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C4K734

- DDL_HAMD5

UniProt

C4K734 - DDL_HAMD5

Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Hamiltonella defensa subsp. Acyrthosiphon pisum (strain 5AT)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 39 (01 Oct 2014)
      Sequence version 1 (07 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 bindingi271 – 2711Magnesium or manganese 1UniRule annotation
    Metal bindingi284 – 2841Magnesium or manganese 1UniRule annotation
    Metal bindingi284 – 2841Magnesium or manganese 2UniRule annotation
    Metal bindingi286 – 2861Magnesium or manganese 2UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi148 – 20356ATPUniRule 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

    BioCyciHDEF572265:GJAB-1797-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:HDEF_1781
    OrganismiHamiltonella defensa subsp. Acyrthosiphon pisum (strain 5AT)
    Taxonomic identifieri572265 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeaphid secondary symbiontsCandidatus Hamiltonella
    ProteomesiUP000002334: 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 – 320320D-alanine--D-alanine ligasePRO_1000202200Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi572265.HDEF_1781.

    Structurei

    3D structure databases

    ProteinModelPortaliC4K734.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini101 – 317217ATP-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.
    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.

    C4K734-1 [UniParc]FASTAAdd to Basket

    « Hide

    MPEKVAVLLG GTSSERQISL QSGHAVVAGL REAGIDARPI DTKNFLVTEL    50
    KEKGFTKAFI ALHGRDGEDG HLQAVLEFLK IPYTGSGVMA SALAMDKHRS 100
    KMIFQGAGLP VSPYVALNRE QIWPNVTQNT SNDLLLNNRI SNKLIKNINQ 150
    LGLPLIVKPS REGSSFGMTK VEHLDQLDDA LKKAWHYDEE ILVEKWHFGT 200
    ELTVAILGDT VLPSIRIQVS DIFYDYQAKY VSDKTQYFCP SGLKQEQEKQ 250
    LATLSMNAYR ALGCDGWGRV DVMLDDEGHF YLMEINTAPG MTDHSLFPMA 300
    ARQAGFSFSE LVCKILSLAH 320
    Length:320
    Mass (Da):35,514
    Last modified:July 7, 2009 - v1
    Checksum:iDB889E36FA65CBF2
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001277 Genomic DNA. Translation: ACQ68377.1.
    RefSeqiWP_015874141.1. NC_012751.1.
    YP_002924525.1. NC_012751.1.

    Genome annotation databases

    EnsemblBacteriaiACQ68377; ACQ68377; HDEF_1781.
    GeneIDi7951378.
    KEGGihde:HDEF_1781.
    PATRICi31975020. VBICanHam112931_1765.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001277 Genomic DNA. Translation: ACQ68377.1 .
    RefSeqi WP_015874141.1. NC_012751.1.
    YP_002924525.1. NC_012751.1.

    3D structure databases

    ProteinModelPortali C4K734.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 572265.HDEF_1781.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ACQ68377 ; ACQ68377 ; HDEF_1781 .
    GeneIDi 7951378.
    KEGGi hde:HDEF_1781.
    PATRICi 31975020. VBICanHam112931_1765.

    Phylogenomic databases

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

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci HDEF572265:GJAB-1797-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. "Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors."
      Degnan P.H., Yu Y., Sisneros N., Wing R.A., Moran N.A.
      Proc. Natl. Acad. Sci. U.S.A. 106:9063-9068(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 5AT.

    Entry informationi

    Entry nameiDDL_HAMD5
    AccessioniPrimary (citable) accession number: C4K734
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 22, 2009
    Last sequence update: July 7, 2009
    Last modified: October 1, 2014
    This is version 39 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