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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).By similarity

Catalytic activityi

Orotidine 5'-phosphate = UMP + CO2.

Pathwayi: UMP biosynthesis via de novo pathway

This protein is involved in step 2 of the subpathway that synthesizes UMP from orotate.
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 sitei7Substrate1
Binding sitei29Substrate1
Active sitei59Proton donor1
Binding sitei109Substrate1
Binding sitei185Substrate; via amide nitrogen1
Binding sitei186Substrate1

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 decarboxylase (EC:4.1.1.23)
Alternative name(s):
OMP decarboxylase
Short name:
OMPDCase
Short name:
OMPdecase
Gene namesi
Name:pyrF
Ordered Locus Names:PH0731
OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Taxonomic identifieri70601 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000000752 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001346161 – 208Orotidine 5'-phosphate decarboxylaseAdd BLAST208

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi70601.PH0731.

Structurei

Secondary structure

1208
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 5Combined sources4
Helixi11 – 21Combined sources11
Helixi22 – 24Combined sources3
Beta strandi26 – 31Combined sources6
Helixi32 – 38Combined sources7
Helixi42 – 50Combined sources9
Beta strandi53 – 60Combined sources8
Helixi64 – 76Combined sources13
Beta strandi80 – 86Combined sources7
Helixi90 – 97Combined sources8
Beta strandi100 – 105Combined sources6
Helixi111 – 114Combined sources4
Turni115 – 117Combined sources3
Helixi118 – 120Combined sources3
Helixi121 – 131Combined sources11
Beta strandi134 – 137Combined sources4
Helixi144 – 152Combined sources9
Beta strandi158 – 161Combined sources4
Beta strandi166 – 169Combined sources4
Helixi170 – 177Combined sources8
Beta strandi180 – 184Combined sources5
Helixi186 – 189Combined sources4
Beta strandi191 – 193Combined sources3
Helixi194 – 205Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2CZ5X-ray1.85A/B1-208[»]
2CZDX-ray1.60A/B1-208[»]
2CZEX-ray1.85A/B1-208[»]
2CZFX-ray1.85A/B1-208[»]
ProteinModelPortaliO58462.
SMRiO58462.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO58462.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni57 – 66Substrate binding10
Regioni162 – 172Substrate bindingAdd BLAST11

Sequence similaritiesi

Phylogenomic databases

eggNOGiarCOG00081. Archaea.
COG0284. LUCA.
HOGENOMiHOG000226069.
KOiK01591.
OMAiVTEMSHP.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01200_A. OMPdecase_type1_A. 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.

O58462-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIVLALDVYE GERAIKIAKS VKDYISMIKV NWPLILGSGV DIIRRLKEET
60 70 80 90 100
GVEIIADLKL ADIPNTNRLI ARKVFGAGAD YVIVHTFVGR DSVMAVKELG
110 120 130 140 150
EIIMVVEMSH PGALEFINPL TDRFIEVANE IEPFGVIAPG TRPERIGYIR
160 170 180 190 200
DRLKEGIKIL APGIGAQGGK AKDAVKAGAD YIIVGRAIYN APNPREAAKA

IYDEIRGV
Length:208
Mass (Da):22,692
Last modified:January 23, 2002 - v2
Checksum:iF0D3124758EB4C43
GO

Sequence cautioni

The sequence BAA29822 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA29822.1. Different initiation.
PIRiD71120.
RefSeqiWP_048053207.1. NC_000961.1.

Genome annotation databases

EnsemblBacteriaiBAA29822; BAA29822; BAA29822.
GeneIDi1443064.
KEGGipho:PH0731.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA29822.1. Different initiation.
PIRiD71120.
RefSeqiWP_048053207.1. NC_000961.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2CZ5X-ray1.85A/B1-208[»]
2CZDX-ray1.60A/B1-208[»]
2CZEX-ray1.85A/B1-208[»]
2CZFX-ray1.85A/B1-208[»]
ProteinModelPortaliO58462.
SMRiO58462.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi70601.PH0731.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA29822; BAA29822; BAA29822.
GeneIDi1443064.
KEGGipho:PH0731.

Phylogenomic databases

eggNOGiarCOG00081. Archaea.
COG0284. LUCA.
HOGENOMiHOG000226069.
KOiK01591.
OMAiVTEMSHP.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.

Miscellaneous databases

EvolutionaryTraceiO58462.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01200_A. OMPdecase_type1_A. 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_PYRHO
AccessioniPrimary (citable) accession number: O58462
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: January 23, 2002
Last modified: November 2, 2016
This is version 106 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.