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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Leptothrix cholodnii (strain ATCC 51168 / LMG 8142 / SP-6) (Leptothrix discophora (strain SP-6))
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-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

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
  • UP000001693 Componenti: Chromosome

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.
OMAiRFTKMQG.
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.
PATRICi22390527. VBILepCho83238_0133.

Cross-referencesi

Sequence databases

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

3D structure databases

ProteinModelPortaliB1Y6S6.
SMRiB1Y6S6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi395495.Lcho_0129.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACB32404; ACB32404; Lcho_0129.
KEGGilch:Lcho_0129.
PATRICi22390527. VBILepCho83238_0133.

Phylogenomic databases

eggNOGiENOG4105E4Z. Bacteria.
COG0253. LUCA.
HOGENOMiHOG000220466.
KOiK01778.
OMAiRFTKMQG.
OrthoDBiPOG091H01QC.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.

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.
ProtoNetiSearch...

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 15, 2017
This is version 55 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.