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B2K072

- DAPF_YERPB

UniProt

B2K072 - DAPF_YERPB

Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Yersinia pseudotuberculosis serotype IB (strain PB1/+)
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 (10 Jun 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 sitei11 – 111SubstrateUniRule annotation
    Binding sitei44 – 441SubstrateUniRule annotation
    Binding sitei64 – 641SubstrateUniRule annotation
    Active sitei73 – 731Proton donor/acceptorUniRule annotation
    Binding sitei157 – 1571SubstrateUniRule annotation
    Sitei159 – 1591Important for catalytic activityUniRule annotation
    Binding sitei190 – 1901SubstrateUniRule annotation
    Sitei208 – 2081Important for catalytic activityUniRule annotation
    Active sitei217 – 2171Proton 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

    BioCyciYPSE502801:GHIH-297-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:YPTS_0203
    OrganismiYersinia pseudotuberculosis serotype IB (strain PB1/+)
    Taxonomic identifieri502801 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeYersinia
    ProteomesiUP000001193: 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 – 274274Diaminopimelate epimerasePRO_1000099274Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi73 ↔ 217

    Keywords - PTMi

    Disulfide bond

    Interactioni

    Protein-protein interaction databases

    STRINGi502801.YPTS_0203.

    Structurei

    3D structure databases

    ProteinModelPortaliB2K072.
    SMRiB2K072. Positions 1-274.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni8 – 92Substrate bindingUniRule annotation
    Regioni73 – 753Substrate bindingUniRule annotation
    Regioni208 – 2092Substrate bindingUniRule annotation

    Sequence similaritiesi

    Belongs to the diaminopimelate epimerase family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0253.
    HOGENOMiHOG000220466.
    KOiK01778.
    OMAiLIVEPPY.
    OrthoDBiEOG6ND0M5.

    Family and domain databases

    HAMAPiMF_00197. DAP_epimerase.
    InterProiIPR018510. DAP_epimerase_AS.
    IPR001653. DAP_epimerase_DapF.
    [Graphical view]
    PANTHERiPTHR31689. PTHR31689. 1 hit.
    PfamiPF01678. DAP_epimerase. 2 hits.
    [Graphical view]
    TIGRFAMsiTIGR00652. DapF. 1 hit.
    PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    B2K072-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQFSKMHGLG NDFMVVDAVT QNVYFSPELI RRLADRHTGV GFDQMLVVEP    50
    PYDPELDFHY RIFNADGSEV SQCGNGARCF ARFVRLKGLT NKREISVSTQ 100
    TGRMILSVTE DEQVCVNMGE PDFEPQTVPF RAAKAEKTYI LRAAEHTVLC 150
    GVVSMGNPHC VMQVDDVSVA NVALLGPVLE NHERFPERAN IGFMQVVSRD 200
    HIRLRVYERG AGETQACGSG ACAAVAVGVV QDLLNENVHV ELPGGSLHIR 250
    WQGPGHPLYM TGPATHVYDG FIHL 274
    Length:274
    Mass (Da):30,252
    Last modified:June 10, 2008 - v1
    Checksum:i8B66E79E67EB9FF1
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001048 Genomic DNA. Translation: ACC87200.1.
    RefSeqiYP_001870657.1. NC_010634.1.

    Genome annotation databases

    EnsemblBacteriaiACC87200; ACC87200; YPTS_0203.
    GeneIDi6260715.
    KEGGiypb:YPTS_0203.
    PATRICi18647911. VBIYerPse20639_0216.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001048 Genomic DNA. Translation: ACC87200.1 .
    RefSeqi YP_001870657.1. NC_010634.1.

    3D structure databases

    ProteinModelPortali B2K072.
    SMRi B2K072. Positions 1-274.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 502801.YPTS_0203.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ACC87200 ; ACC87200 ; YPTS_0203 .
    GeneIDi 6260715.
    KEGGi ypb:YPTS_0203.
    PATRICi 18647911. VBIYerPse20639_0216.

    Phylogenomic databases

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

    Enzyme and pathway databases

    UniPathwayi UPA00034 ; UER00025 .
    BioCyci YPSE502801:GHIH-297-MONOMER.

    Family and domain databases

    HAMAPi MF_00197. DAP_epimerase.
    InterProi IPR018510. DAP_epimerase_AS.
    IPR001653. DAP_epimerase_DapF.
    [Graphical view ]
    PANTHERi PTHR31689. PTHR31689. 1 hit.
    Pfami PF01678. DAP_epimerase. 2 hits.
    [Graphical view ]
    TIGRFAMsi TIGR00652. DapF. 1 hit.
    PROSITEi PS01326. DAP_EPIMERASE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Complete sequence of Yersinia pseudotuberculosis PB1/+."
      Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Munk A.C., Brettin T., Detter J.C., Han C., Tapia R., Schmutz J., Larimer F., Land M., Hauser L.
      , Challacombe J.F., Green L., Lindler L.E., Nikolich M.P., Richardson P.
      Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: PB1/+.

    Entry informationi

    Entry nameiDAPF_YERPB
    AccessioniPrimary (citable) accession number: B2K072
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 24, 2009
    Last sequence update: June 10, 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

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3