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A5VAG4

- DAPF_SPHWW

UniProt

A5VAG4 - DAPF_SPHWW

Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 50 (01 Oct 2014)
      Sequence version 1 (10 Jul 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 sitei47 – 471SubstrateUniRule annotation
    Binding sitei65 – 651SubstrateUniRule annotation
    Active sitei74 – 741Proton donor/acceptorUniRule annotation
    Binding sitei149 – 1491SubstrateUniRule annotation
    Sitei151 – 1511Important for catalytic activityUniRule annotation
    Binding sitei182 – 1821SubstrateUniRule annotation
    Sitei200 – 2001Important for catalytic activityUniRule annotation
    Active sitei209 – 2091Proton 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

    BioCyciSWIT392499:GHZK-2962-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:Swit_2928
    OrganismiSphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273)
    Taxonomic identifieri392499 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeSphingomonas
    ProteomesiUP000001989: 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 – 274274Diaminopimelate epimerasePRO_1000011973Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi74 ↔ 209

    Keywords - PTMi

    Disulfide bond

    Proteomic databases

    PRIDEiA5VAG4.

    Interactioni

    Protein-protein interaction databases

    STRINGi392499.Swit_2928.

    Structurei

    3D structure databases

    ProteinModelPortaliA5VAG4.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni10 – 112Substrate bindingUniRule annotation
    Regioni74 – 763Substrate bindingUniRule annotation
    Regioni200 – 2012Substrate bindingUniRule annotation
    Regioni210 – 2112Substrate bindingUniRule annotation

    Sequence similaritiesi

    Belongs to the diaminopimelate epimerase family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0253.
    HOGENOMiHOG000220466.
    KOiK01778.
    OMAiLIVEPPY.
    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.

    A5VAG4-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQVRFHKMHG LGNDFVVIDA RATAPVEMTA ARARALADRK TGVGCDQLIL    50
    LEPSAVADAR MRIFNADGSE VEACGNATRC VVSLLGGSAR IETVAGLLEG 100
    RSADGQVSVE LGEPRFDWDA IPLAYAMDTR AMPVAWEELE APMAANVGNP 150
    HVVFFVPETD AVALDRLGPR IETDPLFPAR INVNVATVDD RANIRLRVWE 200
    RGVGLTDACG TGACATAVSA IRAGLVDSPV RVTLPGGPLT IDWAPGRPIV 250
    MTGPATHVFT AETDLSAFGA DSRG 274
    Length:274
    Mass (Da):28,927
    Last modified:July 10, 2007 - v1
    Checksum:iBCCDAFE707FFEC04
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000699 Genomic DNA. Translation: ABQ69280.1.
    RefSeqiYP_001263418.1. NC_009511.1.

    Genome annotation databases

    EnsemblBacteriaiABQ69280; ABQ69280; Swit_2928.
    GeneIDi5199935.
    KEGGiswi:Swit_2928.
    PATRICi23685041. VBISphWit55028_3464.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000699 Genomic DNA. Translation: ABQ69280.1 .
    RefSeqi YP_001263418.1. NC_009511.1.

    3D structure databases

    ProteinModelPortali A5VAG4.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 392499.Swit_2928.

    Proteomic databases

    PRIDEi A5VAG4.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABQ69280 ; ABQ69280 ; Swit_2928 .
    GeneIDi 5199935.
    KEGGi swi:Swit_2928.
    PATRICi 23685041. VBISphWit55028_3464.

    Phylogenomic databases

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

    Enzyme and pathway databases

    UniPathwayi UPA00034 ; UER00025 .
    BioCyci SWIT392499:GHZK-2962-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: RW1 / DSM 6014 / JCM 10273.

    Entry informationi

    Entry nameiDAPF_SPHWW
    AccessioniPrimary (citable) accession number: A5VAG4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 15, 2008
    Last sequence update: July 10, 2007
    Last modified: October 1, 2014
    This is version 50 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