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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Heliobacterium modesticaldum (strain ATCC 51547 / Ice1)
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 sitei65SubstrateUniRule annotation1
Active sitei74Proton donorUniRule annotation1
Binding sitei164SubstrateUniRule annotation1
Sitei166Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei197SubstrateUniRule annotation1
Sitei215Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei224Proton acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciHMOD498761:G1GB0-1934-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:Helmi_20550
ORF Names:HM1_2123
OrganismiHeliobacterium modesticaldum (strain ATCC 51547 / Ice1)
Taxonomic identifieri498761 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesHeliobacteriaceaeHeliobacterium
Proteomesi

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000992381 – 281Diaminopimelate epimeraseAdd BLAST281

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi498761.HM1_2123

Structurei

3D structure databases

ProteinModelPortaliB0TGR9
SMRiB0TGR9
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni75 – 76Substrate bindingUniRule annotation2
Regioni215 – 216Substrate bindingUniRule annotation2
Regioni225 – 226Substrate 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.

B0TGR9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEFVKMHGLG NDFIVVNAME PPLLDREDWE EIAVRICDRH YGIGGDGLIL
60 70 80 90 100
LFPSDKADIR WRILNSDGSE PEMCGNGIRC LARYVYERGI VAKRRIEVET
110 120 130 140 150
LAGIIVPEII TDAAGAVTGV CVDMGEPRLQ RHQIPMVGPE GPAVNQELVV
160 170 180 190 200
GDAVVRVTAL SMGNPHCLIY VNDIDEAPVT TLGPKVEVHP AFPAKTNVEF
210 220 230 240 250
VQVVAPDEVQ MRVWERGAGP TLACGTGACA TVVGSVLNGY TDRKVTVHLA
260 270 280
GGPLHIEWRE ENNRVYMTGP AVEVFRGELP L
Length:281
Mass (Da):30,627
Last modified:April 8, 2008 - v1
Checksum:i6412759EBF2E3EEE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000930 Genomic DNA Translation: ABZ84680.1
RefSeqiWP_012283180.1, NC_010337.2

Genome annotation databases

EnsemblBacteriaiABZ84680; ABZ84680; HM1_2123
KEGGihmo:HM1_2123

Entry informationi

Entry nameiDAPF_HELMI
AccessioniPrimary (citable) accession number: B0TGR9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: April 8, 2008
Last modified: March 28, 2018
This is version 61 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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