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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757)
Status
Reviewed-Annotation score: -Protein inferred from homologyi

Functioni

Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan.UniRule annotation

Catalytic activityi

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.UniRule annotation

Pathwayi: L-lysine biosynthesis via DAP pathway

This protein is involved in step 1 of the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Diaminopimelate epimerase (dapF)
This subpathway is part of the pathway L-lysine biosynthesis via DAP pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate, the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei13SubstrateUniRule annotation1
Binding sitei46SubstrateUniRule annotation1
Binding sitei66SubstrateUniRule annotation1
Active sitei75Proton donorUniRule annotation1
Binding sitei159SubstrateUniRule annotation1
Sitei161Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei192SubstrateUniRule annotation1
Sitei210Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei219Proton acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciCVIO243365:G1G08-2524-MONOMER
UniPathwayiUPA00034; UER00025

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimeraseUniRule annotation (EC:5.1.1.7UniRule annotation)
Short name:
DAP epimeraseUniRule annotation
Alternative name(s):
PLP-independent amino acid racemaseUniRule annotation
Gene namesi
Name:dapFUniRule annotation
Ordered Locus Names:CV_2528
OrganismiChromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757)
Taxonomic identifieri243365 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaNeisserialesChromobacteriaceaeChromobacterium
Proteomesi
  • UP000001424 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000118691 – 276Diaminopimelate epimeraseAdd BLAST276

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi243365.CV_2528

Structurei

3D structure databases

ProteinModelPortaliQ7NV18
SMRiQ7NV18
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni76 – 77Substrate bindingUniRule annotation2
Regioni210 – 211Substrate bindingUniRule annotation2
Regioni220 – 221Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z Bacteria
COG0253 LUCA
HOGENOMiHOG000220466
KOiK01778
OMAiSMCGNGG
OrthoDBiPOG091H01QC

Family and domain databases

HAMAPiMF_00197 DAP_epimerase, 1 hit
InterProiView protein in InterPro
IPR018510 DAP_epimerase_AS
IPR001653 DAP_epimerase_DapF
PANTHERiPTHR31689 PTHR31689, 1 hit
PfamiView protein in Pfam
PF01678 DAP_epimerase, 2 hits
TIGRFAMsiTIGR00652 DapF, 1 hit
PROSITEiView protein in PROSITE
PS01326 DAP_EPIMERASE, 1 hit

Sequencei

Sequence statusi: Complete.

Q7NV18-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLKFSKMHG LGNDFMVIDG VRQTVSLTPE QIRLLGNRQL GIGFDQLLLV
60 70 80 90 100
EPAREAGHDF RYRIFNNDGG EVEQCGNGAR CFAKFVRDQG LTGKSRIEVE
110 120 130 140 150
TARGVIAPEY LGDGLARVDM GVPRFRPADL PFLADAEALT YSLPLPEGRC
160 170 180 190 200
EIGIASMGNP HAVQRVDDVD AAPVAEVGPA IESHPAFPQR VNAGFMQIVN
210 220 230 240 250
RGEIRLRVYE RGAGETLACG TGACAAVVCG IRQGLLDARV TVHARGGDIV
260 270
IEWAGEGSPV IMTGPAVTVF QGEIEL
Length:276
Mass (Da):29,652
Last modified:December 15, 2003 - v1
Checksum:i5FAAA1F9C1DBF4B6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016825 Genomic DNA Translation: AAQ60199.1
RefSeqiWP_011136075.1, NC_005085.1

Genome annotation databases

EnsemblBacteriaiAAQ60199; AAQ60199; CV_2528
GeneIDi24948271
KEGGicvi:CV_2528

Similar proteinsi

Entry informationi

Entry nameiDAPF_CHRVO
AccessioniPrimary (citable) accession number: Q7NV18
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: December 15, 2003
Last modified: March 28, 2018
This is version 90 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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Main funding by: National Institutes of Health