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Q3JNE1

- DDL_BURP1

UniProt

Q3JNE1 - DDL_BURP1

Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Burkholderia pseudomallei (strain 1710b)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 70 (01 Oct 2014)
      Sequence version 1 (08 Nov 2005)
      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 bindingi262 – 2621Magnesium or manganese 1UniRule annotation
    Metal bindingi275 – 2751Magnesium or manganese 1UniRule annotation
    Metal bindingi275 – 2751Magnesium or manganese 2UniRule annotation
    Metal bindingi277 – 2771Magnesium or manganese 2UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi138 – 19356ATPUniRule 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

    BioCyciBPSE320372:GBYB-3542-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:BURPS1710b_3542
    OrganismiBurkholderia pseudomallei (strain 1710b)
    Taxonomic identifieri320372 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeBurkholderiapseudomallei group
    ProteomesiUP000002700: Chromosome I

    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 – 312312D-alanine--D-alanine ligasePRO_0000341076Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi320372.BURPS1710b_3542.

    Structurei

    Secondary structure

    1
    312
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi11 – 155
    Helixi23 – 3917
    Beta strandi43 – 475
    Turni49 – 513
    Helixi56 – 594
    Beta strandi64 – 674
    Helixi72 – 743
    Helixi78 – 858
    Beta strandi89 – 924
    Helixi95 – 1028
    Helixi104 – 11411
    Beta strandi121 – 1255
    Helixi130 – 14112
    Beta strandi143 – 1497
    Beta strandi159 – 1613
    Helixi164 – 1663
    Helixi167 – 17711
    Beta strandi179 – 1857
    Beta strandi192 – 1987
    Beta strandi206 – 2083
    Beta strandi229 – 2313
    Helixi236 – 25217
    Beta strandi257 – 2659
    Beta strandi271 – 2799
    Helixi287 – 2948
    Helixi299 – 30810

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4EGQX-ray2.20A/B/C/D1-312[»]
    ProteinModelPortaliQ3JNE1.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini108 – 308201ATP-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.
    OMAiKLAFQYD.
    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.

    Q3JNE1-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSGIDPKRFG KVAVLLGGDS AEREVSLNSG RLVLQGLRDA GIDAHPFDPA    50
    QRPLAALKDE GFVRAFNALH GGYGENGQIQ GALDFYGIRY TGSGVLGSAL 100
    GLDKFRTKLV WQQTGIPTPP FETVMRGDDY AARAQDIVAK LGVPLFVKPA 150
    SEGSSVAVEK VKSADALPAA LEEAAKHDKI VIVEKSIEGG GEYTACIAAD 200
    LDLPLIRIVP AGEFYDYHAK YIANDTQYLI PCGLDAAKEA EFKRIARRAF 250
    DVLGCTDWGR ADFMLDAAGN PYFLEVNTAP GMTDHSLPPK AARAVGIGYS 300
    ELVVKVLSLT LD 312
    Length:312
    Mass (Da):33,341
    Last modified:November 8, 2005 - v1
    Checksum:iCCD89397BEAE5E22
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000124 Genomic DNA. Translation: ABA49167.1.
    RefSeqiYP_334912.1. NC_007434.1.

    Genome annotation databases

    EnsemblBacteriaiABA49167; ABA49167; BURPS1710b_3542.
    GeneIDi3690512.
    KEGGibpm:BURPS1710b_3542.
    PATRICi19239676. VBIBurPse115837_3687.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000124 Genomic DNA. Translation: ABA49167.1 .
    RefSeqi YP_334912.1. NC_007434.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4EGQ X-ray 2.20 A/B/C/D 1-312 [» ]
    ProteinModelPortali Q3JNE1.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 320372.BURPS1710b_3542.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABA49167 ; ABA49167 ; BURPS1710b_3542 .
    GeneIDi 3690512.
    KEGGi bpm:BURPS1710b_3542.
    PATRICi 19239676. VBIBurPse115837_3687.

    Phylogenomic databases

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

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci BPSE320372:GBYB-3542-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. Woods D.E., Nierman W.C.
      Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 1710b.

    Entry informationi

    Entry nameiDDL_BURP1
    AccessioniPrimary (citable) accession number: Q3JNE1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 10, 2008
    Last sequence update: November 8, 2005
    Last modified: October 1, 2014
    This is version 70 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

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3