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A8F110

- DDL_RICM5

UniProt

A8F110 - DDL_RICM5

Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Rickettsia massiliae (strain Mtu5)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 52 (01 Oct 2014)
      Sequence version 1 (13 Nov 2007)
      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 bindingi268 – 2681Magnesium or manganese 1UniRule annotation
    Metal bindingi282 – 2821Magnesium or manganese 1UniRule annotation
    Metal bindingi282 – 2821Magnesium or manganese 2UniRule annotation
    Metal bindingi284 – 2841Magnesium or manganese 2UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi147 – 19953ATPUniRule 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

    BioCyciRMAS416276:GJD3-345-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:RMA_0341
    OrganismiRickettsia massiliae (strain Mtu5)
    Taxonomic identifieri416276 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRickettsialesRickettsiaceaeRickettsieaeRickettsiaspotted fever group
    ProteomesiUP000001311: 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 – 321321D-alanine--D-alanine ligasePRO_1000057329Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi416276.RMA_0341.

    Structurei

    3D structure databases

    ProteinModelPortaliA8F110.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini121 – 315195ATP-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.
    PS00843. DALA_DALA_LIGASE_1. 1 hit.
    PS00844. DALA_DALA_LIGASE_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    A8F110-1 [UniParc]FASTAAdd to Basket

    « Hide

    MHKYQTHWVE HSIVKILSSA GKKYIALMAG GMSAEREVSL VSSEGVSKAL    50
    IELGYSVTFI DMGADITVRL QEIKPDIVFN CLHGTYGEDG CLPGLLNIMR 100
    IPYTHSGMLS SALAFNKIHS RSWFLTNNIN MAESIVVNKS DNIKNDPMKR 150
    PYVIKPLTQG SSIGVEVIFA EDNFNFADYD FPYGDQVIIE QYIKGRELQV 200
    AVLNGKALGV LEIKLLKNRF YDYETKYTEG FADHLCPAPL PANLYEKLLI 250
    ESEKIYKTMN CKGPARAEFI LEEQTNKLYA LELNTHPGMT PLSIVPEIAA 300
    YAGINFTNLI EEIIKTASFE S 321
    Length:321
    Mass (Da):35,920
    Last modified:November 13, 2007 - v1
    Checksum:i3DD68EED3FE3EA73
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000683 Genomic DNA. Translation: ABV84596.1.
    RefSeqiWP_012152573.1. NC_009900.1.
    YP_001499143.1. NC_009900.1.

    Genome annotation databases

    EnsemblBacteriaiABV84596; ABV84596; RMA_0341.
    GeneIDi5665609.
    KEGGirms:RMA_0341.
    PATRICi17894889. VBIRicMas83254_0432.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000683 Genomic DNA. Translation: ABV84596.1 .
    RefSeqi WP_012152573.1. NC_009900.1.
    YP_001499143.1. NC_009900.1.

    3D structure databases

    ProteinModelPortali A8F110.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 416276.RMA_0341.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABV84596 ; ABV84596 ; RMA_0341 .
    GeneIDi 5665609.
    KEGGi rms:RMA_0341.
    PATRICi 17894889. VBIRicMas83254_0432.

    Phylogenomic databases

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

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci RMAS416276:GJD3-345-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. "Lateral gene transfer between obligate intracellular bacteria: evidence from the Rickettsia massiliae genome."
      Blanc G., Ogata H., Robert C., Audic S., Claverie J.-M., Raoult D.
      Genome Res. 17:1657-1664(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Mtu5.

    Entry informationi

    Entry nameiDDL_RICM5
    AccessioniPrimary (citable) accession number: A8F110
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 5, 2008
    Last sequence update: November 13, 2007
    Last modified: October 1, 2014
    This is version 52 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

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3