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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-Experimental evidence at protein leveli

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei13 – 131SubstrateUniRule annotation
Binding sitei46 – 461SubstrateUniRule annotation
Binding sitei66 – 661SubstrateUniRule annotation
Active sitei76 – 761Proton donor/acceptorUniRule annotation
Binding sitei174 – 1741SubstrateUniRule annotation
Sitei176 – 1761Important for catalytic activityUniRule annotation
Binding sitei207 – 2071SubstrateUniRule annotation
Sitei225 – 2251Important for catalytic activityUniRule annotation
Active sitei234 – 2341Proton donor/acceptorUniRule annotation

GO - Molecular functioni

  1. diaminopimelate epimerase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. lysine biosynthetic process via diaminopimelate Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciLCHO395495:GHYL-129-MONOMER.
UniPathwayiUPA00034; UER00025.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimeraseUniRule annotation (EC:5.1.1.7UniRule annotation)
Short name:
DAP epimeraseUniRule 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
ProteomesiUP000001693: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 297297Diaminopimelate epimerasePRO_1000099244Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi76 ↔ 234

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi395495.Lcho_0129.

Structurei

3D structure databases

ProteinModelPortaliB1Y6S6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni76 – 783Substrate bindingUniRule annotation
Regioni225 – 2262Substrate bindingUniRule annotation
Regioni235 – 2362Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
InterProiIPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
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.
RefSeqiYP_001789169.1. NC_010524.1.

Genome annotation databases

EnsemblBacteriaiACB32404; ACB32404; Lcho_0129.
GeneIDi6162710.
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.
RefSeqiYP_001789169.1. NC_010524.1.

3D structure databases

ProteinModelPortaliB1Y6S6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi395495.Lcho_0129.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACB32404; ACB32404; Lcho_0129.
GeneIDi6162710.
KEGGilch:Lcho_0129.
PATRICi22390527. VBILepCho83238_0133.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiMKFTKMH.
OrthoDBiEOG6ND0M5.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciLCHO395495:GHYL-129-MONOMER.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
InterProiIPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 51168 / LMG 8142 / SP-6.

Entry informationi

Entry nameiDAPF_LEPCP
AccessioniPrimary (citable) accession number: B1Y6S6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: May 20, 2008
Last modified: February 4, 2015
This is version 48 of the entry and version 1 of the sequence. [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

External Data

Dasty 3

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 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.