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C1B393

- DAPF_RHOOB

UniProt

C1B393 - DAPF_RHOOB

Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Rhodococcus opacus (strain B4)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 39 (01 Oct 2014)
      Sequence version 1 (26 May 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 sitei11 – 111SubstrateUniRule annotation
    Binding sitei44 – 441SubstrateUniRule annotation
    Binding sitei78 – 781SubstrateUniRule annotation
    Active sitei87 – 871Proton donor/acceptorUniRule annotation
    Binding sitei163 – 1631SubstrateUniRule annotation
    Sitei165 – 1651Important for catalytic activityUniRule annotation
    Binding sitei199 – 1991SubstrateUniRule annotation
    Sitei217 – 2171Important for catalytic activityUniRule annotation
    Active sitei226 – 2261Proton 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

    BioCyciROPA632772:GH0Q-6813-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:ROP_67630
    OrganismiRhodococcus opacus (strain B4)
    Taxonomic identifieri632772 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeNocardiaceaeRhodococcus
    ProteomesiUP000002212: 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 – 289289Diaminopimelate epimerasePRO_1000124430Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi87 ↔ 226

    Keywords - PTMi

    Disulfide bond

    Interactioni

    Protein-protein interaction databases

    STRINGi632772.ROP_67630.

    Structurei

    3D structure databases

    ProteinModelPortaliC1B393.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni87 – 893Substrate bindingUniRule annotation
    Regioni217 – 2182Substrate bindingUniRule annotation
    Regioni227 – 2282Substrate bindingUniRule annotation

    Sequence similaritiesi

    Belongs to the diaminopimelate epimerase family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0253.
    HOGENOMiHOG000220467.
    KOiK01778.
    OMAiITIEMGT.
    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.

    C1B393-1 [UniParc]FASTAAdd to Basket

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    MDFSKGHGTE NDFVVLPDPD VRIDLSAPRV AALCDRRRGL GADGILRVAK    50
    AGALAAAGVL AELPDGTSED DWFMDYRNAD GSIAEMCGNG VRVFAHYLRS 100
    TGLETRDEFV VGSRAGGKPV IVHSADGSAG EVTVDMGVVR DLGTSAATID 150
    GKVFNGIGID VGNPHLACVD AHLTAASLSA LDLTAAPGFD PGFFPHGVNV 200
    EILTRIDSGA VDMRVHERGV GETRSCGTGT VAAATAALRF DGADSGEVKV 250
    RIPGGQVTVA LSGGRATLRG PSVLVASGNL DDSWWNGLS 289
    Length:289
    Mass (Da):29,725
    Last modified:May 26, 2009 - v1
    Checksum:i01ED7A2C9E5309E7
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP011115 Genomic DNA. Translation: BAH55010.1.
    RefSeqiWP_015890446.1. NC_012522.1.
    YP_002783955.1. NC_012522.1.

    Genome annotation databases

    EnsemblBacteriaiBAH55010; BAH55010; ROP_67630.
    GeneIDi7745421.
    KEGGirop:ROP_67630.
    PATRICi23230959. VBIRhoOpa21106_6844.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP011115 Genomic DNA. Translation: BAH55010.1 .
    RefSeqi WP_015890446.1. NC_012522.1.
    YP_002783955.1. NC_012522.1.

    3D structure databases

    ProteinModelPortali C1B393.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 632772.ROP_67630.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAH55010 ; BAH55010 ; ROP_67630 .
    GeneIDi 7745421.
    KEGGi rop:ROP_67630.
    PATRICi 23230959. VBIRhoOpa21106_6844.

    Phylogenomic databases

    eggNOGi COG0253.
    HOGENOMi HOG000220467.
    KOi K01778.
    OMAi ITIEMGT.
    OrthoDBi EOG6ND0M5.

    Enzyme and pathway databases

    UniPathwayi UPA00034 ; UER00025 .
    BioCyci ROPA632772:GH0Q-6813-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. "Comparison of the complete genome sequences of Rhodococcus erythropolis PR4 and Rhodococcus opacus B4."
      Takarada H., Sekine M., Hosoyama A., Yamada R., Fujisawa T., Omata S., Shimizu A., Tsukatani N., Tanikawa S., Fujita N., Harayama S.
      Submitted (MAR-2009) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: B4.

    Entry informationi

    Entry nameiDAPF_RHOOB
    AccessioniPrimary (citable) accession number: C1B393
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 28, 2009
    Last sequence update: May 26, 2009
    Last modified: October 1, 2014
    This is version 39 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