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B8DKC9 (PYRF_DESVM) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 37. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·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:DvMF_1137
OrganismDesulfovibrio vulgaris (strain Miyazaki F / DSM 19637) [Complete proteome] [HAMAP]
Taxonomic identifier883 [NCBI]
Taxonomic lineageBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio

Protein attributes

Sequence length250 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP) By similarity. HAMAP-Rule MF_01200

Catalytic activity

Orotidine 5'-phosphate = UMP + CO2. HAMAP-Rule MF_01200

Pathway

Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from orotate: step 2/2. HAMAP-Rule MF_01200

Subunit structure

Homodimer By similarity. HAMAP-Rule MF_01200

Sequence similarities

Belongs to the OMP decarboxylase family. Type 1 subfamily.

Ontologies

Keywords
   Biological processPyrimidine biosynthesis
   Molecular functionDecarboxylase
Lyase
   Technical termComplete 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 electronic annotation. Source: InterPro

   Molecular_functionorotidine-5'-phosphate decarboxylase activity

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 250250Orotidine 5'-phosphate decarboxylase HAMAP-Rule MF_01200
PRO_1000138521

Regions

Region67 – 7610Substrate binding By similarity

Sites

Active site691Proton donor By similarity
Binding site91Substrate By similarity
Binding site401Substrate By similarity
Binding site1321Substrate By similarity
Binding site1901Substrate By similarity
Binding site2041Substrate By similarity
Binding site2241Substrate; via amide nitrogen By similarity
Binding site2251Substrate By similarity

Sequences

Sequence LengthMass (Da)Tools
B8DKC9 [UniParc].

Last modified March 3, 2009. Version 1.
Checksum: 168C6FEB875A9ED7

FASTA25025,514
        10         20         30         40         50         60 
MAELVIALDY PTMDAALATA RALRGATDTA GDAGGRLWMK VGLELFTASG PEVVARLKDM 

        70         80         90        100        110        120 
GFPVFLDLKF HDIPNTVRGA VRSAVATGAD MCNIHLPGGE RMCRAAVEGL AEGAAARGHG 

       130        140        150        160        170        180 
AAPILLGVTV LTSVAPGELP GGADPSAEAA RLAVCGREWG LGGVVCSGYE AAGIKQRCGR 

       190        200        210        220        230        240 
DFICLTPGIR PAAPQRSGSG DDDQRRVMTP AEAVRAGSDY LVVGRPVTGA AGPDGPAEAA 

       250 
RRILAEMRGA 

« Hide

References

[1]"Complete sequence of Desulfovibrio vulgaris str. 'Miyazaki F'."
Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Hazen T.C., Richardson P.
Submitted (OCT-2008) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: Miyazaki F / DSM 19637.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP001197 Genomic DNA. Translation: ACL08091.1.
RefSeqYP_002435559.1. NC_011769.1.

3D structure databases

ProteinModelPortalB8DKC9.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING883.DvMF_1137.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACL08091; ACL08091; DvMF_1137.
GeneID7173038.
KEGGdvm:DvMF_1137.
PATRIC21772345. VBIDesVul86729_1209.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0284.
HOGENOMHOG000226070.
KOK01591.
OMAVIASPHE.
OrthoDBEOG6N6815.

Enzyme and pathway databases

BioCycDVUL883:GCJ5-1172-MONOMER.
UniPathwayUPA00070; UER00120.

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...

Entry information

Entry namePYRF_DESVM
AccessionPrimary (citable) accession number: B8DKC9
Entry history
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: March 3, 2009
Last modified: May 14, 2014
This is version 37 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

PATHWAY comments

Index of metabolic and biosynthesis pathways