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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
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 sitei61Proton donorUniRule annotation1
Binding sitei115SubstrateUniRule annotation1
Binding sitei191Substrate; via amide nitrogenUniRule annotation1
Binding sitei192SubstrateUniRule 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:MJ0252
OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Taxonomic identifieri243232 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
Proteomesi
  • UP000000805 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001346101 – 213Orotidine 5'-phosphate decarboxylaseAdd BLAST213

Proteomic databases

PRIDEiQ57700.

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi243232.MJ_0252.

Structurei

Secondary structure

1213
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 7Combined sources5
Helixi13 – 23Combined sources11
Turni24 – 26Combined sources3
Beta strandi28 – 33Combined sources6
Helixi34 – 38Combined sources5
Helixi43 – 52Combined sources10
Beta strandi54 – 62Combined sources9
Helixi66 – 76Combined sources11
Turni77 – 79Combined sources3
Beta strandi81 – 87Combined sources7
Helixi91 – 103Combined sources13
Beta strandi107 – 111Combined sources5
Helixi117 – 120Combined sources4
Turni121 – 123Combined sources3
Helixi124 – 126Combined sources3
Helixi127 – 137Combined sources11
Beta strandi140 – 143Combined sources4
Helixi149 – 159Combined sources11
Beta strandi163 – 166Combined sources4
Helixi175 – 177Combined sources3
Helixi179 – 181Combined sources3
Beta strandi187 – 190Combined sources4
Helixi192 – 195Combined sources4
Helixi200 – 209Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4LUIX-ray1.60A/B1-213[»]
4LUJX-ray1.60A/B1-213[»]
ProteinModelPortaliQ57700.
SMRiQ57700.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni59 – 68Substrate 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.
InParanoidiQ57700.
KOiK01591.
OMAiVTEMSHP.
PhylomeDBiQ57700.

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.

Q57700-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPKLMLALDV LDRDRALKIV EDVKDYVDAI KVGYPLVLST GTEIIKEIKK
60 70 80 90 100
LCNKEVIADF KVADIPATNE KIAKITLKYA DGIIVHGFVG EDSVKAVQDV
110 120 130 140 150
AKKLNKKVIM VTEMSHPGAV QFLQPIADKL SEMAKKLKVD AIVAPSTRPE
160 170 180 190 200
RLKEIKEIAE LPVITPGVGA QGGKIEDILN ILDENDYVIV GRAIYQSQNP
210
KEEAKKYKEM LNK
Length:213
Mass (Da):23,592
Last modified:January 23, 2002 - v2
Checksum:i0B073BE37D50C556
GO

Sequence cautioni

The sequence AAB98239 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB98239.1. Different initiation.
PIRiE64331.
RefSeqiWP_064496436.1. NC_000909.1.

Genome annotation databases

EnsemblBacteriaiAAB98239; AAB98239; MJ_0252.
GeneIDi1451106.
KEGGimja:MJ_0252.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB98239.1. Different initiation.
PIRiE64331.
RefSeqiWP_064496436.1. NC_000909.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4LUIX-ray1.60A/B1-213[»]
4LUJX-ray1.60A/B1-213[»]
ProteinModelPortaliQ57700.
SMRiQ57700.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243232.MJ_0252.

Proteomic databases

PRIDEiQ57700.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB98239; AAB98239; MJ_0252.
GeneIDi1451106.
KEGGimja:MJ_0252.

Phylogenomic databases

eggNOGiarCOG00081. Archaea.
COG0284. LUCA.
InParanoidiQ57700.
KOiK01591.
OMAiVTEMSHP.
PhylomeDBiQ57700.

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.
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_METJA
AccessioniPrimary (citable) accession number: Q57700
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: January 23, 2002
Last modified: November 2, 2016
This is version 98 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. Methanococcus jannaschii
    Methanococcus jannaschii: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.