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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

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

Pathwayi: 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)DescriptionActionsGraphical viewLength
Binding sitei9SubstrateUniRule annotation1
Binding sitei31SubstrateUniRule annotation1
Active sitei59Proton donorUniRule annotation1
Binding sitei114SubstrateUniRule annotation1
Binding sitei187Substrate; via amide nitrogenUniRule annotation1
Binding sitei188SubstrateUniRule annotation1

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 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:AF_0929
OrganismiArchaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Taxonomic identifieri224325 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaArchaeoglobiArchaeoglobalesArchaeoglobaceaeArchaeoglobus
Proteomesi
  • UP000002199 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001346081 – 209Orotidine 5'-phosphate decarboxylaseAdd BLAST209

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi224325.AF0929.

Structurei

Secondary structure

1209
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 7Combined sources5
Helixi13 – 23Combined sources11
Helixi24 – 26Combined sources3
Beta strandi28 – 33Combined sources6
Helixi34 – 40Combined sources7
Helixi44 – 49Combined sources6
Beta strandi54 – 60Combined sources7
Helixi64 – 76Combined sources13
Beta strandi80 – 85Combined sources6
Helixi86 – 88Combined sources3
Helixi90 – 102Combined sources13
Beta strandi106 – 110Combined sources5
Helixi116 – 119Combined sources4
Helixi122 – 136Combined sources15
Beta strandi140 – 142Combined sources3
Helixi148 – 158Combined sources11
Beta strandi162 – 165Combined sources4
Beta strandi169 – 171Combined sources3
Helixi175 – 179Combined sources5
Beta strandi182 – 187Combined sources6
Helixi188 – 191Combined sources4
Beta strandi192 – 194Combined sources3
Helixi196 – 207Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4MUZX-ray1.39A/B1-209[»]
4N2YX-ray1.55A/B/C/D1-209[»]
ProteinModelPortaliO29333.
SMRiO29333.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni57 – 66Substrate bindingUniRule annotation10
Regioni166 – 176Substrate bindingUniRule annotationAdd BLAST11

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiarCOG00081. Archaea.
COG0284. LUCA.
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.
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.

Sequencei

Sequence statusi: Complete.

O29333-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKQLILALDV MDGEKAMEIA KKVAEHVDRI KVNYPLVLSA GVGIMKRLSE
60 70 80 90 100
IKPVIADFKI ADVPYTSSLI ARIAFENSAE SVIVHGFVGS DTLREVCRVA
110 120 130 140 150
EEFGGKVYAV TELSSPGGEE FMSAVSLKIV EKAKEAGCHG LIAPSTRIER
160 170 180 190 200
LREIRKAAGD MEILCPGIGA QKGSIEAVKY ADGIIVGRGI YASGNPAEEA

RKLRRVLKI
Length:209
Mass (Da):22,538
Last modified:January 23, 2002 - v2
Checksum:iC6CBB39E9C105B66
GO

Sequence cautioni

The sequence AAB90309 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB90309.1. Different initiation.
PIRiA69366.
RefSeqiWP_048064309.1. NC_000917.1.

Genome annotation databases

EnsemblBacteriaiAAB90309; AAB90309; AF_0929.
GeneIDi1484152.
KEGGiafu:AF_0929.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB90309.1. Different initiation.
PIRiA69366.
RefSeqiWP_048064309.1. NC_000917.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4MUZX-ray1.39A/B1-209[»]
4N2YX-ray1.55A/B/C/D1-209[»]
ProteinModelPortaliO29333.
SMRiO29333.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224325.AF0929.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB90309; AAB90309; AF_0929.
GeneIDi1484152.
KEGGiafu:AF_0929.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01200_A. OMPdecase_type1_A. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR014732. OMPdecase.
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.
ProtoNetiSearch...

Entry informationi

Entry nameiPYRF_ARCFU
AccessioniPrimary (citable) accession number: O29333
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: January 23, 2002
Last modified: November 2, 2016
This is version 101 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, Reference 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.