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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Paraburkholderia xenovorans (strain LB400)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-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

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.
OMAiMCGNGGR.
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

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.

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: June 7, 2017
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

Documents

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