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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Variovorax paradoxus (strain S110)
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 sitei69SubstrateUniRule annotation1
Active sitei78Proton donorUniRule annotation1
Binding sitei173SubstrateUniRule annotation1
Sitei175Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei206SubstrateUniRule annotation1
Sitei224Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei233Proton acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciVPAR543728:G1GF3-896-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:Vapar_0899
OrganismiVariovorax paradoxus (strain S110)
Taxonomic identifieri543728 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesComamonadaceaeVariovorax
Proteomesi
  • UP000000453 Componenti: Chromosome 1

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10002040701 – 294Diaminopimelate epimeraseAdd BLAST294

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi543728.Vapar_0899

Structurei

3D structure databases

ProteinModelPortaliC5CND4
SMRiC5CND4
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni79 – 80Substrate bindingUniRule annotation2
Regioni224 – 225Substrate bindingUniRule annotation2
Regioni234 – 235Substrate 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.

C5CND4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRIRFTKMQG AGNDFVVLDE TRGTLGLTAA QYRFLADRHF GVGADQILTV
60 70 80 90 100
RPPSKGAAEG VDFQYVIHNA DGGEVEQCGN GARCFMRFVR EHHLTDKDTV
110 120 130 140 150
RVETLAGIIE PRMGADGRVT VDMGPPIFEP ARVPFDTAGL DPQPTGSWHT
160 170 180 190 200
WHLALGTHAD SAIVSVAVLS MGNPHAVQVV DNVDTAPVAR QGPLIEHHPR
210 220 230 240 250
FAQRVNAGFM QVVDRSHIKL RVFERGAGET LACGTGACAA VVAGIRLGLL
260 270 280 290
ERRVDVQTHG GVLTIGWEGE GHPVLMTGPA TTVFEGDIEV PELP
Length:294
Mass (Da):31,618
Last modified:July 28, 2009 - v1
Checksum:i5279A4320AD6A5F4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001635 Genomic DNA Translation: ACS17550.1
RefSeqiWP_012746049.1, NC_012791.1

Genome annotation databases

EnsemblBacteriaiACS17550; ACS17550; Vapar_0899
KEGGivap:Vapar_0899

Similar proteinsi

Entry informationi

Entry nameiDAPF_VARPS
AccessioniPrimary (citable) accession number: C5CND4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: July 28, 2009
Last modified: March 28, 2018
This is version 52 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
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Main funding by: National Institutes of Health