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Q1LIM8

- DDL_RALME

UniProt

Q1LIM8 - DDL_RALME

Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Ralstonia metallidurans (strain CH34 / ATCC 43123 / DSM 2839)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 67 (01 Oct 2014)
      Sequence version 1 (30 May 2006)
      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 bindingi266 – 2661Magnesium or manganese 1UniRule annotation
    Metal bindingi279 – 2791Magnesium or manganese 1UniRule annotation
    Metal bindingi279 – 2791Magnesium or manganese 2UniRule annotation
    Metal bindingi281 – 2811Magnesium 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

    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

    BioCyciCMET266264:GJ5G-3335-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:Rmet_3126
    OrganismiRalstonia metallidurans (strain CH34 / ATCC 43123 / DSM 2839)
    Taxonomic identifieri266264 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeCupriavidus
    ProteomesiUP000002429: 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 – 327327D-alanine--D-alanine ligasePRO_0000341160Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi266264.Rmet_3126.

    Structurei

    3D structure databases

    ProteinModelPortaliQ1LIM8.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini113 – 312200ATP-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.
    OMAiKLAFQYD.
    OrthoDBiEOG6ND0KB.

    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.

    Q1LIM8-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSFVAHPNID PKSLGKVGVL LGGKSAEREI SLLSGNGVLA ALKSRGVDAH    50
    PFDPGLQPIS ELAAAGFDRV FIALHGRYGE DGTMQGLLEQ LGIPYTGSGV 100
    LASALAMDKQ ATKRLWMTHG LATPRFAMLY ANTDFDAVVA DLGLPLIVKP 150
    AREGSSIGLT KVIAADQMRA AFEKAAGLDA DVIAETFIDG AELTCPIVGE 200
    GPTAEALPVI KIVAPESNYD YQNKYFTDDT QYLCPSTLPD ALEREVRALA 250
    VEAFRVLGCR GWARADVMLT RDGKPYLLEM NTSPGMTGHS LVPMAARANG 300
    ISYEDFVMQV LAAATLDLHP NEHWKPE 327
    Length:327
    Mass (Da):34,968
    Last modified:May 30, 2006 - v1
    Checksum:iE9968DC61E896386
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000352 Genomic DNA. Translation: ABF09998.1.
    RefSeqiWP_011517618.1. NC_007973.1.
    YP_585267.1. NC_007973.1.

    Genome annotation databases

    EnsemblBacteriaiABF09998; ABF09998; Rmet_3126.
    GeneIDi4039955.
    KEGGirme:Rmet_3126.
    PATRICi20290887. VBIRalMet4734_3518.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000352 Genomic DNA. Translation: ABF09998.1 .
    RefSeqi WP_011517618.1. NC_007973.1.
    YP_585267.1. NC_007973.1.

    3D structure databases

    ProteinModelPortali Q1LIM8.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 266264.Rmet_3126.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABF09998 ; ABF09998 ; Rmet_3126 .
    GeneIDi 4039955.
    KEGGi rme:Rmet_3126.
    PATRICi 20290887. VBIRalMet4734_3518.

    Phylogenomic databases

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

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci CMET266264:GJ5G-3335-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: CH34 / ATCC 43123 / DSM 2839.

    Entry informationi

    Entry nameiDDL_RALME
    AccessioniPrimary (citable) accession number: Q1LIM8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 10, 2008
    Last sequence update: May 30, 2006
    Last modified: October 1, 2014
    This is version 67 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