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Q2P8P8

- Q2P8P8_XANOM

UniProt

Q2P8P8 - Q2P8P8_XANOM

Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Xanthomonas oryzae pv. oryzae (strain MAFF 311018)
Status
Unreviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 77 (01 Oct 2014)
      Sequence version 1 (07 Feb 2006)
      Previous versions | rss
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    Functioni

    Cell wall formation.UniRule annotationSAAS annotation

    Catalytic activityi

    ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.UniRule annotationSAAS annotation

    Cofactori

    Binds 2 magnesium or manganese ions per subunit.UniRule annotationSAAS annotation

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei141 – 1411ATPImported
    Binding sitei192 – 1921ADP; via amide nitrogen
    Binding sitei192 – 1921ATPImported
    Binding sitei228 – 2281ADP
    Binding sitei228 – 2281ATPImported
    Metal bindingi302 – 3021Magnesium or manganese 1UniRule annotation
    Metal bindingi315 – 3151Magnesium or manganese 1UniRule annotation
    Metal bindingi315 – 3151Magnesium or manganese 2UniRule annotation
    Binding sitei315 – 3151ATPImported
    Metal bindingi317 – 3171Magnesium or manganese 2UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi175 – 23056ATPUniRule annotationAdd
    BLAST
    Nucleotide bindingi183 – 1853ADP
    Nucleotide bindingi183 – 1853ATPImported
    Nucleotide bindingi221 – 2244ADP
    Nucleotide bindingi221 – 2244ATPImported

    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

    LigaseUniRule annotationSAAS annotationImported

    Keywords - Biological processi

    Cell shape, Cell wall biogenesis/degradationUniRule annotationSAAS annotation, Peptidoglycan synthesisUniRule annotationSAAS annotation

    Keywords - Ligandi

    ATP-bindingUniRule annotationSAAS annotationImported, MagnesiumUniRule annotationSAAS annotation, ManganeseUniRule annotationSAAS annotation, Metal-bindingUniRule annotationSAAS annotation, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciXORY342109:GIX9-329-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:XOO0324Imported
    OrganismiXanthomonas oryzae pv. oryzae (strain MAFF 311018)Imported
    Taxonomic identifieri342109 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXanthomonas
    ProteomesiUP000001957: Chromosome

    Subcellular locationi

    Cytoplasm UniRule annotationSAAS annotation

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    CytoplasmUniRule annotationSAAS annotation

    Interactioni

    Protein-protein interaction databases

    STRINGi342109.XOO_0324.

    Structurei

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3E5NX-ray2.00A1-367[»]
    3R5FX-ray2.07A1-367[»]
    3RFCX-ray2.10A1-367[»]
    ProteinModelPortaliQ2P8P8.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ2P8P8.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini145 – 348204ATP-graspUniRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the D-alanine--D-alanine ligase family.UniRule annotation
    Contains 1 ATP-grasp domain.UniRule annotation
    Contains ATP-grasp domain.SAAS annotation

    Phylogenomic databases

    eggNOGiCOG1181.
    KOiK01921.
    OMAiQIDVIFP.
    OrthoDBiEOG64BQ73.

    Family and domain databases

    Gene3Di3.30.1490.20. 1 hit.
    3.30.470.20. 1 hit.
    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. 1 hit.
    [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.

    Q2P8P8-1 [UniParc]FASTAAdd to Basket

    « Hide

    MRKIRVGLIF GGKSAEHEVS LQSARNILDA LDPQRFEPVL IGIDKQGQWH    50
    VNDPDSFLLH ADDPARIALH RSGRGVALLP GAQQQQLRPI QPEQALAQID 100
    VVFPIVHGTL GEDGSLQGLL RMANLPFVGS GVLGSAVAMD KDMAKRVLRD 150
    ARLAVAPFVC FDRHTAAHAD VDTLIAQLGL PLFVKPANQG SSVGVSQVRT 200
    ADAFAAALAL ALAYDHKVLV EAAVAGREIE CAVLGNAVPH ASVCGEVVVH 250
    DAFYSYATKY ISEHGAEIVI PADIDAQTQQ RIQQIAVQAY QALGCAGMAR 300
    VDVFLCADGR IVINEVNTLP GFTRISMYPK LWQASGLDYR GLITRLIELA 350
    LERHTDDQLL RSAVELH 367
    Length:367
    Mass (Da):39,613
    Last modified:February 7, 2006 - v1
    Checksum:i4318A8A5DA76F328
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP008229 Genomic DNA. Translation: BAE67079.1.
    RefSeqiWP_011257296.1. NC_007705.1.
    YP_449353.1. NC_007705.1.

    Genome annotation databases

    EnsemblBacteriaiBAE67079; BAE67079; BAE67079.
    GeneIDi3856807.
    KEGGixom:XOO_0324.
    PATRICi24109825. VBIXanOry49434_0366.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP008229 Genomic DNA. Translation: BAE67079.1 .
    RefSeqi WP_011257296.1. NC_007705.1.
    YP_449353.1. NC_007705.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3E5N X-ray 2.00 A 1-367 [» ]
    3R5F X-ray 2.07 A 1-367 [» ]
    3RFC X-ray 2.10 A 1-367 [» ]
    ProteinModelPortali Q2P8P8.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 342109.XOO_0324.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAE67079 ; BAE67079 ; BAE67079 .
    GeneIDi 3856807.
    KEGGi xom:XOO_0324.
    PATRICi 24109825. VBIXanOry49434_0366.

    Phylogenomic databases

    eggNOGi COG1181.
    KOi K01921.
    OMAi QIDVIFP.
    OrthoDBi EOG64BQ73.

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci XORY342109:GIX9-329-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q2P8P8.

    Family and domain databases

    Gene3Di 3.30.1490.20. 1 hit.
    3.30.470.20. 1 hit.
    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. 1 hit.
    [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. "Genome sequence of Xanthomonas oryzae pv. oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity."
      Ochiai H., Inoue Y., Takeya M., Sasaki A., Kaku H.
      Jpn. Agric. Res. Q. 39:275-287(2005)
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: MAFF 311018Imported.
    2. "Crystal strucutre of D-alanine-D-alanine ligase from Xanthomonas oryzae pv. oryzae KACC10331."
      Doan T.N.T., Kim J.K., Kim H.S., Ahn Y.J., Kim J.G., Lee B.M., Kang L.W.
      Submitted (AUG-2008) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS).
    3. "Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ATP."
      Doan T.T.N., Kim J.K., Kang L.W.
      Submitted (MAR-2011) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.07 ANGSTROMS) IN COMPLEX WITH ATP.
    4. "Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP."
      Doan T.T.N., Kim J.K., Ahn Y.J., Kang L.W.
      Submitted (APR-2011) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH ADP.

    Entry informationi

    Entry nameiQ2P8P8_XANOM
    AccessioniPrimary (citable) accession number: Q2P8P8
    Entry historyi
    Integrated into UniProtKB/TrEMBL: February 7, 2006
    Last sequence update: February 7, 2006
    Last modified: October 1, 2014
    This is version 77 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiUnreviewed (UniProtKB/TrEMBL)

    Miscellaneousi

    Keywords - Technical termi

    3D-structureImported, Complete proteomeImported

    External Data

    Dasty 3