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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / KCTC 32145 / OM5)
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 sitei17SubstrateUniRule annotation1
Binding sitei49SubstrateUniRule annotation1
Binding sitei69SubstrateUniRule annotation1
Active sitei78Proton donorUniRule annotation1
Binding sitei166SubstrateUniRule annotation1
Sitei168Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei199SubstrateUniRule annotation1
Sitei217Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei226Proton acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciOCAR504832:G1GTX-260-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:OCAR_4263, OCA5_c02550
OrganismiOligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / KCTC 32145 / OM5)
Taxonomic identifieri504832 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeOligotropha
Proteomesi

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000992531 – 290Diaminopimelate epimeraseAdd BLAST290

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi504832.OCA5_c02550

Structurei

3D structure databases

ProteinModelPortaliB6JAP3
SMRiB6JAP3
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni79 – 80Substrate bindingUniRule annotation2
Regioni217 – 218Substrate bindingUniRule annotation2
Regioni227 – 228Substrate 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.

B6JAP3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTVLANHSFA KMNGIGNEIV IVDLRNTDSQ LSAAEARAIA APGGVPYDQL
60 70 80 90 100
MVLQKPRMPG TTAFVRIYNN DGSEAGACGN GMRCVAKRVF GESGAQAATF
110 120 130 140 150
ETRAGLLNCW QGPSPDLYTV DMGTPKFGWQ DIPLAEEFRD TRYIELQIGP
160 170 180 190 200
IDAPVLHSPS VVSMGNPHAI FWVDDIEAYD LERLGPLLEN HPIFPERANI
210 220 230 240 250
TLAHVVDRNH IRMRTWERGA GLTLACGSAA CATAVAAARL KRTDRTVEMS
260 270 280 290
LPGGDLTIEW RESDDHVLMT GAAVLEYEGL FDPDLFAALA
Length:290
Mass (Da):31,496
Last modified:December 16, 2008 - v1
Checksum:i55349272902037E0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001196 Genomic DNA Translation: ACI91412.1
CP002826 Genomic DNA Translation: AEI04984.1
RefSeqiWP_012561443.1, NC_015684.1

Genome annotation databases

EnsemblBacteriaiACI91412; ACI91412; OCAR_4263
AEI04984; AEI04984; OCA5_c02550
KEGGioca:OCAR_4263
ocg:OCA5_c02550
PATRICifig|504832.7.peg.271

Similar proteinsi

Entry informationi

Entry nameiDAPF_OLICO
AccessioniPrimary (citable) accession number: B6JAP3
Secondary accession number(s): F8BTD9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: December 16, 2008
Last modified: March 28, 2018
This is version 53 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

Documents

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

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