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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
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. 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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei14 – 141SubstrateUniRule annotation
Binding sitei36 – 361SubstrateUniRule annotation
Active sitei65 – 651Proton donorUniRule annotation
Binding sitei118 – 1181SubstrateUniRule annotation
Binding sitei179 – 1791SubstrateUniRule annotation
Binding sitei188 – 1881SubstrateUniRule annotation
Binding sitei208 – 2081Substrate; via amide nitrogenUniRule annotation
Binding sitei209 – 2091SubstrateUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Pyrimidine biosynthesis

Enzyme and pathway databases

BioCyciSMEL266834:GJF6-343-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:R00332
ORF Names:SMc00412
OrganismiRhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
Taxonomic identifieri266834 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeSinorhizobium/Ensifer groupSinorhizobium
ProteomesiUP000001976 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 234234Orotidine 5'-phosphate decarboxylasePRO_0000134569Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi266834.SMc00412.

Structurei

3D structure databases

ProteinModelPortaliQ92SN8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni63 – 7210Substrate 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.

Q92SN8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTSARDRLI VGLDLPTVTE AEKIVSTLGE EVLFYKIGYQ LAFAGGLDFA
60 70 80 90 100
RDLAASGKQV FLDMKLLDID NTVAKGVENI VKMGVSMLTL HAYPKAMKSA
110 120 130 140 150
VEAARGSNLC LLGVTVLTSM DEQDVIDAGY EYDPHSLVLR RAEQARAAGM
160 170 180 190 200
GGIVCSAEEA AAVRKIIGGD MALVTPGIRP AGAEKGDQKR VMTPADALRA
210 220 230
GSSHLVVGRP IVAAPDPLAA SRAILAEMES ALSR
Length:234
Mass (Da):24,611
Last modified:December 1, 2001 - v1
Checksum:i01E59B87DC49B1B4
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti197 – 1982AL → V in AAG10239 (PubMed:10972799).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF201699 Genomic DNA. Translation: AAG10239.1.
AL591688 Genomic DNA. Translation: CAC41769.1.
RefSeqiNP_384438.1. NC_003047.1.
WP_010968510.1. NC_003047.1.

Genome annotation databases

EnsemblBacteriaiCAC41769; CAC41769; SMc00412.
GeneIDi1231966.
KEGGisme:SMc00412.
PATRICi23629867. VBISinMel96828_1703.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF201699 Genomic DNA. Translation: AAG10239.1.
AL591688 Genomic DNA. Translation: CAC41769.1.
RefSeqiNP_384438.1. NC_003047.1.
WP_010968510.1. NC_003047.1.

3D structure databases

ProteinModelPortaliQ92SN8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi266834.SMc00412.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAC41769; CAC41769; SMc00412.
GeneIDi1231966.
KEGGisme:SMc00412.
PATRICi23629867. VBISinMel96828_1703.

Phylogenomic databases

eggNOGiCOG0284.
HOGENOMiHOG000226070.
KOiK01591.
OMAiNFKIFLD.
OrthoDBiEOG6N6815.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.
BioCyciSMEL266834:GJF6-343-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

« Hide 'large scale' publications
  1. "Inactivation of the gene for phospholipid N-methyltransferase in Sinorhizobium meliloti: phosphatidylcholine is required for normal growth."
    de Rudder K.E.E., Lopez-Lara I.M., Geiger O.
    Mol. Microbiol. 37:763-772(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 1021.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 1021.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 1021.

Entry informationi

Entry nameiPYRF_RHIME
AccessioniPrimary (citable) accession number: Q92SN8
Secondary accession number(s): Q9F953
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 23, 2002
Last sequence update: December 1, 2001
Last modified: May 27, 2015
This is version 85 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.