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Protein

D-alanyl-D-alanine dipeptidase

Gene

ddpX

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes hydrolysis of the D-alanyl-D-alanine dipeptide. May have a role in cell-wall turnover.UniRule annotation1 Publication

Catalytic activityi

D-Ala-D-Ala + H2O = 2 D-Ala.UniRule annotation1 Publication

Cofactori

Zn2+1 PublicationNote: Binds 1 zinc ion per subunit.1 Publication

Kineticsi

Kcat is 170 sec(-1) with D-Ala-D-Ala. Kcat is 70 sec(-1) with L-Ala-D-Ala.

  1. KM=1.4 mM for D-Ala-D-Ala1 Publication
  2. KM=550 mM for L-Ala-D-Ala1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sitei71Transition state stabilizerUniRule annotation1
    Metal bindingi98Zinc; via tele nitrogen; catalyticUniRule annotation1
    Metal bindingi105Zinc; catalyticUniRule annotation1
    Active sitei162Proton donor/acceptorUniRule annotation1
    Metal bindingi165Zinc; via pros nitrogen; catalyticUniRule annotation1

    GO - Molecular functioni

    • dipeptidase activity Source: UniProtKB-HAMAP
    • zinc D-Ala-D-Ala carboxypeptidase activity Source: EcoCyc
    • zinc ion binding Source: UniProtKB-HAMAP

    GO - Biological processi

    • cell wall organization Source: UniProtKB-KW
    • peptidoglycan biosynthetic process Source: EcoCyc
    • response to starvation Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Dipeptidase, Hydrolase, Metalloprotease, Protease

    Keywords - Biological processi

    Cell wall biogenesis/degradation

    Keywords - Ligandi

    Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:G6782-MONOMER.
    ECOL316407:JW1483-MONOMER.
    MetaCyc:G6782-MONOMER.

    Protein family/group databases

    MEROPSiM15.011.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-alanyl-D-alanine dipeptidaseUniRule annotation (EC:3.4.13.22UniRule annotation)
    Short name:
    D-Ala-D-Ala dipeptidaseUniRule annotation
    Gene namesi
    Name:ddpXUniRule annotation
    Synonyms:vanX, yddT
    Ordered Locus Names:b1488, JW1483
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG13791. ddpX.

    Subcellular locationi

    • Cytoplasm 1 Publication

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00002178371 – 193D-alanyl-D-alanine dipeptidaseAdd BLAST193

    Proteomic databases

    PaxDbiP77790.
    PRIDEiP77790.

    Interactioni

    Protein-protein interaction databases

    BioGridi4259362. 255 interactors.
    DIPiDIP-9418N.
    STRINGi511145.b1488.

    Structurei

    3D structure databases

    ProteinModelPortaliP77790.
    SMRiP77790.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the peptidase M15D family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4108UQS. Bacteria.
    COG2173. LUCA.
    HOGENOMiHOG000200848.
    InParanoidiP77790.
    KOiK08641.
    OMAiCYRPVRS.
    PhylomeDBiP77790.

    Family and domain databases

    Gene3Di3.30.1380.10. 1 hit.
    HAMAPiMF_01924. A_A_dipeptidase. 1 hit.
    InterProiIPR000755. A_A_dipeptidase.
    IPR009045. Hedgehog_sig/DD-Pept_Zn-bd_dom.
    [Graphical view]
    PfamiPF01427. Peptidase_M15. 1 hit.
    [Graphical view]
    PIRSFiPIRSF026671. AA_dipeptidase. 1 hit.
    SUPFAMiSSF55166. SSF55166. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P77790-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSDTTELVDL AVIFPDLEIE LKYACADNIT GKAIYQQARC LLHKDAITAL
    60 70 80 90 100
    AKSISIAQLS GLQLVIYDAY RPQQAQAMLW QACPDPQYVV DVTVGSNHSR
    110 120 130 140 150
    GTAIDLTLRD EHGNILDMGA GFDEMHERSH AYHPSVPPAA QRNRLLLNAI
    160 170 180 190
    MTGGGFVGIS SEWWHFELPQ AASYPLLADQ FSCFISPGTQ HVS
    Length:193
    Mass (Da):21,213
    Last modified:February 1, 1997 - v1
    Checksum:i6933AAD3FCCD684F
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC74561.1.
    AP009048 Genomic DNA. Translation: BAA15143.1.
    PIRiC64902.
    RefSeqiNP_416005.1. NC_000913.3.
    WP_001285833.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74561; AAC74561; b1488.
    BAA15143; BAA15143; BAA15143.
    GeneIDi945532.
    KEGGiecj:JW1483.
    eco:b1488.
    PATRICi32118270. VBIEscCol129921_1555.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC74561.1.
    AP009048 Genomic DNA. Translation: BAA15143.1.
    PIRiC64902.
    RefSeqiNP_416005.1. NC_000913.3.
    WP_001285833.1. NZ_LN832404.1.

    3D structure databases

    ProteinModelPortaliP77790.
    SMRiP77790.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4259362. 255 interactors.
    DIPiDIP-9418N.
    STRINGi511145.b1488.

    Protein family/group databases

    MEROPSiM15.011.

    Proteomic databases

    PaxDbiP77790.
    PRIDEiP77790.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC74561; AAC74561; b1488.
    BAA15143; BAA15143; BAA15143.
    GeneIDi945532.
    KEGGiecj:JW1483.
    eco:b1488.
    PATRICi32118270. VBIEscCol129921_1555.

    Organism-specific databases

    EchoBASEiEB3552.
    EcoGeneiEG13791. ddpX.

    Phylogenomic databases

    eggNOGiENOG4108UQS. Bacteria.
    COG2173. LUCA.
    HOGENOMiHOG000200848.
    InParanoidiP77790.
    KOiK08641.
    OMAiCYRPVRS.
    PhylomeDBiP77790.

    Enzyme and pathway databases

    BioCyciEcoCyc:G6782-MONOMER.
    ECOL316407:JW1483-MONOMER.
    MetaCyc:G6782-MONOMER.

    Miscellaneous databases

    PROiP77790.

    Family and domain databases

    Gene3Di3.30.1380.10. 1 hit.
    HAMAPiMF_01924. A_A_dipeptidase. 1 hit.
    InterProiIPR000755. A_A_dipeptidase.
    IPR009045. Hedgehog_sig/DD-Pept_Zn-bd_dom.
    [Graphical view]
    PfamiPF01427. Peptidase_M15. 1 hit.
    [Graphical view]
    PIRSFiPIRSF026671. AA_dipeptidase. 1 hit.
    SUPFAMiSSF55166. SSF55166. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiDDPX_ECOLI
    AccessioniPrimary (citable) accession number: P77790
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 27, 2001
    Last sequence update: February 1, 1997
    Last modified: November 2, 2016
    This is version 125 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. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. Peptidase families
      Classification of peptidase families and list of entries
    3. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.