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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Geobacillus kaustophilus (strain HTA426)
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 sitei10SubstrateUniRule annotation1
Binding sitei32SubstrateUniRule annotation1
Active sitei61Proton donorUniRule annotation1
Binding sitei122SubstrateUniRule annotation1
Binding sitei184SubstrateUniRule annotation1
Binding sitei193SubstrateUniRule annotation1
Binding sitei213Substrate; via amide nitrogenUniRule annotation1
Binding sitei214SubstrateUniRule 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:GK1155
OrganismiGeobacillus kaustophilus (strain HTA426)
Taxonomic identifieri235909 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus
Proteomesi
  • UP000001172 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002418601 – 244Orotidine 5'-phosphate decarboxylaseAdd BLAST244

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi235909.GK1155.

Structurei

Secondary structure

1244
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 8Combined sources4
Helixi14 – 21Combined sources8
Helixi22 – 24Combined sources3
Beta strandi30 – 33Combined sources4
Helixi35 – 41Combined sources7
Helixi43 – 51Combined sources9
Beta strandi55 – 62Combined sources8
Helixi66 – 78Combined sources13
Beta strandi82 – 87Combined sources6
Helixi88 – 90Combined sources3
Helixi92 – 105Combined sources14
Beta strandi108 – 110Combined sources3
Beta strandi114 – 120Combined sources7
Helixi126 – 131Combined sources6
Helixi139 – 153Combined sources15
Beta strandi157 – 159Combined sources3
Helixi162 – 172Combined sources11
Beta strandi176 – 180Combined sources5
Helixi199 – 205Combined sources7
Beta strandi208 – 212Combined sources5
Helixi214 – 217Combined sources4
Beta strandi219 – 221Combined sources3
Helixi222 – 232Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2YYTX-ray2.30A/B/C/D1-244[»]
2YYUX-ray2.20A/B1-244[»]
ProteinModelPortaliQ5L0U0.
SMRiQ5L0U0.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5L0U0.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni59 – 68Substrate bindingUniRule annotation10

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4106EG9. Bacteria.
COG0284. LUCA.
HOGENOMiHOG000226071.
KOiK01591.
OMAiNFKIFLD.
OrthoDBiPOG091H0256.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01200_B. OMPdecase_type1_B. 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.

Q5L0U0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHTPFIVALD FPSKQEVERF LRPFAGTPLF VKVGMELYYQ EGPAIVAFLK
60 70 80 90 100
EQGHAVFLDL KLHDIPNTVK QAMKGLARVG ADLVNVHAAG GRRMMEAAIE
110 120 130 140 150
GLDAGTPSGR MRPRCIAVTQ LTSTDERMLH EELWISRPLV ETVAHYAALA
160 170 180 190 200
KESGLDGVVC SANEAAFIKE RCGASFLAVT PGIRFADDAA HDQVRVVTPR
210 220 230 240
KARALGSDYI VIGRSLTRAA DPLRTYARLQ HEWNGGERES TTPT
Length:244
Mass (Da):26,751
Last modified:February 1, 2005 - v1
Checksum:i41AB5BFD1923C349
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000043 Genomic DNA. Translation: BAD75440.1.
RefSeqiWP_011230655.1. NC_006510.1.

Genome annotation databases

EnsemblBacteriaiBAD75440; BAD75440; GK1155.
GeneIDi3186101.
KEGGigka:GK1155.
PATRICi21963573. VBIGeoKau81518_1256.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000043 Genomic DNA. Translation: BAD75440.1.
RefSeqiWP_011230655.1. NC_006510.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2YYTX-ray2.30A/B/C/D1-244[»]
2YYUX-ray2.20A/B1-244[»]
ProteinModelPortaliQ5L0U0.
SMRiQ5L0U0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi235909.GK1155.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD75440; BAD75440; GK1155.
GeneIDi3186101.
KEGGigka:GK1155.
PATRICi21963573. VBIGeoKau81518_1256.

Phylogenomic databases

eggNOGiENOG4106EG9. Bacteria.
COG0284. LUCA.
HOGENOMiHOG000226071.
KOiK01591.
OMAiNFKIFLD.
OrthoDBiPOG091H0256.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.

Miscellaneous databases

EvolutionaryTraceiQ5L0U0.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01200_B. OMPdecase_type1_B. 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_GEOKA
AccessioniPrimary (citable) accession number: Q5L0U0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 27, 2006
Last sequence update: February 1, 2005
Last modified: November 2, 2016
This is version 79 of the entry and version 1 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.