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B8I9H6

- DAPF_METNO

UniProt

B8I9H6 - DAPF_METNO

Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Methylobacterium nodulans (strain ORS2060 / LMG 21967)
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 (03 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 sitei17 – 171SubstrateUniRule annotation
    Binding sitei49 – 491SubstrateUniRule annotation
    Binding sitei69 – 691SubstrateUniRule annotation
    Active sitei78 – 781Proton donor/acceptorUniRule annotation
    Binding sitei169 – 1691SubstrateUniRule annotation
    Sitei171 – 1711Important for catalytic activityUniRule annotation
    Binding sitei203 – 2031SubstrateUniRule annotation
    Sitei221 – 2211Important for catalytic activityUniRule annotation
    Active sitei230 – 2301Proton 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

    BioCyciMNOD460265:GCZK-184-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:Mnod_0183
    OrganismiMethylobacterium nodulans (strain ORS2060 / LMG 21967)
    Taxonomic identifieri460265 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesMethylobacteriaceaeMethylobacterium
    ProteomesiUP000008207: 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 – 293293Diaminopimelate epimerasePRO_1000124425Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi78 ↔ 230

    Keywords - PTMi

    Disulfide bond

    Interactioni

    Protein-protein interaction databases

    STRINGi460265.Mnod_0183.

    Structurei

    3D structure databases

    ProteinModelPortaliB8I9H6.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni14 – 152Substrate bindingUniRule annotation
    Regioni78 – 803Substrate bindingUniRule annotation
    Regioni221 – 2222Substrate 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.

    B8I9H6-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSPLAHRRFL KMNGLGNEIV VLDLRGTPHI VQPQEARAIA ADPRSRFDQL    50
    MVLHDPVTAG TDAALRIYNT DGSESGACGN GTRCVAWAML EDPVMGRPAE 100
    RLTLQSRAGL LAVTRVSATD FTVDMGPPRL RWDEIPLAEP FPDTRRIELQ 150
    IGPIDDPILH SPGVVSMGNP HAVFFVDRDP ASYDLARIGP LLEAHPIFPE 200
    RANISVAQVR GPEHIVLRVW ERGAGLTRAC GSAACAALVA AARLRLTGRR 250
    AVVTLPGGDL VIDWGEDDHV RMTGPTELEW EGTLAPSLFA GAA 293
    Length:293
    Mass (Da):31,629
    Last modified:March 3, 2009 - v1
    Checksum:i8F57AA6895E459E4
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001349 Genomic DNA. Translation: ACL55229.1.
    RefSeqiYP_002495532.1. NC_011894.1.

    Genome annotation databases

    EnsemblBacteriaiACL55229; ACL55229; Mnod_0183.
    GeneIDi7304502.
    KEGGimno:Mnod_0183.
    PATRICi22542608. VBIMetNod76414_1055.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001349 Genomic DNA. Translation: ACL55229.1 .
    RefSeqi YP_002495532.1. NC_011894.1.

    3D structure databases

    ProteinModelPortali B8I9H6.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 460265.Mnod_0183.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ACL55229 ; ACL55229 ; Mnod_0183 .
    GeneIDi 7304502.
    KEGGi mno:Mnod_0183.
    PATRICi 22542608. VBIMetNod76414_1055.

    Phylogenomic databases

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

    Enzyme and pathway databases

    UniPathwayi UPA00034 ; UER00025 .
    BioCyci MNOD460265:GCZK-184-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 nodulans ORS 2060."
      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., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Ivanova N., Marx C.J., Richardson P.
      Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ORS2060 / LMG 21967.

    Entry informationi

    Entry nameiDAPF_METNO
    AccessioniPrimary (citable) accession number: B8I9H6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 28, 2009
    Last sequence update: March 3, 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