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B8DKC9

- PYRF_DESVM

UniProt

B8DKC9 - PYRF_DESVM

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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi

Functioni

Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).UniRule annotation

Catalytic activityi

Orotidine 5'-phosphate = UMP + CO2.UniRule annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei9 – 91SubstrateUniRule annotation
Binding sitei40 – 401SubstrateUniRule annotation
Active sitei69 – 691Proton donorUniRule annotation
Binding sitei132 – 1321SubstrateUniRule annotation
Binding sitei190 – 1901SubstrateUniRule annotation
Binding sitei204 – 2041SubstrateUniRule annotation
Binding sitei224 – 2241Substrate; via amide nitrogenUniRule annotation
Binding sitei225 – 2251SubstrateUniRule annotation

GO - Molecular functioni

  1. orotidine-5'-phosphate decarboxylase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. 'de novo' pyrimidine nucleobase biosynthetic process Source: InterPro
  2. 'de novo' UMP biosynthetic process Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Pyrimidine biosynthesis

Enzyme and pathway databases

BioCyciDVUL883:GCJ5-1172-MONOMER.
UniPathwayiUPA00070; UER00120.

Names & Taxonomyi

Protein namesi
Recommended name:
Orotidine 5'-phosphate decarboxylaseUniRule annotation (EC:4.1.1.23UniRule annotation)
Alternative name(s):
OMP decarboxylaseUniRule annotation
Short name:
OMPDCaseUniRule annotation
Short name:
OMPdecaseUniRule annotation
Gene namesi
Name:pyrFUniRule annotation
Ordered Locus Names:DvMF_1137
OrganismiDesulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Taxonomic identifieri883 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
ProteomesiUP000001361: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 250250Orotidine 5'-phosphate decarboxylasePRO_1000138521Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi883.DvMF_1137.

Structurei

3D structure databases

ProteinModelPortaliB8DKC9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni67 – 7610Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the OMP decarboxylase family. Type 1 subfamily.UniRule annotation

Phylogenomic databases

eggNOGiCOG0284.
HOGENOMiHOG000226070.
KOiK01591.
OMAiVIASPHE.
OrthoDBiEOG6N6815.

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.

B8DKC9-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAELVIALDY PTMDAALATA RALRGATDTA GDAGGRLWMK VGLELFTASG
60 70 80 90 100
PEVVARLKDM GFPVFLDLKF HDIPNTVRGA VRSAVATGAD MCNIHLPGGE
110 120 130 140 150
RMCRAAVEGL AEGAAARGHG AAPILLGVTV LTSVAPGELP GGADPSAEAA
160 170 180 190 200
RLAVCGREWG LGGVVCSGYE AAGIKQRCGR DFICLTPGIR PAAPQRSGSG
210 220 230 240 250
DDDQRRVMTP AEAVRAGSDY LVVGRPVTGA AGPDGPAEAA RRILAEMRGA
Length:250
Mass (Da):25,514
Last modified:March 3, 2009 - v1
Checksum:i168C6FEB875A9ED7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001197 Genomic DNA. Translation: ACL08091.1.
RefSeqiYP_002435559.1. NC_011769.1.

Genome annotation databases

EnsemblBacteriaiACL08091; ACL08091; DvMF_1137.
GeneIDi7173038.
KEGGidvm:DvMF_1137.
PATRICi21772345. VBIDesVul86729_1209.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001197 Genomic DNA. Translation: ACL08091.1 .
RefSeqi YP_002435559.1. NC_011769.1.

3D structure databases

ProteinModelPortali B8DKC9.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 883.DvMF_1137.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACL08091 ; ACL08091 ; DvMF_1137 .
GeneIDi 7173038.
KEGGi dvm:DvMF_1137.
PATRICi 21772345. VBIDesVul86729_1209.

Phylogenomic databases

eggNOGi COG0284.
HOGENOMi HOG000226070.
KOi K01591.
OMAi VIASPHE.
OrthoDBi EOG6N6815.

Enzyme and pathway databases

UniPathwayi UPA00070 ; UER00120 .
BioCyci DVUL883:GCJ5-1172-MONOMER.

Family and domain databases

Gene3Di 3.20.20.70. 1 hit.
HAMAPi MF_01200_B. OMPdecase_type1_B.
InterProi IPR013785. Aldolase_TIM.
IPR014732. OMPdecase.
IPR018089. OMPdecase_AS.
IPR001754. OMPdeCOase_dom.
IPR011060. RibuloseP-bd_barrel.
[Graphical view ]
Pfami PF00215. OMPdecase. 1 hit.
[Graphical view ]
SMARTi SM00934. OMPdecase. 1 hit.
[Graphical view ]
SUPFAMi SSF51366. SSF51366. 1 hit.
TIGRFAMsi TIGR01740. pyrF. 1 hit.
PROSITEi PS00156. OMPDECASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  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.

Entry informationi

Entry nameiPYRF_DESVM
AccessioniPrimary (citable) accession number: B8DKC9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: March 3, 2009
Last modified: October 29, 2014
This is version 40 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

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3