Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

P08244 (PYRF_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 128. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Orotidine 5'-phosphate decarboxylase

EC=4.1.1.23
Alternative name(s):
OMP decarboxylase
Short name=OMPDCase
Short name=OMPdecase
Gene names
Name:pyrF
Ordered Locus Names:b1281, JW1273
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length245 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP). HAMAP-Rule MF_01200_B

Catalytic activity

Orotidine 5'-phosphate = UMP + CO2. HAMAP-Rule MF_01200_B

Pathway

Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 2/2. HAMAP-Rule MF_01200_B

Subunit structure

Homodimer. Ref.6 Ref.7 Ref.8

Sequence similarities

Belongs to the OMP decarboxylase family. Type 1 subfamily.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

ribAP0A7I72EBI-1123202,EBI-1123314

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 245245Orotidine 5'-phosphate decarboxylase HAMAP-Rule MF_01200_B
PRO_0000134539

Regions

Region71 – 8010Substrate binding HAMAP-Rule MF_01200_B

Sites

Active site731Proton donor
Binding site221Substrate
Binding site441Substrate
Binding site1311Substrate
Binding site1921Substrate
Binding site2011Substrate
Binding site2211Substrate; via amide nitrogen
Binding site2221Substrate

Secondary structure

........................................... 245
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P08244 [UniParc].

Last modified August 1, 1988. Version 1.
Checksum: 556877A222F0F501

FASTA24526,350
        10         20         30         40         50         60 
MTLTASSSSR AVTNSPVVVA LDYHNRDDAL AFVDKIDPRD CRLKVGKEMF TLFGPQFVRE 

        70         80         90        100        110        120 
LQQRGFDIFL DLKFHDIPNT AAHAVAAAAD LGVWMVNVHA SGGARMMTAA REALVPFGKD 

       130        140        150        160        170        180 
APLLIAVTVL TSMEASDLVD LGMTLSPADY AERLAALTQK CGLDGVVCSA QEAVRFKQVF 

       190        200        210        220        230        240 
GQEFKLVTPG IRPQGSEAGD QRRIMTPEQA LSAGVDYMVI GRPVTQSVDP AQTLKAINAS 


LQRSA 

« Hide

References

« Hide 'large scale' references
[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]"A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map."
Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K. expand/collapse author list , Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T.
DNA Res. 3:363-377(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
J02768 Genomic DNA. Translation: AAA24483.1.
U00096 Genomic DNA. Translation: AAC74363.1.
AP009048 Genomic DNA. Translation: BAA14835.1.
M23250 Genomic DNA. No translation available.
PIRDCECOP. A28440.
RefSeqNP_415797.1. NC_000913.3.
YP_489549.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalP08244.
SMRP08244. Positions 12-243.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActP08244. 4 interactions.
STRING511145.b1281.

2D gel databases

SWISS-2DPAGEP08244.

Proteomic databases

PaxDbP08244.
PRIDEP08244.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC74363; AAC74363; b1281.
BAA14835; BAA14835; BAA14835.
GeneID12931138.
947121.
KEGGecj:Y75_p1256.
eco:b1281.
PATRIC32117826. VBIEscCol129921_1333.

Organism-specific databases

EchoBASEEB0802.
EcoGeneEG10809. pyrF.

Phylogenomic databases

eggNOGCOG0284.
HOGENOMHOG000226071.
KOK01591.
OMANFKIFLD.
OrthoDBEOG6N6815.
PhylomeDBP08244.
ProtClustDBPRK00230.

Enzyme and pathway databases

BioCycEcoCyc:OROTPDECARB-MONOMER.
ECOL316407:JW1273-MONOMER.
MetaCyc:OROTPDECARB-MONOMER.
UniPathwayUPA00070; UER00120.

Gene expression databases

GenevestigatorP08244.

Family and domain databases

Gene3D3.20.20.70. 1 hit.
HAMAPMF_01200_B. OMPdecase_type1_B.
InterProIPR013785. Aldolase_TIM.
IPR014732. OMPdecase.
IPR018089. OMPdecase_AS.
IPR001754. OMPdeCOase_dom.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]
PfamPF00215. OMPdecase. 1 hit.
[Graphical view]
SMARTSM00934. OMPdecase. 1 hit.
[Graphical view]
SUPFAMSSF51366. SSF51366. 1 hit.
TIGRFAMsTIGR01740. pyrF. 1 hit.
PROSITEPS00156. OMPDECASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP08244.
PROP08244.

Entry information

Entry namePYRF_ECOLI
AccessionPrimary (citable) accession number: P08244
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: August 1, 1988
Last modified: April 16, 2014
This is version 128 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene