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D8IW66

- D8IW66_HERSS

UniProt

D8IW66 - D8IW66_HERSS

Protein

D-alanine--D-alanine ligase

Gene

ddlB

Organism
Herbaspirillum seropedicae (strain SmR1)
Status
Unreviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 25 (01 Oct 2014)
      Sequence version 1 (05 Oct 2010)
      Previous versions | rss
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    Functioni

    Cell wall formation.UniRule annotationSAAS annotation

    Catalytic activityi

    ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.UniRule annotationSAAS annotation

    Cofactori

    Binds 2 magnesium or manganese ions per subunit.UniRule annotationSAAS annotation

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi266 – 2661Magnesium or manganese 1UniRule annotation
    Metal bindingi282 – 2821Magnesium or manganese 1UniRule annotation
    Metal bindingi282 – 2821Magnesium or manganese 2UniRule annotation
    Metal bindingi284 – 2841Magnesium or manganese 2UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi139 – 19456ATPUniRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-HAMAP
    2. D-alanine-D-alanine ligase activity Source: UniProtKB-HAMAP
    3. magnesium ion binding Source: UniProtKB-HAMAP
    4. manganese ion binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
    2. regulation of cell shape Source: UniProtKB-KW

    Keywords - Molecular functioni

    LigaseUniRule annotationSAAS annotationImported

    Keywords - Biological processi

    Cell shape, Cell wall biogenesis/degradationUniRule annotationSAAS annotation, Peptidoglycan synthesisUniRule annotationSAAS annotation

    Keywords - Ligandi

    ATP-bindingUniRule annotationSAAS annotation, MagnesiumUniRule annotationSAAS annotation, ManganeseUniRule annotationSAAS annotation, Metal-bindingUniRule annotationSAAS annotation, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciHSER757424:GCTT-338-MONOMER.
    UniPathwayiUPA00219.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-alanine--D-alanine ligaseUniRule annotation (EC:6.3.2.4UniRule annotation)
    Alternative name(s):
    D-Ala-D-Ala ligaseUniRule annotation
    D-alanylalanine synthetaseUniRule annotation
    Gene namesi
    Name:ddlBImported
    Synonyms:ddlUniRule annotation
    Ordered Locus Names:Hsero_0338Imported
    OrganismiHerbaspirillum seropedicae (strain SmR1)Imported
    Taxonomic identifieri757424 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesOxalobacteraceaeHerbaspirillum
    ProteomesiUP000000329: Chromosome

    Subcellular locationi

    Cytoplasm UniRule annotationSAAS annotation

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    CytoplasmUniRule annotationSAAS annotation

    Structurei

    3D structure databases

    ProteinModelPortaliD8IW66.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini109 – 315207ATP-graspUniRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the D-alanine--D-alanine ligase family.UniRule annotation
    Contains 1 ATP-grasp domain.UniRule annotation
    Contains ATP-grasp domain.SAAS annotation

    Phylogenomic databases

    HOGENOMiHOG000011592.
    KOiK01921.

    Family and domain databases

    Gene3Di3.30.1490.20. 1 hit.
    3.30.470.20. 2 hits.
    3.40.50.20. 1 hit.
    HAMAPiMF_00047. Dala_Dala_lig.
    InterProiIPR011761. ATP-grasp.
    IPR013815. ATP_grasp_subdomain_1.
    IPR013816. ATP_grasp_subdomain_2.
    IPR000291. D-Ala_lig_Van_CS.
    IPR005905. D_ala_D_ala.
    IPR011095. Dala_Dala_lig_C.
    IPR011127. Dala_Dala_lig_N.
    IPR016185. PreATP-grasp_dom.
    [Graphical view]
    PANTHERiPTHR23132. PTHR23132. 1 hit.
    PfamiPF07478. Dala_Dala_lig_C. 1 hit.
    PF01820. Dala_Dala_lig_N. 2 hits.
    [Graphical view]
    SUPFAMiSSF52440. SSF52440. 1 hit.
    TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
    PROSITEiPS50975. ATP_GRASP. 1 hit.
    PS00843. DALA_DALA_LIGASE_1. 1 hit.
    PS00844. DALA_DALA_LIGASE_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    D8IW66-1 [UniParc]FASTAAdd to Basket

    « Hide

    MISQDQIKAF GRVGVLFGGR SAEREVSMMS GNGVLQALRS KGVDAHPFDP    50
    AERSLGELQA EQFDRVFIAL HGRYGEDGTL QGALEQMGLP YTGPGVMSSS 100
    IAMDKVMTKR IWLSHGLPTP RFLTLDAQAT TREQLRLVPD TLGLPLMLKA 150
    PHEGSTIGIA KVNGYSDMQE GFDLCARYDK VVLAEEFIRG RELTVPVLGT 200
    GSAARALPVI EIRAPEGNYD YQNKYFTDDT KYLCPAPLDE ELTRHLQNLA 250
    VQAFNALGCR GWSRVDFMLR EVDGKAEPYL LEINTSPGMT GHSLVPMAAK 300
    AVGMSYEDLC CEILQMAALD MTPSKDWTPQ AGQS 334
    Length:334
    Mass (Da):36,592
    Last modified:October 5, 2010 - v1
    Checksum:i45DB9F217E8665B4
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP002039 Genomic DNA. Translation: ADJ61864.1.
    RefSeqiWP_013232386.1. NC_014323.1.
    YP_003773772.1. NC_014323.1.

    Genome annotation databases

    EnsemblBacteriaiADJ61864; ADJ61864; Hsero_0338.
    GeneIDi9400939.
    KEGGihse:Hsero_0338.
    PATRICi42359345. VBIHerSer153339_0347.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP002039 Genomic DNA. Translation: ADJ61864.1 .
    RefSeqi WP_013232386.1. NC_014323.1.
    YP_003773772.1. NC_014323.1.

    3D structure databases

    ProteinModelPortali D8IW66.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ADJ61864 ; ADJ61864 ; Hsero_0338 .
    GeneIDi 9400939.
    KEGGi hse:Hsero_0338.
    PATRICi 42359345. VBIHerSer153339_0347.

    Phylogenomic databases

    HOGENOMi HOG000011592.
    KOi K01921.

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci HSER757424:GCTT-338-MONOMER.

    Family and domain databases

    Gene3Di 3.30.1490.20. 1 hit.
    3.30.470.20. 2 hits.
    3.40.50.20. 1 hit.
    HAMAPi MF_00047. Dala_Dala_lig.
    InterProi IPR011761. ATP-grasp.
    IPR013815. ATP_grasp_subdomain_1.
    IPR013816. ATP_grasp_subdomain_2.
    IPR000291. D-Ala_lig_Van_CS.
    IPR005905. D_ala_D_ala.
    IPR011095. Dala_Dala_lig_C.
    IPR011127. Dala_Dala_lig_N.
    IPR016185. PreATP-grasp_dom.
    [Graphical view ]
    PANTHERi PTHR23132. PTHR23132. 1 hit.
    Pfami PF07478. Dala_Dala_lig_C. 1 hit.
    PF01820. Dala_Dala_lig_N. 2 hits.
    [Graphical view ]
    SUPFAMi SSF52440. SSF52440. 1 hit.
    TIGRFAMsi TIGR01205. D_ala_D_alaTIGR. 1 hit.
    PROSITEi PS50975. ATP_GRASP. 1 hit.
    PS00843. DALA_DALA_LIGASE_1. 1 hit.
    PS00844. DALA_DALA_LIGASE_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The genome of Herbaspirillum seropedicae SmR1, an endophytic, nitrogen-fixing, plant-growth promoting beta-Proteobacteria."
      Pedrosa F.O., Monteiro R.A., Wassem R., Cruz L.M., Ayub R.A., Colauto N.B., Fernandez M.A., Fungaro M.H.P., Grisard E.C., Hungria M., Madeira H.M.F., Nodari R.O., Osaku C.A., Petzl-Erler M.L., Terenzi H., Vieira L.G.E., Almeida M.I.M., Alves L.R.
      , Arantes O.M.N., Balsanelli E., Barcellos F.G., Baura V.A., Binde D.R., Campo R.J., Chubatsu L.S., Chueire L.M.O., Ciferri R.R., Correa L.C., da Conceicao Silva J.L., Dabul A.N.G., Dambros B.P., Faoro H., Favetti A., Friedermann G., Furlaneto M.C., Gasques L.S., Gimenes C.C.T., Gioppo N.M.R., Glienke-Blanco C., Godoy L.P., Guerra M.P., Karp S., Kava-Cordeiro V., Margarido V.P., Mathioni S.M., Menck-Soares M.A., Murace N.K., Nicolas M.F., Oliveira C.E.C., Pagnan N.A.B., Pamphile J.A., Patussi E.V., Pereira L.F.P., Pereira-Ferrari L., Pinto F.G.S., Precoma C., Prioli A.J., Prioli S.M.A.P., Raittz R.T., Ramos H.J.O., Ribeiro E.M.S.F., Rigo L.U., Rocha C.L.M.S.C., Rocha S.N., Santos K., Satori D., Silva A.G., Simao R.C.G., Soares M.A.M., Souza E.M., Steffens M.B.R., Steindel M., Tadra-Sfeir M.Z., Takahashi E.K., Torres R.A., Valle J.S., Vernal J.I., Vilas-Boas L.A., Watanabe M.A.E., Weiss V.A., Yates M.A., Souza E.M.
      Submitted (APR-2010) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: SmR1Imported.

    Entry informationi

    Entry nameiD8IW66_HERSS
    AccessioniPrimary (citable) accession number: D8IW66
    Entry historyi
    Integrated into UniProtKB/TrEMBL: October 5, 2010
    Last sequence update: October 5, 2010
    Last modified: October 1, 2014
    This is version 25 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiUnreviewed (UniProtKB/TrEMBL)

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteomeImported

    External Data

    Dasty 3