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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Methylocella silvestris (strain DSM 15510 / CIP 108128 / LMG 27833 / NCIMB 13906 / BL2)
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 sitei17SubstrateUniRule annotation1
Binding sitei49SubstrateUniRule annotation1
Binding sitei69SubstrateUniRule annotation1
Active sitei78Proton donorUniRule annotation1
Binding sitei165SubstrateUniRule annotation1
Sitei167Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei198SubstrateUniRule annotation1
Sitei216Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei225Proton acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciMSIL395965:G1GUA-1895-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:Msil_1850
OrganismiMethylocella silvestris (strain DSM 15510 / CIP 108128 / LMG 27833 / NCIMB 13906 / BL2)
Taxonomic identifieri395965 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBeijerinckiaceaeMethylocella
Proteomesi
  • UP000002257 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10001244261 – 290Diaminopimelate epimeraseAdd BLAST290

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi395965.Msil_1850

Structurei

3D structure databases

ProteinModelPortaliB8EM14
SMRiB8EM14
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni79 – 80Substrate bindingUniRule annotation2
Regioni216 – 217Substrate bindingUniRule annotation2
Regioni226 – 227Substrate 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.

B8EM14-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNPLANRLAV KMNGIGNEIL IVDLRGAGAG VTGPQARAIA RTKGLAFDQL
60 70 80 90 100
MVLEDPRSKG CAAFVTIFNA DGSQSAACGN GTRCVAWTLL KDGARDEVLL
110 120 130 140 150
ETAAGRLACR RVSELVFSVE MGRPRLKAAE IPLSRDAPDT SAVDLSFGPA
160 170 180 190 200
DSPILKNPAV VNMGNPHAIF FVEDIGAYDL AAIGPVLEHD PLFPERANIS
210 220 230 240 250
LARIVSPERI ELKVWERGVG LTLACGSAAC AALVAAARRG LTGRRATVAL
260 270 280 290
PGGELDIFWR ESDDMVVMTG PVAFEFETRL DPAIFADAAA
Length:290
Mass (Da):30,607
Last modified:March 3, 2009 - v1
Checksum:iCBA2F8F9AD691263
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001280 Genomic DNA Translation: ACK50795.1
RefSeqiWP_012590865.1, NC_011666.1

Genome annotation databases

EnsemblBacteriaiACK50795; ACK50795; Msil_1850
KEGGimsl:Msil_1850

Similar proteinsi

Entry informationi

Entry nameiDAPF_METSB
AccessioniPrimary (citable) accession number: B8EM14
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: March 3, 2009
Last modified: March 28, 2018
This is version 50 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
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Main funding by: National Institutes of Health