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O58462 (PYRF_PYRHO) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 93. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Orotidine 5'-phosphate decarboxylase

EC=4.1.1.23
Alternative name(s):
OMP decarboxylase
Short name=OMPDCase
Short name=OMPdecase
Gene names
Name:pyrF
Ordered Locus Names:PH0731
OrganismPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) [Complete proteome] [HAMAP]
Taxonomic identifier70601 [NCBI]
Taxonomic lineageArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus

Protein attributes

Sequence length208 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP) By similarity. HAMAP-Rule MF_01200_A

Catalytic activity

Orotidine 5'-phosphate = UMP + CO2. HAMAP-Rule MF_01200_A

Pathway

Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 2/2. HAMAP-Rule MF_01200_A

Subunit structure

Homodimer. Ref.2

Sequence similarities

Belongs to the OMP decarboxylase family. Type 1 subfamily.

Sequence caution

The sequence BAA29822.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 208208Orotidine 5'-phosphate decarboxylase HAMAP-Rule MF_01200_A
PRO_0000134616

Regions

Region57 – 6610Substrate binding HAMAP-Rule MF_01200_A
Region162 – 17211Substrate binding HAMAP-Rule MF_01200_A

Sites

Active site591Proton donor
Binding site71Substrate
Binding site291Substrate
Binding site1091Substrate
Binding site1851Substrate; via amide nitrogen
Binding site1861Substrate

Secondary structure

.......................................... 208
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O58462 [UniParc].

Last modified January 23, 2002. Version 2.
Checksum: F0D3124758EB4C43

FASTA20822,692
        10         20         30         40         50         60 
MIVLALDVYE GERAIKIAKS VKDYISMIKV NWPLILGSGV DIIRRLKEET GVEIIADLKL 

        70         80         90        100        110        120 
ADIPNTNRLI ARKVFGAGAD YVIVHTFVGR DSVMAVKELG EIIMVVEMSH PGALEFINPL 

       130        140        150        160        170        180 
TDRFIEVANE IEPFGVIAPG TRPERIGYIR DRLKEGIKIL APGIGAQGGK AKDAVKAGAD 

       190        200 
YIIVGRAIYN APNPREAAKA IYDEIRGV 

« Hide

References

« Hide 'large scale' references
[1]"Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3."
Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S., Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K., Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T. expand/collapse author list , Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T., Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.
DNA Res. 5:55-76(1998) [PubMed] [Europe PMC] [Abstract]
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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
BA000001 Genomic DNA. Translation: BAA29822.1. Different initiation.
PIRD71120.
RefSeqNP_142676.1. NC_000961.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2CZ5X-ray1.85A/B1-208[»]
2CZDX-ray1.60A/B1-208[»]
2CZEX-ray1.85A/B1-208[»]
2CZFX-ray1.85A/B1-208[»]
ProteinModelPortalO58462.
SMRO58462. Positions 1-208.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING70601.PH0731.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaBAA29822; BAA29822; BAA29822.
GeneID1443064.
KEGGpho:PH0731.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0284.
HOGENOMHOG000226069.
KOK01591.
OMATEMSHPG.

Enzyme and pathway databases

BioCycPHOR70601:GJWR-730-MONOMER.
UniPathwayUPA00070; UER00120.

Family and domain databases

Gene3D3.20.20.70. 1 hit.
HAMAPMF_01200_A. OMPdecase_type1_A.
InterProIPR013785. Aldolase_TIM.
IPR014732. OMPdecase.
IPR018089. OMPdecase_AS.
IPR001754. OMPdeCOase_dom.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]
PfamPF00215. OMPdecase. 1 hit.
[Graphical view]
SMARTSM00934. OMPdecase. 1 hit.
[Graphical view]
SUPFAMSSF51366. SSF51366. 1 hit.
TIGRFAMsTIGR01740. pyrF. 1 hit.
PROSITEPS00156. OMPDECASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceO58462.

Entry information

Entry namePYRF_PYRHO
AccessionPrimary (citable) accession number: O58462
Entry history
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 statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways