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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / JCM 1027 / KCTC 2358 / NCIMB 9240)
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 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
Sitei270Important for dimerizationUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciAHYD380703:G1G7B-475-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:AHA_0474
OrganismiAeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / JCM 1027 / KCTC 2358 / NCIMB 9240)
Taxonomic identifieri380703 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaAeromonadalesAeromonadaceaeAeromonas
Proteomesi
  • UP000000756 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000118291 – 276Diaminopimelate epimeraseAdd BLAST276

Proteomic databases

PRIDEiA0KFI1

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi380703.AHA_0474

Structurei

3D structure databases

ProteinModelPortaliA0KFI1
SMRiA0KFI1
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
HOGENOMiHOG000220466
KOiK01778
OMAiSMCGNGG

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.

A0KFI1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLIDFSKMHG LGNDFMVVDG VTQKVFFSNE VIKKLADRHF GIGFDQLLLV
60 70 80 90 100
EPPYDPELDF HYRIFNADGS EVEQCGNGAR CFARFVRLKG LINRDRIAVS
110 120 130 140 150
TARGRIVLQL EGENQVTVNM GVPQFEPGKI PFRAQKAEKT YLLRAQEHTV
160 170 180 190 200
MCGAVSMGNP HCVIEVPSVA DAPVATLGPI MERHERFPER VNVGFMEMVN
210 220 230 240 250
ASEIKLRVFE RGVGETLACG TGACAAVVVG ISQGKLKERV TVTLPGGKLT
260 270
IAWKGPGQPV YMTGPAEHVF DGQIEL
Length:276
Mass (Da):30,315
Last modified:December 12, 2006 - v1
Checksum:iF2B901F8F9FADDD4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000462 Genomic DNA Translation: ABK38916.1
RefSeqiWP_011704447.1, NC_008570.1
YP_855007.1, NC_008570.1

Genome annotation databases

EnsemblBacteriaiABK38916; ABK38916; AHA_0474
GeneIDi4488892
KEGGiaha:AHA_0474
PATRICifig|380703.7.peg.467

Similar proteinsi

Entry informationi

Entry nameiDAPF_AERHH
AccessioniPrimary (citable) accession number: A0KFI1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: December 12, 2006
Last modified: May 23, 2018
This is version 72 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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