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A5F4I6

- DAPF_VIBC3

UniProt

A5F4I6 - DAPF_VIBC3

Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 53 (01 Oct 2014)
      Sequence version 1 (12 Jun 2007)
      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 sitei75 – 751Proton donor/acceptorUniRule annotation
    Binding sitei159 – 1591SubstrateUniRule annotation
    Sitei161 – 1611Important for catalytic activityUniRule annotation
    Binding sitei192 – 1921SubstrateUniRule annotation
    Sitei210 – 2101Important for catalytic activityUniRule annotation
    Active sitei219 – 2191Proton 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

    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:VC0395_A2393, VC395_0054
    OrganismiVibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)
    Taxonomic identifieri345073 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
    ProteomesiUP000000249: Chromosome 2, UP000001630: Chromosome I

    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 – 276276Diaminopimelate epimerasePRO_1000071717Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi75 ↔ 219

    Keywords - PTMi

    Disulfide bond

    Interactioni

    Protein-protein interaction databases

    STRINGi345073.VC0395_A2393.

    Structurei

    3D structure databases

    ProteinModelPortaliA5F4I6.
    SMRiA5F4I6. Positions 4-275.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni10 – 112Substrate bindingUniRule annotation
    Regioni75 – 773Substrate bindingUniRule annotation
    Regioni210 – 2112Substrate bindingUniRule annotation

    Sequence similaritiesi

    Belongs to the diaminopimelate epimerase family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0253.
    HOGENOMiHOG000220466.
    KOiK01778.
    OMAiLIVEPPY.

    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.

    A5F4I6-1 [UniParc]FASTAAdd to Basket

    « Hide

    MHFHFSKMHG LGNDFMVVDC ITQNVFFSPE LIRRLADRHT GVGFDQLLVV    50
    EAPYDPESDF HYRIFNADGS EVEQCGNGAR CFARFVRMKG LTNKYTIHVS 100
    TKKGKMVLNV EEEDLITVNM GVPEFEPNKI PFRAKQSEKT YILRVGEHTL 150
    FCGAVSMGNP HVVTVVDDIR TAAVETLGPL LESHERFPER VNAGFMQVVS 200
    RDEINLRVYE RGAGETQACG SGACAAVAVG ILQGLLDEQV RVHLPGGELE 250
    IHWQGPGKPL YMTGPATHIY DGQISC 276
    Length:276
    Mass (Da):30,651
    Last modified:June 12, 2007 - v1
    Checksum:i8FCFEC10E5DD714B
    GO

    Sequence cautioni

    The sequence ACP08082.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000627 Genomic DNA. Translation: ABQ19755.1.
    CP001235 Genomic DNA. Translation: ACP08082.1. Different initiation.
    RefSeqiYP_001218293.1. NC_009457.1.
    YP_002818318.1. NC_012582.1.

    Genome annotation databases

    EnsemblBacteriaiABQ19755; ABQ19755; VC0395_A2393.
    ACP08082; ACP08082; VC395_0054.
    GeneIDi5137009.
    7776703.
    KEGGivco:VC0395_A2393.
    vcr:VC395_0054.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000627 Genomic DNA. Translation: ABQ19755.1 .
    CP001235 Genomic DNA. Translation: ACP08082.1 . Different initiation.
    RefSeqi YP_001218293.1. NC_009457.1.
    YP_002818318.1. NC_012582.1.

    3D structure databases

    ProteinModelPortali A5F4I6.
    SMRi A5F4I6. Positions 4-275.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 345073.VC0395_A2393.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABQ19755 ; ABQ19755 ; VC0395_A2393 .
    ACP08082 ; ACP08082 ; VC395_0054 .
    GeneIDi 5137009.
    7776703.
    KEGGi vco:VC0395_A2393.
    vcr:VC395_0054.

    Phylogenomic databases

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

    Enzyme and pathway databases

    UniPathwayi UPA00034 ; UER00025 .

    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. Heidelberg J.
      Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 39541 / Classical Ogawa 395 / O395.
    2. "A recalibrated molecular clock and independent origins for the cholera pandemic clones."
      Feng L., Reeves P.R., Lan R., Ren Y., Gao C., Zhou Z., Ren Y., Cheng J., Wang W., Wang J., Qian W., Li D., Wang L.
      PLoS ONE 3:E4053-E4053(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 39541 / Classical Ogawa 395 / O395.

    Entry informationi

    Entry nameiDAPF_VIBC3
    AccessioniPrimary (citable) accession number: A5F4I6
    Secondary accession number(s): C3M2B8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 26, 2008
    Last sequence update: June 12, 2007
    Last modified: October 1, 2014
    This is version 53 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