – 2171SubstrateUniRule 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

BioCyciGSP316067:GHSV-2429-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:Geob_2402
OrganismiGeobacter daltonii (strain DSM 22248 / JCM 15807 / FRC-32)
Taxonomic identifieri316067 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfuromonadalesGeobacteraceaeGeobacter
ProteomesiUP000007721: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 239239Orotidine 5'-phosphate decarboxylasePRO_1000164571Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi316067.Geob_2402.

Structurei

3D structure databases

ProteinModelPortaliB9LZK2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni64 – 7310Substrate bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0284.
HOGENOMiHOG000226070.
KOiK01591.
OMAiNFKIFLD.
OrthoDBiEOG6N6815.

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.

B9LZK2-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MTRDEARAKI IFALDVNEFS DVEKWADLLS PHVGMFKVGK QLYTACGPAV
60 70 80 90 100
VRMIQKYGGE VFLDLKYHDI PNTVAMASLE AARMGVKLFN LHALGGYEMM
110 120 130 140 150
AKTVETLDKE FKGEERGKVL AVTILTSSNE QTLQEVGINL PVPEMVVKLA
160 170 180 190 200
ALAKKAGIDG VVASPQEVPL IREACGNDFL IVTPGVRPAF AAADDQKRIM
210 220 230
TPAEAVKSGA DYLVIGRPIA AAPNPAEAAQ AIVAEIVAG
Length:239
Mass (Da):25,577
Last modified:March 24, 2009 - v1
Checksum:iE5FB83DE1E2E4BF6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001390 Genomic DNA. Translation: ACM20755.1.
RefSeqiYP_002537856.1. NC_011979.1.

Genome annotation databases

EnsemblBacteriaiACM20755; ACM20755; Geob_2402.
GeneIDi7363916.
KEGGigeo:Geob_2402.
PATRICi22011445. VBIGeoSp137169_2484.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001390 Genomic DNA. Translation: ACM20755.1.
RefSeqiYP_002537856.1. NC_011979.1.

3D structure databases

ProteinModelPortaliB9LZK2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi316067.Geob_2402.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACM20755; ACM20755; Geob_2402.
GeneIDi7363916.
KEGGigeo:Geob_2402.
PATRICi22011445. VBIGeoSp137169_2484.

Phylogenomic databases

eggNOGiCOG0284.
HOGENOMiHOG000226070.
KOiK01591.
OMAiNFKIFLD.
OrthoDBiEOG6N6815.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.
BioCyciGSP316067:GHSV-2429-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: DSM 22248 / JCM 15807 / FRC-32.

Entry informationi

Entry nameiPYRF_GEODF
AccessioniPrimary (citable) accession number: B9LZK2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: March 24, 2009
Last modified: January 7, 2015
This is version 39 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.