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C4XRH9

- DDL_DESMR

UniProt

C4XRH9 - DDL_DESMR

Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Desulfovibrio magneticus (strain ATCC 700980 / DSM 13731 / RS-1)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 40 (01 Oct 2014)
      Sequence version 1 (28 Jul 2009)
      Previous versions | rss
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    Functioni

    Cell wall formation.UniRule annotation

    Catalytic activityi

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

    Cofactori

    Binds 2 magnesium or manganese ions per subunit.By similarity

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi249 – 2491Magnesium or manganese 1UniRule annotation
    Metal bindingi261 – 2611Magnesium or manganese 1UniRule annotation
    Metal bindingi261 – 2611Magnesium or manganese 2UniRule annotation
    Metal bindingi263 – 2631Magnesium or manganese 2UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi126 – 18055ATPUniRule 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

    Ligase

    Keywords - Biological processi

    Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

    Keywords - Ligandi

    ATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciDMAG573370:GHJL-2055-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 annotation
    Ordered Locus Names:DMR_20330
    OrganismiDesulfovibrio magneticus (strain ATCC 700980 / DSM 13731 / RS-1)
    Taxonomic identifieri573370 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
    ProteomesiUP000009071: 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 – 304304D-alanine--D-alanine ligasePRO_1000202198Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi573370.DMR_20330.

    Structurei

    3D structure databases

    ProteinModelPortaliC4XRH9.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini100 – 294195ATP-graspUniRule annotationAdd
    BLAST

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiCOG1181.
    HOGENOMiHOG000011592.
    KOiK01921.
    OMAiGCDARSS.
    OrthoDBiEOG6ND0KB.

    Family and domain databases

    Gene3Di3.30.1490.20. 1 hit.
    3.30.470.20. 1 hit.
    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.
    PROSITEiPS50975. ATP_GRASP. 1 hit.
    PS00844. DALA_DALA_LIGASE_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    C4XRH9-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKILLVAGGW SSERAVSLSG AVQIEKALTS LGHEVVPYDL SHDFPGFVRR    50
    AKACDFVFLS LHGAPGEDGL PQALLDAAGV PYQGSGPAGS FLALNKAASK 100
    QLFLEACLPT PRWTFVPRDA GTSARPDFPL PWFVKPNLGG SSIHMTLVRR 150
    AEELPAALEK VFAHGDDALI EEGLSGPELT CAVLGDEALP PILIRPKAGE 200
    FFDYASKYEP DAADEICPAP VEPAVTEELS RLSLAAHRVL GLCGYSRADF 250
    ILAPEGLRLL EVNTLPGMTP TSLLPRAAAT AGLSFADLIA RLIELGLAQQ 300
    AKRP 304
    Length:304
    Mass (Da):32,255
    Last modified:July 28, 2009 - v1
    Checksum:i285C53A06A55A506
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP010904 Genomic DNA. Translation: BAH75524.1.
    RefSeqiWP_015860715.1. NC_012796.1.
    YP_002953410.1. NC_012796.1.

    Genome annotation databases

    EnsemblBacteriaiBAH75524; BAH75524; DMR_20330.
    GeneIDi7983730.
    KEGGidma:DMR_20330.
    PATRICi21750329. VBIDesMag26496_1935.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP010904 Genomic DNA. Translation: BAH75524.1 .
    RefSeqi WP_015860715.1. NC_012796.1.
    YP_002953410.1. NC_012796.1.

    3D structure databases

    ProteinModelPortali C4XRH9.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 573370.DMR_20330.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAH75524 ; BAH75524 ; DMR_20330 .
    GeneIDi 7983730.
    KEGGi dma:DMR_20330.
    PATRICi 21750329. VBIDesMag26496_1935.

    Phylogenomic databases

    eggNOGi COG1181.
    HOGENOMi HOG000011592.
    KOi K01921.
    OMAi GCDARSS.
    OrthoDBi EOG6ND0KB.

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci DMAG573370:GHJL-2055-MONOMER.

    Family and domain databases

    Gene3Di 3.30.1490.20. 1 hit.
    3.30.470.20. 1 hit.
    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.
    PROSITEi PS50975. ATP_GRASP. 1 hit.
    PS00844. DALA_DALA_LIGASE_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Whole genome sequence of Desulfovibrio magneticus strain RS-1 revealed common gene clusters in magnetotactic bacteria."
      Nakazawa H., Arakaki A., Narita-Yamada S., Yashiro I., Jinno K., Aoki N., Tsuruyama A., Okamura Y., Tanikawa S., Fujita N., Takeyama H., Matsunaga T.
      Genome Res. 19:1801-1808(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 700980 / DSM 13731 / RS-1.

    Entry informationi

    Entry nameiDDL_DESMR
    AccessioniPrimary (citable) accession number: C4XRH9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 22, 2009
    Last sequence update: July 28, 2009
    Last modified: October 1, 2014
    This is version 40 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