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D3PM04

- D3PM04_MEIRD

UniProt

D3PM04 - D3PM04_MEIRD

Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Meiothermus ruber (strain ATCC 35948 / DSM 1279 / VKM B-1258 / 21) (Thermus ruber)
Status
Unreviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 38 (01 Oct 2014)
      Sequence version 1 (20 Apr 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 bindingi271 – 2711Magnesium or manganese 1UniRule annotation
    Metal bindingi284 – 2841Magnesium or manganese 1UniRule annotation
    Metal bindingi284 – 2841Magnesium or manganese 2UniRule annotation
    Metal bindingi286 – 2861Magnesium or manganese 2UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi146 – 19954ATPUniRule 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

    BioCyciMRUB504728:GI6U-342-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:ddlUniRule annotationImported
    Ordered Locus Names:Mrub_0337Imported
    ORF Names:K649_01305Imported
    OrganismiMeiothermus ruber (strain ATCC 35948 / DSM 1279 / VKM B-1258 / 21) (Thermus ruber)Imported
    Taxonomic identifieri504728 [NCBI]
    Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeMeiothermus
    ProteomesiUP000006655: Chromosome, UP000013026: Chromosome

    Subcellular locationi

    Cytoplasm UniRule annotationSAAS annotation

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    CytoplasmUniRule annotationSAAS annotation

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini120 – 317198ATP-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

    HOGENOMiHOG000011593.
    KOiK01921.
    OMAiQIDVIFP.

    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. 1 hit.
    [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.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    D3PM04-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKVLLLAGGP PGEHEVSLSS ARGVLAAMPH PTELVVIAKD GRWLLGEDAY    50
    EALRAGVAEQ GTHPFPPPVP WQHYDVVFPL LHGPLGEDGV IQGFLQLLRR 100
    PYVGAGVASS ALCMDKDLCK RVLRQAGIPV VPWVTLYKGE PTPQPPFPPP 150
    YFVKPANTGS SVGISKVKAD QDATRALAEA FAWDDKVLVE QGIEGVRELE 200
    VALLGNIHAE ASVVGEITYQ SEFYDYETKY TEGKAQLHLP APIPPELSDE 250
    IRATALEAYR ILGVRGMARV DFFLSPQGEL YLNEFNTIPG FTPTSMYPKL 300
    WQATGLAYPD LLDRLVRLAL ER 322
    Length:322
    Mass (Da):35,231
    Last modified:April 20, 2010 - v1
    Checksum:i396C70BD2892732B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001743 Genomic DNA. Translation: ADD27115.1.
    CP005385 Genomic DNA. Translation: AGK03569.1.
    RefSeqiWP_013012634.1. NC_021081.1.
    YP_003506135.1. NC_013946.1.
    YP_007879066.1. NC_021081.1.

    Genome annotation databases

    EnsemblBacteriaiADD27115; ADD27115; Mrub_0337.
    AGK03569; AGK03569; K649_01305.
    GeneIDi15334879.
    8878408.
    KEGGimrb:Mrub_0337.
    mre:K649_01305.
    PATRICi35356778. VBIMeiRub128672_0343.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001743 Genomic DNA. Translation: ADD27115.1 .
    CP005385 Genomic DNA. Translation: AGK03569.1 .
    RefSeqi WP_013012634.1. NC_021081.1.
    YP_003506135.1. NC_013946.1.
    YP_007879066.1. NC_021081.1.

    3D structure databases

    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ADD27115 ; ADD27115 ; Mrub_0337 .
    AGK03569 ; AGK03569 ; K649_01305 .
    GeneIDi 15334879.
    8878408.
    KEGGi mrb:Mrub_0337.
    mre:K649_01305.
    PATRICi 35356778. VBIMeiRub128672_0343.

    Phylogenomic databases

    HOGENOMi HOG000011593.
    KOi K01921.
    OMAi QIDVIFP.

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci MRUB504728:GI6U-342-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. 1 hit.
    [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.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 35948 / DSM 1279 / VKM B-1258 / 21Imported.
    2. "Non-Hybrid, Finished Microbial Genome Assemblies from Long-Read SMRT Sequencing Data."
      Klammer A., Drake J., Heiner C., Clum A., Copeland A., Huddleston J., Eichler E., Turner S.W.
      Submitted (APR-2013) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE.
      Strain: DSM 1279Imported.
    3. Chin J., Alexander D.H., Marks P., Korlach J., Clum A., Copeland A.
      Submitted (APR-2013) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE.
      Strain: DSM 1279Imported.

    Entry informationi

    Entry nameiD3PM04_MEIRD
    AccessioniPrimary (citable) accession number: D3PM04
    Entry historyi
    Integrated into UniProtKB/TrEMBL: April 20, 2010
    Last sequence update: April 20, 2010
    Last modified: October 1, 2014
    This is version 38 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