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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Yersinia pestis
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 sitei22 – 221SubstrateUniRule annotation
Binding sitei44 – 441SubstrateUniRule annotation
Active sitei73 – 731Proton donorUniRule annotation
Binding sitei131 – 1311SubstrateUniRule annotation
Binding sitei192 – 1921SubstrateUniRule annotation
Binding sitei201 – 2011SubstrateUniRule annotation
Binding sitei221 – 2211Substrate; via amide nitrogenUniRule annotation
Binding sitei222 – 2221SubstrateUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Pyrimidine biosynthesis

Enzyme and pathway databases

BioCyciYPES214092:GKDD-2197-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:YPO2227, y2069, YP_2026
OrganismiYersinia pestis
Taxonomic identifieri632 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeYersinia
ProteomesiUP000000815 Componenti: Chromosome UP000002490 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 245245Orotidine 5'-phosphate decarboxylasePRO_0000134606Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

IntActiP58644. 4 interactions.
STRINGi214092.YPO2227.

Structurei

3D structure databases

ProteinModelPortaliP58644.
SMRiP58644. Positions 14-243.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni71 – 8010Substrate bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0284.
HOGENOMiHOG000226071.
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.

P58644-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTSATKTNNS GSISSPIVVA LDYANKDAAL AFADQVSPQD CRLKVGKEMF
60 70 80 90 100
TLYGPELIRD LHQRGFDVFL DLKFHDIPNT TARAVAAAAE LGVWMVNVHA
110 120 130 140 150
SGGARMMSAA KEALLPYGAQ APLLIAVTVL TSMDGEDLRD IGITISPAEQ
160 170 180 190 200
AERLAKLTWD CGLDGVVCSA HEAVRLKQVC GEDFSLVTPG IRPQGSEAGD
210 220 230 240
QRRIMTPEQA VAVGVDYMVI GRPITQSPDP EKTLREILAS LTKVA
Length:245
Mass (Da):26,207
Last modified:January 23, 2002 - v1
Checksum:i3663A90EBE1E381A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL590842 Genomic DNA. Translation: CAL20857.1.
AE009952 Genomic DNA. Translation: AAM85633.1.
AE017042 Genomic DNA. Translation: AAS62242.1.
PIRiAF0271.
RefSeqiNP_669382.1. NC_004088.1.
NP_993365.1. NC_005810.1.
WP_002210613.1. NZ_KN150724.1.
YP_002347199.1. NC_003143.1.

Genome annotation databases

EnsemblBacteriaiAAM85633; AAM85633; y2069.
AAS62242; AAS62242; YP_2026.
GeneIDi1175061.
KEGGiype:YPO2227.
ypk:y2069.
ypm:YP_2026.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL590842 Genomic DNA. Translation: CAL20857.1.
AE009952 Genomic DNA. Translation: AAM85633.1.
AE017042 Genomic DNA. Translation: AAS62242.1.
PIRiAF0271.
RefSeqiNP_669382.1. NC_004088.1.
NP_993365.1. NC_005810.1.
WP_002210613.1. NZ_KN150724.1.
YP_002347199.1. NC_003143.1.

3D structure databases

ProteinModelPortaliP58644.
SMRiP58644. Positions 14-243.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP58644. 4 interactions.
STRINGi214092.YPO2227.

Protocols and materials databases

DNASUi1147016.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAM85633; AAM85633; y2069.
AAS62242; AAS62242; YP_2026.
GeneIDi1175061.
KEGGiype:YPO2227.
ypk:y2069.
ypm:YP_2026.

Phylogenomic databases

eggNOGiCOG0284.
HOGENOMiHOG000226071.
KOiK01591.
OMAiNFKIFLD.
OrthoDBiEOG6N6815.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.
BioCyciYPES214092:GKDD-2197-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: CO-92 / Biovar Orientalis.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: KIM10+ / Biovar Mediaevalis.
  3. "Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans."
    Song Y., Tong Z., Wang J., Wang L., Guo Z., Han Y., Zhang J., Pei D., Zhou D., Qin H., Pang X., Han Y., Zhai J., Li M., Cui B., Qi Z., Jin L., Dai R.
    , Chen F., Li S., Ye C., Du Z., Lin W., Wang J., Yu J., Yang H., Wang J., Huang P., Yang R.
    DNA Res. 11:179-197(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 91001 / Biovar Mediaevalis.

Entry informationi

Entry nameiPYRF_YERPE
AccessioniPrimary (citable) accession number: P58644
Secondary accession number(s): Q0WET9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 23, 2002
Last sequence update: January 23, 2002
Last modified: June 24, 2015
This is version 104 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.