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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Leifsonia xyli subsp. xyli (strain CTCB07)
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 sitei14SubstrateUniRule annotation1
Binding sitei78SubstrateUniRule annotation1
Active sitei87Proton donorUniRule annotation1
Binding sitei164SubstrateUniRule annotation1
Sitei166Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei197SubstrateUniRule annotation1
Sitei221Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei230Proton acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciLXYL281090:G1G06-1640-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:Lxx15970
OrganismiLeifsonia xyli subsp. xyli (strain CTCB07)
Taxonomic identifieri281090 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaMicrococcalesMicrobacteriaceaeLeifsonia
Proteomesi
  • UP000001306 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001498461 – 292Diaminopimelate epimeraseAdd BLAST292

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi281090.Lxx15970

Structurei

3D structure databases

ProteinModelPortaliQ6AE05
SMRiQ6AE05
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni88 – 89Substrate bindingUniRule annotation2
Regioni221 – 222Substrate bindingUniRule annotation2
Regioni231 – 232Substrate 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.

Q6AE05-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATLHFTKGQ GTGNDFVLYA DPDGTLPLSA GQIAEICDRH FGVGADGVIR
60 70 80 90 100
AVRSKRLPEG AEALADDEAA EWFMDYYNAD GSAAEMCGNG IRVYVRYLIE
110 120 130 140 150
SRLVQLADGD TLPIGTRSGV RDVQRTLSGF QVDLGRWRLA GGEPLVRAKE
160 170 180 190 200
LPVARLGLGI DLGNPHVVVA LADESELESA DLTYIPHLEP APQGGANVEF
210 220 230 240 250
VVPHEPLVKD GVGRIRMRVH ERGSGETLSC GTGAAAAALA VRHWAGENAP
260 270 280 290
GQWWVDVPGG TVGVRMFPTE DGEHVALSGP AELVYTGALE LA
Length:292
Mass (Da):30,987
Last modified:September 13, 2004 - v1
Checksum:i9A7944AB9769542C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016822 Genomic DNA Translation: AAT89391.1
RefSeqiWP_011186380.1, NC_006087.1

Genome annotation databases

EnsemblBacteriaiAAT89391; AAT89391; Lxx15970
KEGGilxx:Lxx15970

Similar proteinsi

Entry informationi

Entry nameiDAPF_LEIXX
AccessioniPrimary (citable) accession number: Q6AE05
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 2, 2005
Last sequence update: September 13, 2004
Last modified: March 28, 2018
This is version 79 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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