Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: 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).

Catalytic activityi

Orotidine 5'-phosphate = UMP + CO2.

Pathwayi: UMP biosynthesis via de novo pathway

This protein is involved in step 2 of the subpathway that synthesizes UMP from orotate.
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 sitei11Substrate1
Binding sitei33Substrate1
Active sitei62Proton donor1
Binding sitei123Substrate1
Binding sitei185Substrate1
Binding sitei194Substrate1
Binding sitei214Substrate; via amide nitrogen1
Binding sitei215Substrate1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Pyrimidine biosynthesis

Enzyme and pathway databases

BioCyciBSUB:BSU15550-MONOMER.
BRENDAi4.1.1.23. 658.
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:BSU15550
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001345271 – 239Orotidine 5'-phosphate decarboxylaseAdd BLAST239

Proteomic databases

PaxDbiP25971.
PRIDEiP25971.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

IntActiP25971. 1 interactor.
MINTiMINT-8366633.
STRINGi224308.Bsubs1_010100008591.

Structurei

Secondary structure

1239
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi7 – 9Combined sources3
Helixi15 – 21Combined sources7
Helixi23 – 25Combined sources3
Beta strandi31 – 34Combined sources4
Helixi36 – 42Combined sources7
Helixi44 – 52Combined sources9
Beta strandi56 – 63Combined sources8
Helixi67 – 78Combined sources12
Turni79 – 81Combined sources3
Beta strandi83 – 88Combined sources6
Helixi89 – 91Combined sources3
Helixi93 – 106Combined sources14
Beta strandi115 – 119Combined sources5
Helixi127 – 132Combined sources6
Helixi140 – 153Combined sources14
Beta strandi157 – 160Combined sources4
Helixi163 – 165Combined sources3
Helixi166 – 169Combined sources4
Turni170 – 172Combined sources3
Beta strandi178 – 181Combined sources4
Helixi200 – 205Combined sources6
Beta strandi209 – 213Combined sources5
Helixi215 – 218Combined sources4
Helixi223 – 235Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DBTX-ray2.40A/B/C1-239[»]
ProteinModelPortaliP25971.
SMRiP25971.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP25971.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni60 – 69Substrate binding10

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4106EG9. Bacteria.
COG0284. LUCA.
HOGENOMiHOG000226071.
InParanoidiP25971.
KOiK01591.
OMAiNFKIFLD.
PhylomeDBiP25971.

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.

P25971-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKNNLPIIAL DFASAEETLA FLAPFQQEPL FVKVGMELFY QEGPSIVKQL
60 70 80 90 100
KERNCELFLD LKLHDIPTTV NKAMKRLASL GVDLVNVHAA GGKKMMQAAL
110 120 130 140 150
EGLEEGTPAG KKRPSLIAVT QLTSTSEQIM KDELLIEKSL IDTVVHYSKQ
160 170 180 190 200
AEESGLDGVV CSVHEAKAIY QAVSPSFLTV TPGIRMSEDA ANDQVRVATP
210 220 230
AIAREKGSSA IVVGRSITKA EDPVKAYKAV RLEWEGIKS
Length:239
Mass (Da):25,992
Last modified:May 1, 1992 - v1
Checksum:iDB1743714ED052E7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M59757 Genomic DNA. Translation: AAA21273.1.
AL009126 Genomic DNA. Translation: CAB13429.1.
PIRiI39845.
RefSeqiNP_389438.1. NC_000964.3.
WP_003232107.1. NZ_JNCM01000035.1.

Genome annotation databases

EnsemblBacteriaiCAB13429; CAB13429; BSU15550.
GeneIDi935960.
KEGGibsu:BSU15550.
PATRICi18974917. VBIBacSub10457_1650.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M59757 Genomic DNA. Translation: AAA21273.1.
AL009126 Genomic DNA. Translation: CAB13429.1.
PIRiI39845.
RefSeqiNP_389438.1. NC_000964.3.
WP_003232107.1. NZ_JNCM01000035.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DBTX-ray2.40A/B/C1-239[»]
ProteinModelPortaliP25971.
SMRiP25971.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP25971. 1 interactor.
MINTiMINT-8366633.
STRINGi224308.Bsubs1_010100008591.

Proteomic databases

PaxDbiP25971.
PRIDEiP25971.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB13429; CAB13429; BSU15550.
GeneIDi935960.
KEGGibsu:BSU15550.
PATRICi18974917. VBIBacSub10457_1650.

Phylogenomic databases

eggNOGiENOG4106EG9. Bacteria.
COG0284. LUCA.
HOGENOMiHOG000226071.
InParanoidiP25971.
KOiK01591.
OMAiNFKIFLD.
PhylomeDBiP25971.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.
BioCyciBSUB:BSU15550-MONOMER.
BRENDAi4.1.1.23. 658.

Miscellaneous databases

EvolutionaryTraceiP25971.

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_BACSU
AccessioniPrimary (citable) accession number: P25971
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: May 1, 1992
Last modified: November 2, 2016
This is version 123 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. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  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.