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Protein

Orotidine 5'-phosphate decarboxylase

Gene

pyrF

Organism
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Status
Reviewed-Annotation score: -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: UMP biosynthesis via de novo pathway

This protein is involved in step 2 of the subpathway that synthesizes UMP from orotate.UniRule annotation
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)DescriptionActionsGraphical viewLength
Binding sitei9SubstrateUniRule annotation1
Binding sitei40SubstrateUniRule annotation1
Active sitei69Proton donorUniRule annotation1
Binding sitei132SubstrateUniRule annotation1
Binding sitei190SubstrateUniRule annotation1
Binding sitei204SubstrateUniRule annotation1
Binding sitei224Substrate; via amide nitrogenUniRule annotation1
Binding sitei225SubstrateUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDecarboxylase, Lyase
Biological processPyrimidine biosynthesis

Enzyme and pathway databases

BioCyciDVUL883:G1GTY-1171-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
Proteomesi
  • UP000001361 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10001385211 – 250Orotidine 5'-phosphate decarboxylaseAdd BLAST250

Proteomic databases

PRIDEiB8DKC9

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi883.DvMF_1137

Structurei

3D structure databases

ProteinModelPortaliB8DKC9
SMRiB8DKC9
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni67 – 76Substrate bindingUniRule annotation10

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4106EG9 Bacteria
COG0284 LUCA
HOGENOMiHOG000226070
KOiK01591
OMAiNFKIFLD
OrthoDBiPOG091H0256

Family and domain databases

Gene3Di3.20.20.70, 1 hit
HAMAPiMF_01200_B OMPdecase_type1_B, 1 hit
InterProiView protein in InterPro
IPR013785 Aldolase_TIM
IPR014732 OMPdecase
IPR018089 OMPdecase_AS
IPR001754 OMPdeCOase_dom
IPR011060 RibuloseP-bd_barrel
PANTHERiPTHR32119:SF2 PTHR32119:SF2, 1 hit
PfamiView protein in Pfam
PF00215 OMPdecase, 1 hit
SMARTiView protein in SMART
SM00934 OMPdecase, 1 hit
SUPFAMiSSF51366 SSF51366, 1 hit
TIGRFAMsiTIGR01740 pyrF, 1 hit
PROSITEiView protein in PROSITE
PS00156 OMPDECASE, 1 hit

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
RefSeqiWP_012612280.1, NC_011769.1

Genome annotation databases

EnsemblBacteriaiACL08091; ACL08091; DvMF_1137
KEGGidvm:DvMF_1137

Similar proteinsi

Entry informationi

Entry nameiPYRF_DESVM
AccessioniPrimary (citable) accession number: B8DKC9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: March 3, 2009
Last modified: May 23, 2018
This is version 54 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

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