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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Desulforudis audaxviator (strain MP104C)
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 sitei11SubstrateUniRule annotation1
Binding sitei63SubstrateUniRule annotation1
Active sitei72Proton donorUniRule annotation1
Binding sitei160SubstrateUniRule annotation1
Sitei162Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei193SubstrateUniRule annotation1
Sitei211Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei220Proton acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciCDES477974:G1GAD-1662-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:Daud_1604
OrganismiDesulforudis audaxviator (strain MP104C)
Taxonomic identifieri477974 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesPeptococcaceaeCandidatus Desulforudis
Proteomesi
  • UP000008544 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000992311 – 278Diaminopimelate epimeraseAdd BLAST278

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi477974.Daud_1604

Structurei

3D structure databases

ProteinModelPortaliB1I545
SMRiB1I545
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni73 – 74Substrate bindingUniRule annotation2
Regioni211 – 212Substrate bindingUniRule annotation2
Regioni221 – 222Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z Bacteria
COG0253 LUCA
HOGENOMiHOG000220467
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.

B1I545-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEFTKMHGLG NDFVIVNGFG QSLPDDPGAL ARRVCDRRLG VGADGLVLLL
60 70 80 90 100
PSAAADLRMR VFNPDGSEPE MCGNAIRCVA LYARRRGLVA KTQLEVETLA
110 120 130 140 150
GLIRPEILLD GDRETVRVDM GRPRLERAEI PMRGPAGPVV GEVLDAGERS
160 170 180 190 200
FMVTAVSMGN PHCVVFGADL DDAGFRKYGP LLEVHPAFPA RTNVEFVEVL
210 220 230 240 250
SPGEVAVRVW ERGVGPTPAC GTGACAVAVA GVLTGRTARR VHVRLPGGVL
260 270
LIEWPDDAGP VYMSGPAEEV FDGKWVRA
Length:278
Mass (Da):29,718
Last modified:April 29, 2008 - v1
Checksum:iB6A521D992514291
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000860 Genomic DNA Translation: ACA60106.1
RefSeqiWP_012302687.1, NC_010424.1

Genome annotation databases

EnsemblBacteriaiACA60106; ACA60106; Daud_1604
KEGGidau:Daud_1604

Similar proteinsi

Entry informationi

Entry nameiDAPF_DESAP
AccessioniPrimary (citable) accession number: B1I545
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: April 29, 2008
Last modified: March 28, 2018
This is version 62 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
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