Orotidine 5'-phosphate decarboxylase - Escherichia coli (strain K12)

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P08244 (PYRF_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 122. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended 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

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	245 AA.
Sequence status	Complete.
Protein existence	Evidence 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.

Ontologies

Keywords
Biological process	Pyrimidine biosynthesis
Molecular function	Decarboxylase Lyase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	'de novo' UMP biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway 'de novo' pyrimidine nucleobase biosynthetic process Inferred from mutant phenotype PubMed 6370696. Source: EcoCyc nucleobase-containing small molecule interconversion Inferred from direct assay PubMed 6355062. Source: EcoliWiki
Cellular_component	cytoplasm Inferred from direct assay PubMed 6355062. Source: EcoliWiki
Molecular_function	orotidine-5'-phosphate decarboxylase activity Inferred from direct assay PubMed 6355062. Source: EcoCyc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ribA	P0A7I7	2	EBI-1123202,EBI-1123314

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 245

245

Orotidine 5'-phosphate decarboxylase HAMAP-Rule MF_01200_B

PRO_0000134539

Regions

Region

71 – 80

Substrate binding HAMAP-Rule MF_01200_B

Sites

Active site

Proton donor

Binding site

Substrate

Binding site

Substrate

Binding site

131

Substrate

Binding site

192

Substrate

Binding site

201

Substrate

Binding site

221

Substrate; via amide nitrogen

Binding site

222

Substrate

Secondary structure

245

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P08244 [UniParc].

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

FASTA

245

26,350

        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' referencesShow '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. 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 277:1453-1474(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.

PIR

DCECOP. A28440.

RefSeq

NP_415797.1. NC_000913.2.
YP_489549.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1EIX	X-ray	2.50	A/B/C/D	1-245	[»]
1JJK	X-ray	3.00	A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P	1-245	[»]
1L2U	X-ray	2.50	A/B	1-245	[»]

ProteinModelPortal

P08244.

SMR

P08244. Positions 12-243.

ModBase

Search...

Protein-protein interaction databases

IntAct

P08244. 3 interactions.

STRING

511145.b1281.

2D gel databases

SWISS-2DPAGE

P08244.

Proteomic databases

PaxDb

P08244.

PRIDE

P08244.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC74363; AAC74363; b1281.
BAA14835; BAA14835; BAA14835.

GeneID

12931138.
947121.

KEGG

ecj:Y75_p1256.
eco:b1281.

PATRIC

32117826. VBIEscCol129921_1333.

Organism-specific databases

EchoBASE

EB0802.

EcoGene

EG10809. pyrF.

Phylogenomic databases

eggNOG

COG0284.

HOGENOM

HOG000226071.

K01591.

OMA

NFKIFLD.

ProtClustDB

PRK00230.

Enzyme and pathway databases

BioCyc

EcoCyc:OROTPDECARB-MONOMER.
ECOL316407:JW1273-MONOMER.
MetaCyc:OROTPDECARB-MONOMER.

UniPathway

UPA00070; UER00120.

Gene expression databases

Genevestigator

P08244.

Family and domain databases

Gene3D

3.20.20.70. 1 hit.

HAMAP

MF_01200_B. OMPdecase_type1_B.

InterPro

IPR013785. Aldolase_TIM.
IPR014732. OMPdecase.
IPR018089. OMPdecase_AS.
IPR001754. OMPdeCOase_dom.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]

Pfam

PF00215. OMPdecase. 1 hit.
[Graphical view]

SMART

SM00934. OMPdecase. 1 hit.
[Graphical view]

SUPFAM

SSF51366. RibP_bind_barrel. 1 hit.

TIGRFAMs

TIGR01740. pyrF. 1 hit.

PROSITE

PS00156. OMPDECASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P08244.

Entry information

Entry name

PYRF_ECOLI

Accession

Primary (citable) accession number: P08244

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1988
Last sequence update:	August 1, 1988
Last modified:	May 1, 2013
This is version 122 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

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

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2D gel databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents