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B1Y6S6

- DAPF_LEPCP

UniProt

B1Y6S6 - DAPF_LEPCP

Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Leptothrix cholodnii (strain ATCC 51168 / LMG 8142 / SP-6) (Leptothrix discophora (strain SP-6))
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 44 (01 Oct 2014)
      Sequence version 1 (20 May 2008)
      Previous versions | rss
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    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

    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

    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.
    OMAiKMRIFNN.
    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

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    MRLHFTKMQG AGNDFVVLDA TRAPLALSAA DYRFLGDRRF GVGADQILVV    50
    ERSTTPGVDF RYRIFNGGSG DEVEQCGNGA RCFARFVRDN GLSQQVRVKV 100
    ETVNSLIELH VEADGRVTVD MNQPIFEHAL IPFDSAGLSA RPHNGHGNGF 150
    ELWPLQLPGA SLPSVDVAVL SMGNPHAVQR VHDVDTAPVA EIGPRVETHA 200
    RFPRHVNAGF MQVMSRREVR LRVFERGAGE TLACGTGACA AVVAGIRLGW 250
    LDPEVDVQTR GGLLTIAWAG LGHPVLMTGP AQTVFTGDID LPTTSVQ 297
    Length:297
    Mass (Da):32,011
    Last modified:May 20, 2008 - v1
    Checksum:i0F20436686B685E5
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001013 Genomic DNA. Translation: ACB32404.1 .
    RefSeqi YP_001789169.1. NC_010524.1.

    3D structure databases

    ProteinModelPortali B1Y6S6.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 395495.Lcho_0129.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ACB32404 ; ACB32404 ; Lcho_0129 .
    GeneIDi 6162710.
    KEGGi lch:Lcho_0129.
    PATRICi 22390527. VBILepCho83238_0133.

    Phylogenomic databases

    eggNOGi COG0253.
    HOGENOMi HOG000220466.
    KOi K01778.
    OMAi KMRIFNN.
    OrthoDBi EOG6ND0M5.

    Enzyme and pathway databases

    UniPathwayi UPA00034 ; UER00025 .
    BioCyci LCHO395495:GHYL-129-MONOMER.

    Family and domain databases

    HAMAPi MF_00197. DAP_epimerase.
    InterProi IPR001653. DAP_epimerase_DapF.
    [Graphical view ]
    PANTHERi PTHR31689. PTHR31689. 1 hit.
    Pfami PF01678. DAP_epimerase. 2 hits.
    [Graphical view ]
    TIGRFAMsi TIGR00652. DapF. 1 hit.
    ProtoNeti Search...

    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: October 1, 2014
    This is version 44 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