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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.

Pathway:iUMP 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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei22 – 221Substrate
Binding sitei44 – 441Substrate
Active sitei73 – 731Proton donor
Binding sitei131 – 1311Substrate
Binding sitei192 – 1921Substrate
Binding sitei201 – 2011Substrate
Binding sitei221 – 2211Substrate; via amide nitrogen
Binding sitei222 – 2221Substrate

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
  • UMP biosynthetic process Source: GO_Central
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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10809. pyrF.

Subcellular locationi

GO - Cellular componenti

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 245245Orotidine 5'-phosphate decarboxylasePRO_0000134539Add
BLAST

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 interactions.
STRINGi511145.b1281.

Structurei

Secondary structure

1
245
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi17 – 215Combined sources
Helixi26 – 338Combined sources
Turni38 – 403Combined sources
Beta strandi42 – 465Combined sources
Helixi47 – 6317Combined sources
Beta strandi68 – 747Combined sources
Helixi78 – 9114Combined sources
Beta strandi94 – 996Combined sources
Helixi100 – 1023Combined sources
Helixi104 – 1129Combined sources
Helixi113 – 1208Combined sources
Beta strandi123 – 1275Combined sources
Helixi135 – 1395Combined sources
Turni140 – 1423Combined sources
Helixi147 – 16014Combined sources
Beta strandi164 – 1674Combined sources
Helixi170 – 1723Combined sources
Helixi173 – 1808Combined sources
Beta strandi182 – 1887Combined sources
Helixi207 – 2126Combined sources
Beta strandi216 – 2205Combined sources
Helixi222 – 2254Combined sources
Beta strandi227 – 2293Combined sources
Helixi230 – 24011Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 12-243.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP08244.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni71 – 8010Substrate binding

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0284.
HOGENOMiHOG000226071.
InParanoidiP08244.
KOiK01591.
OMAiNFKIFLD.
OrthoDBiEOG6N6815.
PhylomeDBiP08244.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01200_B. OMPdecase_type1_B.
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_CP010445.1.

Genome annotation databases

EnsemblBacteriaiAAC74363; AAC74363; b1281.
BAA14835; BAA14835; BAA14835.
GeneIDi947121.
KEGGieco: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_CP010445.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 12-243.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP08244. 4 interactions.
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.
KEGGieco:b1281.
PATRICi32117826. VBIEscCol129921_1333.

Organism-specific databases

EchoBASEiEB0802.
EcoGeneiEG10809. pyrF.

Phylogenomic databases

eggNOGiCOG0284.
HOGENOMiHOG000226071.
InParanoidiP08244.
KOiK01591.
OMAiNFKIFLD.
OrthoDBiEOG6N6815.
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.
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...

Publicationsi

« Hide 'large scale' publications
  1. "Nucleotide sequence and characterization of the pyrF operon of Escherichia coli K12."
    Turnbough C.L. Jr., Kerr K.H., Funderburg W.R., Donahue J.P., Powell F.E.
    J. Biol. Chem. 262:10239-10245(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "A consensus sequence of three DNA replication terminus sites on the E. coli chromosome is highly homologous to the terR sites of the R6K plasmid."
    Hidaka M., Akiyama M., Horiuchi T.
    Cell 55:467-475(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-14.
  6. "Structural basis for the catalytic mechanism of a proficient enzyme: orotidine 5'-monophosphate decarboxylase."
    Harris P., Poulsen J.-C.N., Jensen K.F., Larsen S.
    Biochemistry 39:4217-4224(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG, SUBUNIT.
    Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
  7. "Selenomethionine substitution of orotidine-5'-monophosphate decarboxylase causes a change in crystal contacts and space group."
    Poulsen J.-C.N., Harris P., Jensen K.F., Larsen S.
    Acta Crystallogr. D 57:1251-1259(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG, SUBUNIT.
    Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
  8. "Substrate binding induces domain movements in orotidine 5'-monophosphate decarboxylase."
    Harris P., Poulsen J.-C.N., Jensen K.F., Larsen S.
    J. Mol. Biol. 318:1019-1029(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF THE NATIVE PROTEIN, SUBUNIT.
    Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.

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: July 22, 2015
This is version 138 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

External Data

Dasty 3

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 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.