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B8ETM9

- DDL_METSB

UniProt

B8ETM9 - DDL_METSB

Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Methylocella silvestris (strain BL2 / DSM 15510 / NCIMB 13906)
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 (03 Mar 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 bindingi251 – 2511Magnesium or manganese 1UniRule annotation
    Metal bindingi268 – 2681Magnesium or manganese 1UniRule annotation
    Metal bindingi268 – 2681Magnesium or manganese 2UniRule annotation
    Metal bindingi270 – 2701Magnesium or manganese 2UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi128 – 18255ATPUniRule 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

    BioCyciMSIL395965:GCND-3545-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:Msil_3492
    OrganismiMethylocella silvestris (strain BL2 / DSM 15510 / NCIMB 13906)
    Taxonomic identifieri395965 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBeijerinckiaceaeMethylocella
    ProteomesiUP000002257: 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 – 307307D-alanine--D-alanine ligasePRO_1000189741Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi395965.Msil_3492.

    Structurei

    3D structure databases

    ProteinModelPortaliB8ETM9.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini101 – 301201ATP-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.
    OMAiANDTQYR.
    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.

    B8ETM9-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSKHVAVLMG GLSAEREVSL RSGAACAKAL EAEGFRVTTL DVDRDIAQKL    50
    AALRPDAALN ALHGRYGEDG VIQGVLEMLA IPYTHSGVLA SALAMQKDRA 100
    KDVLRAAGVP VAEGVTIGRF EAAKAHVMTP PYVVKPLGEG SSFGVIIVRA 150
    DQTHPPQELT RDDWAYGDLV LVERFVAGRE LTCAVIGDKA YGVTEIRAAD 200
    GGWYDYDAKY KAGGSIHILP ANLKEFVYQN VQELALVAHR ALGCRGVSRT 250
    DFRYDDTPQG TGELVVLEVN SQPGMTETSL VPEIAAYAGI SFGELVRWMV 300
    EDASCDR 307
    Length:307
    Mass (Da):32,974
    Last modified:March 3, 2009 - v1
    Checksum:i5A0F70EEF0F984B6
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001280 Genomic DNA. Translation: ACK52381.1.
    RefSeqiYP_002363743.1. NC_011666.1.

    Genome annotation databases

    EnsemblBacteriaiACK52381; ACK52381; Msil_3492.
    GeneIDi7092516.
    KEGGimsl:Msil_3492.
    PATRICi22602784. VBIMetSil55537_3740.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001280 Genomic DNA. Translation: ACK52381.1 .
    RefSeqi YP_002363743.1. NC_011666.1.

    3D structure databases

    ProteinModelPortali B8ETM9.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 395965.Msil_3492.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ACK52381 ; ACK52381 ; Msil_3492 .
    GeneIDi 7092516.
    KEGGi msl:Msil_3492.
    PATRICi 22602784. VBIMetSil55537_3740.

    Phylogenomic databases

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

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci MSIL395965:GCND-3545-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. "Complete genome sequence of the aerobic facultative methanotroph Methylocella silvestris BL2."
      Chen Y., Crombie A., Rahman M.T., Dedysh S.N., Liesack W., Stott M.B., Alam M., Theisen A.R., Murrell J.C., Dunfield P.F.
      J. Bacteriol. 192:3840-3841(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: BL2 / DSM 15510 / NCIMB 13906.

    Entry informationi

    Entry nameiDDL_METSB
    AccessioniPrimary (citable) accession number: B8ETM9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 28, 2009
    Last sequence update: March 3, 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