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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Geobacter sp. (strain M21)
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: 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 sitei15SubstrateUniRule annotation1
Binding sitei37SubstrateUniRule annotation1
Active sitei66Proton donorUniRule annotation1
Binding sitei127SubstrateUniRule annotation1
Binding sitei188SubstrateUniRule annotation1
Binding sitei197SubstrateUniRule annotation1
Binding sitei217Substrate; via amide nitrogenUniRule annotation1
Binding sitei218SubstrateUniRule annotation1

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:GM21_1335
OrganismiGeobacter sp. (strain M21)
Taxonomic identifieri443144 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfuromonadalesGeobacteraceaeGeobacter
Proteomesi
  • UP000002380 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10002138201 – 240Orotidine 5'-phosphate decarboxylaseAdd BLAST240

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi443144.GM21_1335.

Structurei

3D structure databases

ProteinModelPortaliC6E497.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni64 – 73Substrate bindingUniRule annotation10

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4106EG9. Bacteria.
COG0284. LUCA.
HOGENOMiHOG000226070.
KOiK01591.
OMAiNFKIFLD.
OrthoDBiPOG091H0256.

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.

C6E497-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTREEAIKKI IFAMDVKEFS DVQYWAELLS QHVGMFKVGK QLYTACGPAA
60 70 80 90 100
VRMIQKCGGE VFLDLKYHDI PNTVAMATLE AANLGVQLCD LHAMGGYEMM
110 120 130 140 150
NKTMEALDKN FSGCTPRPKV LAITVLTSSN EETLRGIGIE LPVPEMVVKL
160 170 180 190 200
AKLAKSAGVD GVVASPQEVE LIREACGKDF LVVTPGVRPS FASADDQKRI
210 220 230 240
MTPAEAVKAG ADYLVIGRPI AAAQSPVEAA QKIVDEIVAG
Length:240
Mass (Da):25,798
Last modified:September 1, 2009 - v1
Checksum:i066776E115554332
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001661 Genomic DNA. Translation: ACT17395.1.
RefSeqiWP_015836646.1. NC_012918.1.

Genome annotation databases

EnsemblBacteriaiACT17395; ACT17395; GM21_1335.
KEGGigem:GM21_1335.
PATRICi22017126. VBIGeoSp56140_1299.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001661 Genomic DNA. Translation: ACT17395.1.
RefSeqiWP_015836646.1. NC_012918.1.

3D structure databases

ProteinModelPortaliC6E497.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi443144.GM21_1335.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACT17395; ACT17395; GM21_1335.
KEGGigem:GM21_1335.
PATRICi22017126. VBIGeoSp56140_1299.

Phylogenomic databases

eggNOGiENOG4106EG9. Bacteria.
COG0284. LUCA.
HOGENOMiHOG000226070.
KOiK01591.
OMAiNFKIFLD.
OrthoDBiPOG091H0256.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.

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_GEOSM
AccessioniPrimary (citable) accession number: C6E497
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: September 1, 2009
Last modified: November 2, 2016
This is version 40 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

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.