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B9JUB9

- DAPF_AGRVS

UniProt

B9JUB9 - DAPF_AGRVS

Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Agrobacterium vitis (strain S4 / ATCC BAA-846) (Rhizobium vitis (strain S4))
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 37 (01 Oct 2014)
      Sequence version 1 (24 Mar 2009)
      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 sitei15 – 151SubstrateUniRule annotation
    Binding sitei47 – 471SubstrateUniRule annotation
    Binding sitei67 – 671SubstrateUniRule annotation
    Active sitei76 – 761Proton donor/acceptorUniRule annotation
    Binding sitei163 – 1631SubstrateUniRule annotation
    Sitei165 – 1651Important for catalytic activityUniRule annotation
    Binding sitei197 – 1971SubstrateUniRule annotation
    Sitei215 – 2151Important for catalytic activityUniRule annotation
    Active sitei224 – 2241Proton 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

    BioCyciAVIT311402:GH2Y-3159-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:Avi_4198
    OrganismiAgrobacterium vitis (strain S4 / ATCC BAA-846) (Rhizobium vitis (strain S4))
    Taxonomic identifieri311402 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeRhizobium/Agrobacterium groupAgrobacterium
    ProteomesiUP000001596: Chromosome 1

    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 – 303303Diaminopimelate epimerasePRO_1000124397Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi76 ↔ 224

    Keywords - PTMi

    Disulfide bond

    Interactioni

    Protein-protein interaction databases

    STRINGi311402.Avi_4198.

    Structurei

    3D structure databases

    ProteinModelPortaliB9JUB9.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni12 – 132Substrate bindingUniRule annotation
    Regioni76 – 783Substrate bindingUniRule annotation
    Regioni215 – 2162Substrate bindingUniRule annotation

    Sequence similaritiesi

    Belongs to the diaminopimelate epimerase family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0253.
    HOGENOMiHOG000220466.
    KOiK01778.
    OMAiDGVWMTG.
    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.

    B9JUB9-1 [UniParc]FASTAAdd to Basket

    « Hide

    MGNRVEFAKM NGLGNKILVV DMRGRADRVM PQAAIALAGN AETHFDQIMA    50
    IHDPKLAGTF AYIDIINCDG TLAQACGNGT RCVVQALSAE TGLKAFTFQT 100
    LAGILNAVEH DDRTVSVDMG SPVFDWNRIP LSEEFHDTSR IELQIGPIDA 150
    PVLHSPAVMS MGNPHAVFWV DRDPMSYDLE RFGPLLENHP LFPEKANITL 200
    AQVTSRTTMT TRTWERGAGL TLACGSAACA AGVSAARTGR AERKVTITVA 250
    SSPNRQALDI EWRERDGHVI MTGAAEWEWA GQLDPQTGDW QREQQAGHEA 300
    SVS 303
    Length:303
    Mass (Da):32,938
    Last modified:March 24, 2009 - v1
    Checksum:i576CE7C264678232
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000633 Genomic DNA. Translation: ACM38042.1.
    RefSeqiYP_002551054.1. NC_011989.1.

    Genome annotation databases

    EnsemblBacteriaiACM38042; ACM38042; Avi_4198.
    GeneIDi7386963.
    KEGGiavi:Avi_4198.
    PATRICi20831920. VBIAgrVit37146_5599.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000633 Genomic DNA. Translation: ACM38042.1 .
    RefSeqi YP_002551054.1. NC_011989.1.

    3D structure databases

    ProteinModelPortali B9JUB9.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 311402.Avi_4198.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ACM38042 ; ACM38042 ; Avi_4198 .
    GeneIDi 7386963.
    KEGGi avi:Avi_4198.
    PATRICi 20831920. VBIAgrVit37146_5599.

    Phylogenomic databases

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

    Enzyme and pathway databases

    UniPathwayi UPA00034 ; UER00025 .
    BioCyci AVIT311402:GH2Y-3159-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: S4 / ATCC BAA-846.

    Entry informationi

    Entry nameiDAPF_AGRVS
    AccessioniPrimary (citable) accession number: B9JUB9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 28, 2009
    Last sequence update: March 24, 2009
    Last modified: October 1, 2014
    This is version 37 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