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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Azoarcus sp. (strain BH72)
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 sitei159SubstrateUniRule annotation1
Sitei161Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei192SubstrateUniRule annotation1
Sitei210Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei219Proton 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:azo0594
OrganismiAzoarcus sp. (strain BH72)
Taxonomic identifieri62928 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaRhodocyclalesZoogloeaceaeAzoarcus
Proteomesi
  • UP000002588 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000118331 – 277Diaminopimelate epimeraseAdd BLAST277

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi62928.azo0594.

Structurei

3D structure databases

ProteinModelPortaliA1K306.
SMRiA1K306.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni76 – 77Substrate bindingUniRule annotation2
Regioni210 – 211Substrate bindingUniRule annotation2
Regioni220 – 221Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220467.
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.

A1K306-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHIRFTKMHG LGNDFVVIDA TRTPVDLTPA RVKAIADRHF GVGCDQLLVV
60 70 80 90 100
EPPGSDEVDF RYRIFNADGG EVEQCGNGAR CFVRFVHDKG LTDKREIRVE
110 120 130 140 150
TRAGVIAPAL RPDGLVSVDM GVPELSPARI PFVSDSDAWV QPLQLAEDTV
160 170 180 190 200
AITAVSMGNP HAVQVVADVD TAPVARQGAE IECHPRFPAR VNAGFMQVVD
210 220 230 240 250
AGHIRLRVFE RGAGETLACG TGACAAVVAG IGRGLLVSPV RVETRGGELE
260 270
IAWAGPGTPV VMTGPAVTVF EGELELP
Length:277
Mass (Da):29,433
Last modified:February 6, 2007 - v1
Checksum:i2572480EA9E797E6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM406670 Genomic DNA. Translation: CAL93211.1.
RefSeqiWP_011764329.1. NC_008702.1.

Genome annotation databases

EnsemblBacteriaiCAL93211; CAL93211; azo0594.
KEGGiazo:azo0594.

Similar proteinsi

Entry informationi

Entry nameiDAPF_AZOSB
AccessioniPrimary (citable) accession number: A1K306
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: February 6, 2007
Last modified: August 30, 2017
This is version 67 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