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B7KQM2

- DAPF_METC4

UniProt

B7KQM2 - DAPF_METC4

Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Methylobacterium extorquens (strain CM4 / NCIMB 13688) (Methylobacterium chloromethanicum)
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 (10 Feb 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 sitei17 – 171SubstrateUniRule annotation
    Binding sitei49 – 491SubstrateUniRule annotation
    Binding sitei69 – 691SubstrateUniRule annotation
    Active sitei78 – 781Proton donor/acceptorUniRule annotation
    Binding sitei171 – 1711SubstrateUniRule annotation
    Sitei173 – 1731Important for catalytic activityUniRule annotation
    Binding sitei205 – 2051SubstrateUniRule annotation
    Sitei223 – 2231Important for catalytic activityUniRule annotation
    Active sitei232 – 2321Proton 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

    BioCyciMCHL440085:GCXT-3004-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:Mchl_2947
    OrganismiMethylobacterium extorquens (strain CM4 / NCIMB 13688) (Methylobacterium chloromethanicum)
    Taxonomic identifieri440085 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesMethylobacteriaceaeMethylobacterium
    ProteomesiUP000002385: 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 – 296296Diaminopimelate epimerasePRO_1000124420Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi78 ↔ 232

    Keywords - PTMi

    Disulfide bond

    Interactioni

    Protein-protein interaction databases

    STRINGi440085.Mchl_2947.

    Structurei

    3D structure databases

    ProteinModelPortaliB7KQM2.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni78 – 803Substrate bindingUniRule annotation
    Regioni223 – 2242Substrate bindingUniRule annotation
    Regioni233 – 2342Substrate bindingUniRule annotation

    Sequence similaritiesi

    Belongs to the diaminopimelate epimerase family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0253.
    HOGENOMiHOG000220466.
    KOiK01778.
    OMAiRPAENGA.
    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.

    B7KQM2-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSPLANRRFL KMHGAGNAIV VLDLRGTAVR VTPAEARAIA ADVHSRFDQL    50
    MVVHDPVTPG TDAFMRIYNT DGSESGACGN GTRCVGYALL DDPAMARPAE 100
    NGALTLETKA GLVAVKRITE RSFTVDMGQP RLRWDEIPLT EPFLDTRRIE 150
    LQVGPIDDPI LHSPAAVSMG NPHAIFFVER DPDSYDLGRI GPLLEAHPIF 200
    PERANISIAE VTSRDTIKLR VWERGAGLTL ACGTAACATV VAASRLRMIG 250
    RAARVALPGG ELSIEWRADD HVLMTGPVYL EGEGTFSPDL FAGIDG 296
    Length:296
    Mass (Da):31,877
    Last modified:February 10, 2009 - v1
    Checksum:iF01A444D94EAD5F3
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001298 Genomic DNA. Translation: ACK83786.1.
    RefSeqiYP_002421714.1. NC_011757.1.

    Genome annotation databases

    EnsemblBacteriaiACK83786; ACK83786; Mchl_2947.
    GeneIDi7115754.
    KEGGimch:Mchl_2947.
    PATRICi22500176. VBIMetChl132133_2915.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001298 Genomic DNA. Translation: ACK83786.1 .
    RefSeqi YP_002421714.1. NC_011757.1.

    3D structure databases

    ProteinModelPortali B7KQM2.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 440085.Mchl_2947.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ACK83786 ; ACK83786 ; Mchl_2947 .
    GeneIDi 7115754.
    KEGGi mch:Mchl_2947.
    PATRICi 22500176. VBIMetChl132133_2915.

    Phylogenomic databases

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

    Enzyme and pathway databases

    UniPathwayi UPA00034 ; UER00025 .
    BioCyci MCHL440085:GCXT-3004-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 chromosome of Methylobacterium chloromethanicum CM4."
      US DOE Joint Genome Institute
      Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Chertkov O., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Marx C., Richardson P.
      Submitted (DEC-2008) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: CM4 / NCIMB 13688.

    Entry informationi

    Entry nameiDAPF_METC4
    AccessioniPrimary (citable) accession number: B7KQM2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 28, 2009
    Last sequence update: February 10, 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

    Documents

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

    External Data

    Dasty 3