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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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei7 – 71Substrate
Binding sitei29 – 291Substrate
Active sitei59 – 591Proton donor
Binding sitei109 – 1091Substrate
Binding sitei185 – 1851Substrate; via amide nitrogen
Binding sitei186 – 1861Substrate

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Pyrimidine biosynthesis

Enzyme and pathway databases

BioCyciPHOR70601:GJWR-730-MONOMER.
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
ProteomesiUP000000752 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 208208Orotidine 5'-phosphate decarboxylasePRO_0000134616Add
BLAST

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi70601.PH0731.

Structurei

Secondary structure

1
208
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 54Combined sources
Helixi11 – 2111Combined sources
Helixi22 – 243Combined sources
Beta strandi26 – 316Combined sources
Helixi32 – 387Combined sources
Helixi42 – 509Combined sources
Beta strandi53 – 608Combined sources
Helixi64 – 7613Combined sources
Beta strandi80 – 867Combined sources
Helixi90 – 978Combined sources
Beta strandi100 – 1056Combined sources
Helixi111 – 1144Combined sources
Turni115 – 1173Combined sources
Helixi118 – 1203Combined sources
Helixi121 – 13111Combined sources
Beta strandi134 – 1374Combined sources
Helixi144 – 1529Combined sources
Beta strandi158 – 1614Combined sources
Beta strandi166 – 1694Combined sources
Helixi170 – 1778Combined sources
Beta strandi180 – 1845Combined sources
Helixi186 – 1894Combined sources
Beta strandi191 – 1933Combined sources
Helixi194 – 20512Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 1-208.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO58462.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni57 – 6610Substrate binding
Regioni162 – 17211Substrate bindingAdd
BLAST

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0284.
HOGENOMiHOG000226069.
KOiK01591.
OMAiDWVIVGR.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01200_A. OMPdecase_type1_A.
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 BAA29822.1 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.
RefSeqiNP_142676.1. NC_000961.1.
WP_010884829.1. 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.
RefSeqiNP_142676.1. NC_000961.1.
WP_010884829.1. NC_000961.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 1-208.
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

eggNOGiCOG0284.
HOGENOMiHOG000226069.
KOiK01591.
OMAiDWVIVGR.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.
BioCyciPHOR70601:GJWR-730-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO58462.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01200_A. OMPdecase_type1_A.
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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.
  2. "Crystal structure of orotidine 5'-phosphate decarboxylase from Pyrococcus horikoshii OT3."
    RIKEN structural genomics initiative (RSGI)
    Submitted (JAN-2006) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF NATIVE PROTEIN AND COMPLEXES WITH UMP AND XMP, SUBUNIT.
    Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.

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: May 27, 2015
This is version 99 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

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.