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Protein

D-aminoacyl-tRNA deacylase

Gene

dtd

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

Functioni

An aminoacyl-tRNA editing enzyme that deacylates mischarged D-aminoacyl-tRNAs, has no observable editing activity on tRNAs charged with cognate L-amino acid (PubMed:10383414, PubMed:4292198, PubMed:10918062, PubMed:24302572, PubMed:27224426). Edits mischarged glycyl-tRNA(Ala) more efficiently than AlaRS (PubMed:28362257). Acts via tRNA-based rather than protein-based catalysis (PubMed:24302572, PubMed:27224426, PubMed:28362257). Rejects correctly charged L-amino acid-tRNAs from its binding site rather than specifically recognizing incorrectly charged D-amino acid-tRNAs (PubMed:27224426). Hydrolyzes correctly charged, achiral, glycyl-tRNA(Gly); GTP-bound EF-Tu (tested with T.thermophilus EF-Tu AC Q5SHN6) protects charged glycyl-tRNA(Gly) from hydrolysis, while increasing Dtd levels or inactivating EF-Tu decreases protection (PubMed:27224426). Hydrolyzes mischarged glycyl-tRNA(Ala) (but not seryl-tRNA(Ala)) even in the presence of EF-Tu, edits about 4-fold better than the editing domain of AlaRS (PubMed:28362257). Has greater activity on glycyl-tRNA(Ala) than glycyl-tRNA(Gly) due in part to its recognition of the conserved tRNA(Ala) G3.U70 wobble base pair (PubMed:28362257). Binds D-amino acids but not L-amino acids (PubMed:16902403). Overexpression of E.coli or P.falciparum Dtd is toxic in E.coli, toxicity can be rescued by supplementation with Gly (PubMed:27224426). By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality (PubMed:15292242). Hydrolyzes D-tyrosyl-tRNA(Tyr) (PubMed:4292198, PubMed:10383414, PubMed:24302572, PubMed:27224426). Hydrolyzes D-phenylalanyl-tRNA(Phe) (PubMed:4292198, PubMed:24302572). Hydrolyzes D-aspartyl-tRNA(Asp) (PubMed:10918062). Hydrolyzes D-tryptophanyl-tRNA(Trp) (PubMed:10918062). Hydrolyzes glycyl-tRNA(Gly) (PubMed:27224426). Hydrolyzes glycyl-tRNA(Ala) (PubMed:28362257).9 Publications

Catalytic activityi

Glycyl-tRNA(Ala) + H2O = glycine + tRNA(Ala).UniRule annotation1 Publication
A D-aminoacyl-tRNA + H2O = a D-amino acid + tRNA.UniRule annotation3 Publications

Kineticsi

kcat/KM is 6 µM(-1)s(-1) for D-tyrosyl-tRNA(Tyr) (PubMed:10383414). kcat/KM is 2.8 µM(-1)s(-1) for D-tryptophanyl-tRNA(Trp) (PubMed:10918062). kcat/KM is 12 µM(-1)s(-1) for D-aspartyl-tRNA(Asp) (PubMed:10918062). kcat/KM is 10 µM (-1)s(-1) for glycyl-tRNA(Gly) (PubMed:27224426).3 Publications
  1. KM=1.0 µM for D-tyrosyl-tRNA(Tyr)1 Publication
  2. KM=1.0 µM for glycyl-tRNA(Gly)1 Publication

    GO - Molecular functioni

    • aminoacyl-tRNA editing activity Source: EcoCyc
    • D-tyrosyl-tRNA(Tyr) deacylase activity Source: EcoCyc
    • tRNA binding Source: UniProtKB-KW

    GO - Biological processi

    • response to heat Source: EcoCyc
    • tRNA metabolic process Source: EcoCyc

    Keywordsi

    Molecular functionHydrolase, RNA-binding, tRNA-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11852-MONOMER.
    MetaCyc:EG11852-MONOMER.
    BRENDAi3.1.1.96. 2026.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-aminoacyl-tRNA deacylase1 PublicationUniRule annotation (EC:3.1.1.96UniRule annotation3 Publications)
    Short name:
    DTDUniRule annotation
    Alternative name(s):
    D-tyrosyl RNA deacylase1 Publication
    D-tyrosyl-tRNA(Tyr) deacylase1 Publication
    Gly-tRNA(Ala) deacylase1 PublicationUniRule annotation (EC:3.1.1.-UniRule annotation1 Publication)
    Gly-tRNA(Gly) deacylase1 Publication
    Gene namesi
    Name:dtd1 PublicationUniRule annotation
    Synonyms:yihZ
    Ordered Locus Names:b3887, JW3858
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11852. dtd.

    Subcellular locationi

    • Cytoplasm UniRule annotation1 Publication

    GO - Cellular componenti

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Disruption phenotypei

    No phenotype in rich or minimal medium, decreased growth rate in the presence of excess D-tyrosine (PubMed:10383414). A double dtd-dadA deletion mutant has a more pronounced growth defect in the presence of D-Tyr (in strain K12 / EC989) (PubMed:10383414). In a dtd deletion mutant about 40% of tRNA(Tyr) is D-tyrosyl-tRNA(Tyr); overexpressing the gene for tRNA(Tyr) suppresses the toxicity of D-Tyr by increasing the levels of L-tyrosyl-tRNA(Tyr) available for translation (PubMed:15292242). Decreased growth in the presence of D-Asp, D-Ser, D-Gln and D-Trp (PubMed:10918062). Poor growth on 20 mg/ml D-Tyr, no growth on 500 mg/ml D-Tyr or 20 mg/ml D-Trp (PubMed:25441601). Overexpression of genes for tRNA(Asp) or tRNA(Trp) suppresses the toxicity of their respective D-amino acids (PubMed:15292242). No effect seen when grown in 3 or 10 mM Gly; in a mutant that no longer edits mischarged glycyl-tRNA(Ala) or seryl-tRNA(Ala) (triple mutation in alaS) Gly becomes toxic, but excess Ala restores growth (PubMed:28362257).5 Publications

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi77S → A or P: Wild-type deacylation of D-tyrosyl-tRNA(Tyr). 1 Publication1
    Mutagenesisi78Q → A: Wild-type deacylation of D-tyrosyl-tRNA(Tyr). 1 Publication1
    Mutagenesisi80T → A: Wild-type deacylation of D-tyrosyl-tRNA(Tyr). 1 Publication1
    Mutagenesisi102A → F: Loss of deacylation of D-tyrosyl-tRNA(Tyr), loss of deacylation of glycyl-tRNA(Gly), not toxic upon overexpression. 2 Publications1
    Mutagenesisi125F → A: Loss of deacylation of D-tyrosyl-tRNA(Tyr), loss of deacylation of glycyl-tRNA(Gly). 2 Publications1
    Mutagenesisi129M → K: Alters stereospecificity, confers binding of L-amino acids while slightly decreasing binding of D-amino acids. 1 Publication1
    Mutagenesisi137G → A: Loss of deacylation of D-tyrosyl-tRNA(Tyr). 1 Publication1
    Mutagenesisi138P → A: Loss of deacylation of D-tyrosyl-tRNA(Tyr). 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001645371 – 145D-aminoacyl-tRNA deacylaseAdd BLAST145

    Proteomic databases

    PaxDbiP0A6M4.
    PRIDEiP0A6M4.

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    ccaP069612EBI-562575,EBI-545256

    Protein-protein interaction databases

    BioGridi4262640. 2 interactors.
    DIPiDIP-47962N.
    IntActiP0A6M4. 9 interactors.
    STRINGi316385.ECDH10B_4077.

    Structurei

    Secondary structure

    1145
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi2 – 15Combined sources14
    Beta strandi18 – 32Combined sources15
    Helixi39 – 51Combined sources13
    Beta strandi62 – 64Combined sources3
    Turni66 – 70Combined sources5
    Beta strandi72 – 77Combined sources6
    Helixi79 – 82Combined sources4
    Beta strandi86 – 90Combined sources5
    Beta strandi94 – 96Combined sources3
    Helixi99 – 115Combined sources17
    Beta strandi120 – 122Combined sources3
    Beta strandi129 – 144Combined sources16

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1JKEX-ray1.55A/B/C/D1-145[»]
    ProteinModelPortaliP0A6M4.
    SMRiP0A6M4.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A6M4.

    Family & Domainsi

    Motif

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Motifi137 – 138Gly-cisPro motif, important for rejection of L-amino acidsUniRule annotation1 Publication2

    Domaini

    A Gly-cisPro motif from one monomer fits into the active site of the other monomer to allow specific chiral rejection of L-amino acids (PubMed:24302572, PubMed:27224426).UniRule annotation2 Publications

    Sequence similaritiesi

    Belongs to the DTD family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4108YYA. Bacteria.
    COG1490. LUCA.
    HOGENOMiHOG000113982.
    InParanoidiP0A6M4.
    KOiK07560.
    PhylomeDBiP0A6M4.

    Family and domain databases

    CDDicd00563. Dtyr_deacylase. 1 hit.
    Gene3Di3.50.80.10. 1 hit.
    HAMAPiMF_00518. Deacylase_Dtd. 1 hit.
    InterProiView protein in InterPro
    IPR003732. Daa-tRNA_deacyls_DTD.
    IPR023509. DTD-like_dom_sf.
    PANTHERiPTHR10472. PTHR10472. 1 hit.
    PfamiView protein in Pfam
    PF02580. Tyr_Deacylase. 1 hit.
    SUPFAMiSSF69500. SSF69500. 1 hit.
    TIGRFAMsiTIGR00256. TIGR00256. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P0A6M4-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MIALIQRVTR ASVTVEGEVT GEIGAGLLVL LGVEKDDDEQ KANRLCERVL
    60 70 80 90 100
    GYRIFSDAEG KMNLNVQQAG GSVLVVSQFT LAADTERGMR PSFSKGASPD
    110 120 130 140
    RAEALYDYFV ERCRQQEMNT QTGRFAADMQ VSLVNDGPVT FWLQV
    Length:145
    Mass (Da):15,950
    Last modified:May 10, 2005 - v1
    Checksum:i5CF0C0DB0819EC9B
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L19201 Genomic DNA. Translation: AAB03020.1.
    U00096 Genomic DNA. Translation: AAD13449.1.
    AP009048 Genomic DNA. Translation: BAE77422.1.
    PIRiS40831.
    RefSeqiNP_418323.1. NC_000913.3.
    WP_000560983.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAD13449; AAD13449; b3887.
    BAE77422; BAE77422; BAE77422.
    GeneIDi948378.
    KEGGiecj:JW3858.
    eco:b3887.
    PATRICifig|1411691.4.peg.2824.

    Similar proteinsi

    Entry informationi

    Entry nameiDTD_ECOLI
    AccessioniPrimary (citable) accession number: P0A6M4
    Secondary accession number(s): P32147, Q2M8I4
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 10, 2005
    Last sequence update: May 10, 2005
    Last modified: November 22, 2017
    This is version 107 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Caution

    Initially the conserved reside Thr-80 was thought to be a nucleophile; mutagenesis in this organism and P.falciparum indicates it is not.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families