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Q83BZ9

- DDL_COXBU

UniProt

Q83BZ9 - DDL_COXBU

Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Coxiella burnetii (strain RSA 493 / Nine Mile phase I)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 79 (01 Oct 2014)
      Sequence version 1 (01 Jun 2003)
      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 bindingi303 – 3031Magnesium or manganese 1UniRule annotation
    Metal bindingi316 – 3161Magnesium or manganese 1UniRule annotation
    Metal bindingi316 – 3161Magnesium or manganese 2UniRule annotation
    Metal bindingi318 – 3181Magnesium or manganese 2UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi176 – 23156ATPUniRule 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

    BioCyciCBUR227377:GJ7S-1329-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:CBU_1338
    OrganismiCoxiella burnetii (strain RSA 493 / Nine Mile phase I)
    Taxonomic identifieri227377 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaLegionellalesCoxiellaceaeCoxiella
    ProteomesiUP000002671: 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 – 372372D-alanine--D-alanine ligasePRO_0000177813Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi227377.CBU_1338.

    Structurei

    Secondary structure

    1
    372
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 129
    Helixi18 – 3114
    Turni34 – 363
    Beta strandi37 – 448
    Beta strandi50 – 534
    Helixi56 – 616
    Helixi64 – 707
    Beta strandi73 – 786
    Beta strandi87 – 893
    Beta strandi100 – 1045
    Turni109 – 1124
    Helixi115 – 1228
    Beta strandi127 – 1293
    Helixi132 – 1398
    Helixi141 – 15010
    Beta strandi159 – 1613
    Helixi170 – 1778
    Beta strandi183 – 1897
    Helixi193 – 1953
    Beta strandi196 – 1994
    Helixi202 – 21211
    Turni213 – 2153
    Beta strandi219 – 2235
    Beta strandi227 – 23913
    Beta strandi246 – 2494
    Beta strandi268 – 2714
    Helixi277 – 29317
    Beta strandi298 – 3069
    Beta strandi312 – 3209
    Helixi328 – 3358
    Helixi340 – 37031

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3TQTX-ray1.88A/B1-372[»]
    ProteinModelPortaliQ83BZ9.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini145 – 349205ATP-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.
    HOGENOMiHOG000011593.
    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.

    Q83BZ9-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAEKLHISVL CGGQSTEHEI SIQSAKNIVN TLDAAKYLIS VIFIDHVGRW    50
    YLIDQPEMFL AHSPDHLVKE GSARPITIAF GDAAKPWQSL NGDGRRYSAD 100
    CVFPMVHGTQ GEDGALQGLL ELLNLPYVGA NVQSSAVCME KDLTKTVLRA 150
    GGIPVVDWHT LSPRDATEGV YQRLLDRWGT SELFVKAVSL GSSVATLPVK 200
    TETEFTKAVK EVFRYDDRLM VEPRIRGREI ECAVLGNGAP KASLPGEIIP 250
    HHDYYSYDAK YLDPNGATTT TSVDLSESVT KQIQQIAIDA FKMVHCSGMA 300
    RVDFFVTPNN KVLVNEINTI PGFTNISMYP KMWEASGLPC PNLLDQLIEL 350
    AIDRHQEQQK LIRCYEVKAR SL 372
    Length:372
    Mass (Da):41,218
    Last modified:June 1, 2003 - v1
    Checksum:iC983B28F92B519EC
    GO

    Sequence cautioni

    The sequence AAO90841.2 differs from that shown. Reason: Erroneous initiation.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE016828 Genomic DNA. Translation: AAO90841.2. Different initiation.
    RefSeqiNP_820327.2. NC_002971.3.

    Genome annotation databases

    EnsemblBacteriaiAAO90841; AAO90841; CBU_1338.
    GeneIDi1209244.
    KEGGicbu:CBU_1338.
    PATRICi17931413. VBICoxBur82552_1330.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE016828 Genomic DNA. Translation: AAO90841.2 . Different initiation.
    RefSeqi NP_820327.2. NC_002971.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3TQT X-ray 1.88 A/B 1-372 [» ]
    ProteinModelPortali Q83BZ9.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 227377.CBU_1338.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAO90841 ; AAO90841 ; CBU_1338 .
    GeneIDi 1209244.
    KEGGi cbu:CBU_1338.
    PATRICi 17931413. VBICoxBur82552_1330.

    Phylogenomic databases

    eggNOGi COG1181.
    HOGENOMi HOG000011593.
    KOi K01921.
    OMAi QIDVIFP.
    OrthoDBi EOG64BQ73.

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci CBUR227377:GJ7S-1329-MONOMER.

    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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: RSA 493 / Nine Mile phase I.

    Entry informationi

    Entry nameiDDL_COXBU
    AccessioniPrimary (citable) accession number: Q83BZ9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 15, 2003
    Last sequence update: June 1, 2003
    Last modified: October 1, 2014
    This is version 79 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

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Coxiella burnetii
      Coxiella burnetii (strain RSA 493): entries and gene names
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3