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B3DVV9

- DDL_METI4

UniProt

B3DVV9 - DDL_METI4

Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Methylacidiphilum infernorum (isolate V4) (Methylokorus infernorum (strain V4))
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 48 (01 Oct 2014)
      Sequence version 1 (22 Jul 2008)
      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 bindingi247 – 2471Magnesium or manganese 1UniRule annotation
    Metal bindingi260 – 2601Magnesium or manganese 1UniRule annotation
    Metal bindingi260 – 2601Magnesium or manganese 2UniRule annotation
    Metal bindingi262 – 2621Magnesium or manganese 2UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi130 – 17950ATPUniRule 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

    BioCyciMINF481448:GJEI-1437-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:Minf_1408
    OrganismiMethylacidiphilum infernorum (isolate V4) (Methylokorus infernorum (strain V4))
    Taxonomic identifieri481448 [NCBI]
    Taxonomic lineageiBacteriaVerrucomicrobiaunclassified VerrucomicrobiaMethylacidiphilalesMethylacidiphilaceaeMethylacidiphilum
    ProteomesiUP000009149: 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 – 303303D-alanine--D-alanine ligasePRO_1000091194Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi481448.Minf_1408.

    Structurei

    3D structure databases

    ProteinModelPortaliB3DVV9.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini103 – 293191ATP-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.
    OMAiEDPARES.
    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.
    PS00844. DALA_DALA_LIGASE_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    B3DVV9-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNPALPRHIA VLKGGPSEER EISLRTAKAV EDALSSLGYE ISSIDVTTEK    50
    FEIPRDAEIC FLCIHGSFGE DGQIQRLLMR RGIPFTGSDA SSSEKAFDKA 100
    WSKTLFIKGG IPTPPFCVVG DGKKIPFDPP YVIKPSRQGS SIGIEFVYDI 150
    KELDQAIKKS TQYDHVVLAE ALITGKELTV GILDGKALPV VEIKPKEGFY 200
    DYHHKYTKGA STYFCPAPLT VDQTSAVQKT ALDAFNVLGC SVYGRVDIIL 250
    SDNGIPWVLE INTIPGMTET SLFPMAAKAS GMNFAQLCEK ILEISYLRWK 300
    AHG 303
    Length:303
    Mass (Da):33,194
    Last modified:July 22, 2008 - v1
    Checksum:i4B0BC4D8738D0BEA
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000975 Genomic DNA. Translation: ACD83462.1.
    RefSeqiYP_001940060.1. NC_010794.1.

    Genome annotation databases

    EnsemblBacteriaiACD83462; ACD83462; Minf_1408.
    GeneIDi6352347.
    KEGGimin:Minf_1408.
    PATRICi22491981. VBIMetInf111569_1473.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000975 Genomic DNA. Translation: ACD83462.1 .
    RefSeqi YP_001940060.1. NC_010794.1.

    3D structure databases

    ProteinModelPortali B3DVV9.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 481448.Minf_1408.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ACD83462 ; ACD83462 ; Minf_1408 .
    GeneIDi 6352347.
    KEGGi min:Minf_1408.
    PATRICi 22491981. VBIMetInf111569_1473.

    Phylogenomic databases

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

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci MINF481448:GJEI-1437-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.
    PS00844. DALA_DALA_LIGASE_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia."
      Hou S., Makarova K.S., Saw J.H., Senin P., Ly B.V., Zhou Z., Ren Y., Wang J., Galperin M.Y., Omelchenko M.V., Wolf Y.I., Yutin N., Koonin E.V., Stott M.B., Mountain B.W., Crowe M.A., Smirnova A.V., Dunfield P.F.
      , Feng L., Wang L., Alam M.
      Biol. Direct 3:26-26(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Isolate V4.

    Entry informationi

    Entry nameiDDL_METI4
    AccessioniPrimary (citable) accession number: B3DVV9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 24, 2009
    Last sequence update: July 22, 2008
    Last modified: October 1, 2014
    This is version 48 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