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O58462

- PYRF_PYRHO

UniProt

O58462 - PYRF_PYRHO

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Protein

Orotidine 5'-phosphate decarboxylase

Gene
pyrF, PH0731
Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Status
Reviewed - 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.UniRule annotation

Catalytic activityi

Orotidine 5'-phosphate = UMP + CO2.UniRule annotation

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

  1. orotidine-5'-phosphate decarboxylase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. 'de novo' pyrimidine nucleobase biosynthetic process Source: InterPro
  2. 'de novo' UMP biosynthetic process Source: UniProtKB-UniPathway
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: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 208208Orotidine 5'-phosphate decarboxylaseUniRule annotationPRO_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 – 54
Helixi11 – 2111
Helixi22 – 243
Beta strandi26 – 316
Helixi32 – 387
Helixi42 – 509
Beta strandi53 – 608
Helixi64 – 7613
Beta strandi80 – 867
Helixi90 – 978
Beta strandi100 – 1056
Helixi111 – 1144
Turni115 – 1173
Helixi118 – 1203
Helixi121 – 13111
Beta strandi134 – 1374
Helixi144 – 1529
Beta strandi158 – 1614
Beta strandi166 – 1694
Helixi170 – 1778
Beta strandi180 – 1845
Helixi186 – 1894
Beta strandi191 – 1933
Helixi194 – 20512

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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.

Miscellaneous databases

EvolutionaryTraceiO58462.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni57 – 6610Substrate bindingUniRule annotation
Regioni162 – 17211Substrate bindingUniRule annotationAdd
BLAST

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0284.
HOGENOMiHOG000226069.
KOiK01591.
OMAiTEMSHPG.

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

MIVLALDVYE GERAIKIAKS VKDYISMIKV NWPLILGSGV DIIRRLKEET    50
GVEIIADLKL ADIPNTNRLI ARKVFGAGAD YVIVHTFVGR DSVMAVKELG 100
EIIMVVEMSH PGALEFINPL TDRFIEVANE IEPFGVIAPG TRPERIGYIR 150
DRLKEGIKIL APGIGAQGGK AKDAVKAGAD YIIVGRAIYN APNPREAAKA 200
IYDEIRGV 208
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.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
BA000001 Genomic DNA. Translation: BAA29822.1. Different initiation.
PIRiD71120.
RefSeqiNP_142676.1. NC_000961.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
BA000001 Genomic DNA. Translation: BAA29822.1 . Different initiation.
PIRi D71120.
RefSeqi NP_142676.1. NC_000961.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2CZ5 X-ray 1.85 A/B 1-208 [» ]
2CZD X-ray 1.60 A/B 1-208 [» ]
2CZE X-ray 1.85 A/B 1-208 [» ]
2CZF X-ray 1.85 A/B 1-208 [» ]
ProteinModelPortali O58462.
SMRi O58462. Positions 1-208.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 70601.PH0731.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAA29822 ; BAA29822 ; BAA29822 .
GeneIDi 1443064.
KEGGi pho:PH0731.

Phylogenomic databases

eggNOGi COG0284.
HOGENOMi HOG000226069.
KOi K01591.
OMAi TEMSHPG.

Enzyme and pathway databases

UniPathwayi UPA00070 ; UER00120 .
BioCyci PHOR70601:GJWR-730-MONOMER.

Miscellaneous databases

EvolutionaryTracei O58462.

Family and domain databases

Gene3Di 3.20.20.70. 1 hit.
HAMAPi MF_01200_A. OMPdecase_type1_A.
InterProi IPR013785. Aldolase_TIM.
IPR014732. OMPdecase.
IPR018089. OMPdecase_AS.
IPR001754. OMPdeCOase_dom.
IPR011060. RibuloseP-bd_barrel.
[Graphical view ]
Pfami PF00215. OMPdecase. 1 hit.
[Graphical view ]
SMARTi SM00934. OMPdecase. 1 hit.
[Graphical view ]
SUPFAMi SSF51366. SSF51366. 1 hit.
TIGRFAMsi TIGR01740. pyrF. 1 hit.
PROSITEi PS00156. OMPDECASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

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 14, 2014
This is version 93 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

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