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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes the ATP-driven ligation of two D-alanine molecules to form the D-alanyl-D-alanine dipeptide. This molecule is a key building block in peptidoglycan biosynthesis.UniRule annotation2 Publications

Miscellaneous

Follows an ordered ter-ter mechanism. ATP is the first substrate to bind and is necessary for subsequent binding of D-alanine or DCS. ADP is the final product to dissociate.1 Publication

Catalytic activityi

ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.UniRule annotation2 Publications

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 2 magnesium or manganese ions per subunit.By similarity

Activity regulationi

Is inhibited by the antituberculous drug D-cycloserine (DCS), which is a structural analog of D-alanine (PubMed:20956591, PubMed:23286234). Is activated by K+ (PubMed:23286234).2 Publications

Kineticsi

kcat is 9.7 sec(-1) (at pH 7.3).1 Publication
  1. KM=0.075 mM for D-Ala (first D-Ala binding site) (at pH 7.3)1 Publication
  2. KM=3.6 mM for D-Ala (second D-Ala binding site) (at pH 7.3)1 Publication
  3. KM=0.31 mM for ATP (at pH 7.3)1 Publication

    Pathwayi: peptidoglycan biosynthesis

    This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.UniRule annotation2 Publications
    View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi318Magnesium or manganese 1UniRule annotation1
    Metal bindingi330Magnesium or manganese 1UniRule annotation1
    Metal bindingi330Magnesium or manganese 2UniRule annotation1
    Metal bindingi332Magnesium or manganese 2UniRule annotation1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi184 – 239ATPUniRule annotationAdd BLAST56

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-KW
    • D-alanine-D-alanine ligase activity Source: MTBBASE
    • metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    Keywordsi

    Molecular functionLigase
    Biological processCell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis
    LigandATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:G185E-7236-MONOMER
    UniPathwayi
    UPA00219

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-alanine--D-alanine ligaseUniRule annotation (EC:6.3.2.4UniRule annotation2 Publications)
    Alternative name(s):
    D-Ala-D-Ala ligaseUniRule annotation
    D-alanine:D-alanine ligase2 Publications
    D-alanylalanine synthetaseUniRule annotation
    Gene namesi
    Name:ddl2 PublicationsUniRule annotation
    Synonyms:ddlA
    Ordered Locus Names:Rv2981c
    ORF Names:MTCY349.06
    OrganismiMycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
    Taxonomic identifieri83332 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
    Proteomesi
    • UP000001584 Componenti: Chromosome

    Organism-specific databases

    TubercuListiRv2981c

    Subcellular locationi

    GO - Cellular componenti

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Chemistry databases

    ChEMBLiCHEMBL2030

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001778441 – 373D-alanine--D-alanine ligaseAdd BLAST373

    Proteomic databases

    PaxDbiP9WP31

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    STRINGi83332.Rv2981c

    Structurei

    Secondary structure

    1373
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    ProteinModelPortaliP9WP31
    SMRiP9WP31
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini156 – 363ATP-graspUniRule annotationAdd BLAST208

    Sequence similaritiesi

    Belongs to the D-alanine--D-alanine ligase family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105CPF Bacteria
    COG1181 LUCA
    KOiK01921
    OMAiYETKYTE
    PhylomeDBiP9WP31

    Family and domain databases

    Gene3Di3.30.1490.20, 1 hit
    HAMAPiMF_00047 Dala_Dala_lig, 1 hit
    InterProiView protein in InterPro
    IPR011761 ATP-grasp
    IPR013815 ATP_grasp_subdomain_1
    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_sf
    PfamiView protein in Pfam
    PF07478 Dala_Dala_lig_C, 1 hit
    PF01820 Dala_Dala_lig_N, 1 hit
    PIRSFiPIRSF039102 Ddl/VanB, 1 hit
    SUPFAMiSSF52440 SSF52440, 1 hit
    TIGRFAMsiTIGR01205 D_ala_D_alaTIGR, 1 hit
    PROSITEiView protein in PROSITE
    PS50975 ATP_GRASP, 1 hit
    PS00843 DALA_DALA_LIGASE_1, 1 hit
    PS00844 DALA_DALA_LIGASE_2, 1 hit

    Sequencei

    Sequence statusi: Complete.

    P9WP31-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MSANDRRDRR VRVAVVFGGR SNEHAISCVS AGSILRNLDS RRFDVIAVGI
    60 70 80 90 100
    TPAGSWVLTD ANPDALTITN RELPQVKSGS GTELALPADP RRGGQLVSLP
    110 120 130 140 150
    PGAGEVLESV DVVFPVLHGP YGEDGTIQGL LELAGVPYVG AGVLASAVGM
    160 170 180 190 200
    DKEFTKKLLA ADGLPVGAYA VLRPPRSTLH RQECERLGLP VFVKPARGGS
    210 220 230 240 250
    SIGVSRVSSW DQLPAAVARA RRHDPKVIVE AAISGRELEC GVLEMPDGTL
    260 270 280 290 300
    EASTLGEIRV AGVRGREDSF YDFATKYLDD AAELDVPAKV DDQVAEAIRQ
    310 320 330 340 350
    LAIRAFAAID CRGLARVDFF LTDDGPVINE INTMPGFTTI SMYPRMWAAS
    360 370
    GVDYPTLLAT MIETTLARGV GLH
    Length:373
    Mass (Da):39,710
    Last modified:April 16, 2014 - v1
    Checksum:iFD7838E8B7526B53
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AL123456 Genomic DNA Translation: CCP45786.1
    PIRiB70673
    RefSeqiNP_217497.1, NC_000962.3
    WP_003912011.1, NZ_KK339370.1

    Genome annotation databases

    EnsemblBacteriaiCCP45786; CCP45786; Rv2981c
    GeneIDi888415
    KEGGimtu:Rv2981c

    Similar proteinsi

    Entry informationi

    Entry nameiDDL_MYCTU
    AccessioniPrimary (citable) accession number: P9WP31
    Secondary accession number(s): L0TBF6, P95114
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 16, 2014
    Last sequence update: April 16, 2014
    Last modified: September 12, 2018
    This is version 28 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome
    UniProt is an ELIXIR core data resource
    Main funding by: National Institutes of Health

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