Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Leptothrix cholodnii (strain ATCC 51168 / LMG 8142 / SP-6) (Leptothrix discophora (strain SP-6))
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 sitei76Proton donorUniRule annotation1
Binding sitei174SubstrateUniRule annotation1
Sitei176Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei207SubstrateUniRule annotation1
Sitei225Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei234Proton acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciLCHO395495:G1GBL-131-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:Lcho_0129
OrganismiLeptothrix cholodnii (strain ATCC 51168 / LMG 8142 / SP-6) (Leptothrix discophora (strain SP-6))
Taxonomic identifieri395495 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesLeptothrix
Proteomesi

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000992441 – 297Diaminopimelate epimeraseAdd BLAST297

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi395495.Lcho_0129

Structurei

3D structure databases

ProteinModelPortaliB1Y6S6
SMRiB1Y6S6
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni77 – 78Substrate bindingUniRule annotation2
Regioni225 – 226Substrate bindingUniRule annotation2
Regioni235 – 236Substrate 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
IPR001653 DAP_epimerase_DapF
PANTHERiPTHR31689 PTHR31689, 1 hit
PfamiView protein in Pfam
PF01678 DAP_epimerase, 2 hits
TIGRFAMsiTIGR00652 DapF, 1 hit

Sequencei

Sequence statusi: Complete.

B1Y6S6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRLHFTKMQG AGNDFVVLDA TRAPLALSAA DYRFLGDRRF GVGADQILVV
60 70 80 90 100
ERSTTPGVDF RYRIFNGGSG DEVEQCGNGA RCFARFVRDN GLSQQVRVKV
110 120 130 140 150
ETVNSLIELH VEADGRVTVD MNQPIFEHAL IPFDSAGLSA RPHNGHGNGF
160 170 180 190 200
ELWPLQLPGA SLPSVDVAVL SMGNPHAVQR VHDVDTAPVA EIGPRVETHA
210 220 230 240 250
RFPRHVNAGF MQVMSRREVR LRVFERGAGE TLACGTGACA AVVAGIRLGW
260 270 280 290
LDPEVDVQTR GGLLTIAWAG LGHPVLMTGP AQTVFTGDID LPTTSVQ
Length:297
Mass (Da):32,011
Last modified:May 20, 2008 - v1
Checksum:i0F20436686B685E5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001013 Genomic DNA Translation: ACB32404.1
RefSeqiWP_012345166.1, NC_010524.1

Genome annotation databases

EnsemblBacteriaiACB32404; ACB32404; Lcho_0129
KEGGilch:Lcho_0129

Entry informationi

Entry nameiDAPF_LEPCP
AccessioniPrimary (citable) accession number: B1Y6S6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: May 20, 2008
Last modified: March 28, 2018
This is version 58 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

Cookie policy

We would like to use anonymized google analytics cookies to gather statistics on how uniprot.org is used in aggregate. Learn more

UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health