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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 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 sitei22Substrate1
Binding sitei44Substrate1
Active sitei73Proton donor1
Binding sitei131Substrate1
Binding sitei192Substrate1
Binding sitei201Substrate1
Binding sitei221Substrate; via amide nitrogen1
Binding sitei222Substrate1

GO - Molecular functioni

  • carboxy-lyase activity Source: EcoliWiki
  • orotidine-5'-phosphate decarboxylase activity Source: EcoCyc

GO - Biological processi

  • 'de novo' pyrimidine nucleobase biosynthetic process Source: EcoCyc
  • 'de novo' UMP biosynthetic process Source: UniProtKB-UniPathway
  • nucleobase-containing small molecule interconversion Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Pyrimidine biosynthesis

Enzyme and pathway databases

BioCyciEcoCyc:OROTPDECARB-MONOMER.
ECOL316407:JW1273-MONOMER.
MetaCyc:OROTPDECARB-MONOMER.
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:b1281, JW1273
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10809. pyrF.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: EcoliWiki
  • cytosol Source: EcoCyc
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001345391 – 245Orotidine 5'-phosphate decarboxylaseAdd BLAST245

Proteomic databases

PaxDbiP08244.
PRIDEiP08244.

2D gel databases

SWISS-2DPAGEP08244.

Interactioni

Subunit structurei

Homodimer.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
ribAP0A7I72EBI-1123202,EBI-1123314

Protein-protein interaction databases

IntActiP08244. 4 interactors.
STRINGi511145.b1281.

Structurei

Secondary structure

1245
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi17 – 21Combined sources5
Helixi26 – 33Combined sources8
Turni38 – 40Combined sources3
Beta strandi42 – 46Combined sources5
Helixi47 – 63Combined sources17
Beta strandi68 – 74Combined sources7
Helixi78 – 91Combined sources14
Beta strandi94 – 99Combined sources6
Helixi100 – 102Combined sources3
Helixi104 – 112Combined sources9
Helixi113 – 120Combined sources8
Beta strandi123 – 127Combined sources5
Helixi135 – 139Combined sources5
Turni140 – 142Combined sources3
Helixi147 – 160Combined sources14
Beta strandi164 – 167Combined sources4
Helixi170 – 172Combined sources3
Helixi173 – 180Combined sources8
Beta strandi182 – 188Combined sources7
Helixi207 – 212Combined sources6
Beta strandi216 – 220Combined sources5
Helixi222 – 225Combined sources4
Beta strandi227 – 229Combined sources3
Helixi230 – 240Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1EIXX-ray2.50A/B/C/D1-245[»]
1JJKX-ray3.00A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P1-245[»]
1L2UX-ray2.50A/B1-245[»]
ProteinModelPortaliP08244.
SMRiP08244.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP08244.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni71 – 80Substrate binding10

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4106EG9. Bacteria.
COG0284. LUCA.
HOGENOMiHOG000226071.
InParanoidiP08244.
KOiK01591.
OMAiNFKIFLD.
PhylomeDBiP08244.

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.

P08244-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTLTASSSSR AVTNSPVVVA LDYHNRDDAL AFVDKIDPRD CRLKVGKEMF
60 70 80 90 100
TLFGPQFVRE LQQRGFDIFL DLKFHDIPNT AAHAVAAAAD LGVWMVNVHA
110 120 130 140 150
SGGARMMTAA REALVPFGKD APLLIAVTVL TSMEASDLVD LGMTLSPADY
160 170 180 190 200
AERLAALTQK CGLDGVVCSA QEAVRFKQVF GQEFKLVTPG IRPQGSEAGD
210 220 230 240
QRRIMTPEQA LSAGVDYMVI GRPVTQSVDP AQTLKAINAS LQRSA
Length:245
Mass (Da):26,350
Last modified:August 1, 1988 - v1
Checksum:i556877A222F0F501
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02768 Genomic DNA. Translation: AAA24483.1.
U00096 Genomic DNA. Translation: AAC74363.1.
AP009048 Genomic DNA. Translation: BAA14835.1.
M23250 Genomic DNA. No translation available.
PIRiA28440. DCECOP.
RefSeqiNP_415797.1. NC_000913.3.
WP_000176270.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74363; AAC74363; b1281.
BAA14835; BAA14835; BAA14835.
GeneIDi947121.
KEGGiecj:JW1273.
eco:b1281.
PATRICi32117826. VBIEscCol129921_1333.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02768 Genomic DNA. Translation: AAA24483.1.
U00096 Genomic DNA. Translation: AAC74363.1.
AP009048 Genomic DNA. Translation: BAA14835.1.
M23250 Genomic DNA. No translation available.
PIRiA28440. DCECOP.
RefSeqiNP_415797.1. NC_000913.3.
WP_000176270.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1EIXX-ray2.50A/B/C/D1-245[»]
1JJKX-ray3.00A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P1-245[»]
1L2UX-ray2.50A/B1-245[»]
ProteinModelPortaliP08244.
SMRiP08244.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP08244. 4 interactors.
STRINGi511145.b1281.

2D gel databases

SWISS-2DPAGEP08244.

Proteomic databases

PaxDbiP08244.
PRIDEiP08244.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74363; AAC74363; b1281.
BAA14835; BAA14835; BAA14835.
GeneIDi947121.
KEGGiecj:JW1273.
eco:b1281.
PATRICi32117826. VBIEscCol129921_1333.

Organism-specific databases

EchoBASEiEB0802.
EcoGeneiEG10809. pyrF.

Phylogenomic databases

eggNOGiENOG4106EG9. Bacteria.
COG0284. LUCA.
HOGENOMiHOG000226071.
InParanoidiP08244.
KOiK01591.
OMAiNFKIFLD.
PhylomeDBiP08244.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00120.
BioCyciEcoCyc:OROTPDECARB-MONOMER.
ECOL316407:JW1273-MONOMER.
MetaCyc:OROTPDECARB-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP08244.
PROiP08244.

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_ECOLI
AccessioniPrimary (citable) accession number: P08244
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: August 1, 1988
Last modified: November 2, 2016
This is version 146 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. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  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.