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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Burkholderia vietnamiensis (strain G4 / LMG 22486) (Burkholderia cepacia (strain R1808))
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 sitei47SubstrateUniRule annotation1
Binding sitei67SubstrateUniRule annotation1
Active sitei76Proton donorUniRule annotation1
Binding sitei167SubstrateUniRule annotation1
Sitei169Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei200SubstrateUniRule annotation1
Sitei218Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei227Proton acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

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:Bcep1808_3168
OrganismiBurkholderia vietnamiensis (strain G4 / LMG 22486) (Burkholderia cepacia (strain R1808))
Taxonomic identifieri269482 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeBurkholderiaBurkholderia cepacia complex
Proteomesi
  • UP000002287 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_10000118621 – 289Diaminopimelate epimeraseAdd BLAST289

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi269482.Bcep1808_3168

Structurei

3D structure databases

ProteinModelPortaliA4JIQ6
SMRiA4JIQ6
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni77 – 78Substrate bindingUniRule annotation2
Regioni218 – 219Substrate bindingUniRule annotation2
Regioni228 – 229Substrate 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.

A4JIQ6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLSFTKMHG AGNDFVVLDG YSHTLPPLTD VQVRALADRH FGIGADQLLV
60 70 80 90 100
VEKPTVDGAD FKYRIFNCDG GEVEHCGNGA RCFVKFVTDR GLTDKRSVRV
110 120 130 140 150
QVMKGLITLT MQDNGEVVVD MGAPVFEPAQ VPFDASGLDG RTDGNDTLWP
160 170 180 190 200
LDVGGATRWV STVSMGNPHA VQVVDDAEAY PVLAEGPLIE RHARFPKRVN
210 220 230 240 250
AGFMQIVSRH EVKLRVYERG AGETLACGTG ACAAVAAGIR RGLLDTPVTV
260 270 280
HTHGGTLTIS WDGAHDERAA LTMAGPATTV FEGEIELNV
Length:289
Mass (Da):30,997
Last modified:May 1, 2007 - v1
Checksum:iD3EA718F216679FC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000614 Genomic DNA Translation: ABO56159.1

Genome annotation databases

EnsemblBacteriaiABO56159; ABO56159; Bcep1808_3168
KEGGibvi:Bcep1808_3168

Similar proteinsi

Entry informationi

Entry nameiDAPF_BURVG
AccessioniPrimary (citable) accession number: A4JIQ6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: May 1, 2007
Last modified: March 28, 2018
This is version 70 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