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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Nitratiruptor sp. (strain SB155-2)
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 sitei60SubstrateUniRule annotation1
Active sitei69Proton donorUniRule annotation1
Sitei138Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei164SubstrateUniRule annotation1
Sitei182Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei192Proton acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciNSP387092:G1G2O-106-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:NIS_0102
OrganismiNitratiruptor sp. (strain SB155-2)
Taxonomic identifieri387092 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaNitratiruptor
Proteomesi
  • UP000001118 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000119201 – 250Diaminopimelate epimeraseAdd BLAST250

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi387092.NIS_0102

Structurei

3D structure databases

ProteinModelPortaliA6Q160
SMRiA6Q160
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni70 – 71Substrate bindingUniRule annotation2
Regioni182 – 183Substrate bindingUniRule annotation2
Regioni193 – 194Substrate 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.

A6Q160-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQLVKYSASG NDFVIYHTFV KKDRSELAKL LCHRHEGIGA DGLIVLLPHS
60 70 80 90 100
RYDFEWQFYN ADGSEAEMCG NGSRAAAHYA YSYGLASKQM RFLTLAGVIE
110 120 130 140 150
ASVEADVVES QLTKPKILDR KIEENGKRWW LIDTGVPHLV TFVEDLNQFD
160 170 180 190 200
KNESKRLRNK YNANVNYGII RDLENVGVRT YERGVEDETL ACGTGMAATF
210 220 230 240 250
LRAFEEGVVN PTVTVVPKSG EELQLRYENE KLFFKGRVKK VFETFKEGIW
Length:250
Mass (Da):28,476
Last modified:August 21, 2007 - v1
Checksum:iA9EDE4FAA3305FEF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009178 Genomic DNA Translation: BAF69219.1
RefSeqiWP_011979645.1, NC_009662.1

Genome annotation databases

EnsemblBacteriaiBAF69219; BAF69219; NIS_0102
KEGGinis:NIS_0102

Similar proteinsi

Entry informationi

Entry nameiDAPF_NITSB
AccessioniPrimary (citable) accession number: A6Q160
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: August 21, 2007
Last modified: May 23, 2018
This is version 60 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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