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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Paraburkholderia xenovorans (strain LB400)
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

BioCyciBXEN266265:G1G66-90-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:Bxeno_A0089
ORF Names:Bxe_A4373
OrganismiParaburkholderia xenovorans (strain LB400)
Taxonomic identifieri266265 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeParaburkholderia
Proteomesi
  • UP000001817 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_10000118631 – 287Diaminopimelate epimeraseAdd BLAST287

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi266265.Bxe_A4373

Structurei

3D structure databases

ProteinModelPortaliQ146W2
SMRiQ146W2
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.

Q146W2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLKFTKMHG AGNDFVVLDG YTQPVNLTPA QVRALADRHF GVGADQLLLV
60 70 80 90 100
EKPTVAGVDF RYRIFNCDGG EVEHCGNGAR CFVKFVRERG LTDQRSVRVQ
110 120 130 140 150
VQKGTITLTM QENGEVLVDM GTPVFDPERV PFATKGLEGR REGADTLWPL
160 170 180 190 200
DVSGTTRWIS VVSMGNPHAV QVVGDVEAFP VLAEGPVIER HARFPQRVNA
210 220 230 240 250
GFMQIVGRNE IRLRVYERGA GETLACGTGA CAAVAAGIRR GLLDSPVRVH
260 270 280
THGGDLTISW DSTREGEPLL MAGPAVTVFE GEIELPD
Length:287
Mass (Da):31,177
Last modified:August 22, 2006 - v1
Checksum:i0263F6ACC407ED7F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000270 Genomic DNA Translation: ABE28627.1
RefSeqiWP_011486479.1, NZ_CP008760.1

Genome annotation databases

EnsemblBacteriaiABE28627; ABE28627; Bxe_A4373
GeneIDi4005532
KEGGibxb:DR64_2050
bxe:Bxe_A4373
PATRICifig|266265.5.peg.92

Similar proteinsi

Entry informationi

Entry nameiDAPF_PARXL
AccessioniPrimary (citable) accession number: Q146W2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: August 22, 2006
Last modified: March 28, 2018
This is version 72 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