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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815) (Burkholderia phymatum)
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 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

BioCyciBPHY391038:G1GBS-78-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:Bphy_0076
OrganismiParaburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815) (Burkholderia phymatum)
Taxonomic identifieri391038 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeParaburkholderia
Proteomesi
  • UP000001192 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_10000992221 – 286Diaminopimelate epimeraseAdd BLAST286

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi391038.Bphy_0076

Structurei

3D structure databases

ProteinModelPortaliB2JJY4
SMRiB2JJY4
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni76 – 77Substrate 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.

B2JJY4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLKFTKMHG AGNDFVVLDG YTQPLNLTET QVRALANRHF GVGADQLLVV
60 70 80 90 100
EKPTVDGVDF RYRIFNCDGG EVEHCGNGAR CFVKFVRDSR LTDKRSVRVQ
110 120 130 140 150
VQKGVITLTM QDNGEVVVDM GAPVFEPVQV PFDASGVEAR REGNDTLYAL
160 170 180 190 200
EVNGETRWVS VVSMGNPHAV QVVDDVEAFP VLVDGPVIET HPRFPQRVNA
210 220 230 240 250
GFMQIVGRSE VKLRVYERGA GETLACGTGA CAAVAAGIRR GLLDAPVKVH
260 270 280
THGGTLTITW NGESASSLMM AGPAATVFEG EIELAD
Length:286
Mass (Da):30,870
Last modified:June 10, 2008 - v1
Checksum:i79FD072E1C848D9D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001043 Genomic DNA Translation: ACC69271.1
RefSeqiWP_012399501.1, NC_010622.1

Genome annotation databases

EnsemblBacteriaiACC69271; ACC69271; Bphy_0076
GeneIDi27739748
KEGGibph:Bphy_0076

Similar proteinsi

Entry informationi

Entry nameiDAPF_PARP8
AccessioniPrimary (citable) accession number: B2JJY4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: June 10, 2008
Last modified: March 28, 2018
This is version 65 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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