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P0A6M4

- DTD_ECOLI

UniProt

P0A6M4 - DTD_ECOLI

Protein

D-tyrosyl-tRNA(Tyr) deacylase

Gene

dtd

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

    Hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr). Could be a defense mechanism against a harmful effect of D-tyrosine. Can also cleave D-aspartyl-tRNA(Asp) and D-tryptophanyl-tRNA(Trp).

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei80 – 801NucleophileBy similarity

    GO - Molecular functioni

    1. aminoacyl-tRNA editing activity Source: EcoCyc
    2. D-tyrosyl-tRNA(Tyr) deacylase activity Source: EcoCyc

    GO - Biological processi

    1. D-amino acid catabolic process Source: UniProtKB-HAMAP
    2. regulation of translational fidelity Source: GOC
    3. response to heat Source: EcoCyc
    4. tRNA metabolic process Source: EcoCyc

    Keywords - Molecular functioni

    Hydrolase

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11852-MONOMER.
    ECOL316407:JW3858-MONOMER.
    MetaCyc:EG11852-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-tyrosyl-tRNA(Tyr) deacylase (EC:3.1.-.-)
    Gene namesi
    Name:dtd
    Synonyms:yihZ
    Ordered Locus Names:b3887, JW3858
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG11852. dtd.

    Subcellular locationi

    Cytoplasm Curated

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 145145D-tyrosyl-tRNA(Tyr) deacylasePRO_0000164537Add
    BLAST

    Proteomic databases

    PaxDbiP0A6M4.
    PRIDEiP0A6M4.

    Expressioni

    Gene expression databases

    GenevestigatoriP0A6M4.

    Interactioni

    Subunit structurei

    Homodimer.

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    ccaP069611EBI-562575,EBI-545256

    Protein-protein interaction databases

    DIPiDIP-47962N.
    IntActiP0A6M4. 9 interactions.
    STRINGi511145.b3887.

    Structurei

    Secondary structure

    1
    145
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 1514
    Beta strandi18 – 3215
    Helixi39 – 5113
    Beta strandi62 – 643
    Turni66 – 705
    Beta strandi72 – 776
    Helixi79 – 824
    Beta strandi86 – 905
    Beta strandi94 – 963
    Helixi99 – 11517
    Beta strandi120 – 1223
    Beta strandi129 – 14416

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiP0A6M4.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the DTD family.Curated

    Phylogenomic databases

    eggNOGiCOG1490.
    HOGENOMiHOG000113982.
    KOiK07560.
    OMAiGDENDKM.
    OrthoDBiEOG6C2WM2.
    PhylomeDBiP0A6M4.

    Family and domain databases

    Gene3Di3.50.80.10. 1 hit.
    HAMAPiMF_00518. Tyr_Deacylase_Dtd.
    InterProiIPR023509. DTD-like_dom.
    IPR003732. DTyrtRNA_deacyls.
    [Graphical view]
    PANTHERiPTHR10472. PTHR10472. 1 hit.
    PfamiPF02580. Tyr_Deacylase. 1 hit.
    [Graphical view]
    SUPFAMiSSF69500. SSF69500. 1 hit.
    TIGRFAMsiTIGR00256. TIGR00256. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P0A6M4-1 [UniParc]FASTAAdd to Basket

    « Hide

    MIALIQRVTR ASVTVEGEVT GEIGAGLLVL LGVEKDDDEQ KANRLCERVL    50
    GYRIFSDAEG KMNLNVQQAG GSVLVVSQFT LAADTERGMR PSFSKGASPD 100
    RAEALYDYFV ERCRQQEMNT QTGRFAADMQ VSLVNDGPVT FWLQV 145
    Length:145
    Mass (Da):15,950
    Last modified:May 10, 2005 - v1
    Checksum:i5CF0C0DB0819EC9B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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.
    YP_491563.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAD13449; AAD13449; b3887.
    BAE77422; BAE77422; BAE77422.
    GeneIDi12933646.
    948378.
    KEGGiecj:Y75_p3299.
    eco:b3887.
    PATRICi32123277. VBIEscCol129921_3999.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L19201 Genomic DNA. Translation: AAB03020.1 .
    U00096 Genomic DNA. Translation: AAD13449.1 .
    AP009048 Genomic DNA. Translation: BAE77422.1 .
    PIRi S40831.
    RefSeqi NP_418323.1. NC_000913.3.
    YP_491563.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1JKE X-ray 1.55 A/B/C/D 1-145 [» ]
    ProteinModelPortali P0A6M4.
    SMRi P0A6M4. Positions 1-145.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-47962N.
    IntActi P0A6M4. 9 interactions.
    STRINGi 511145.b3887.

    Proteomic databases

    PaxDbi P0A6M4.
    PRIDEi P0A6M4.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAD13449 ; AAD13449 ; b3887 .
    BAE77422 ; BAE77422 ; BAE77422 .
    GeneIDi 12933646.
    948378.
    KEGGi ecj:Y75_p3299.
    eco:b3887.
    PATRICi 32123277. VBIEscCol129921_3999.

    Organism-specific databases

    EchoBASEi EB1798.
    EcoGenei EG11852. dtd.

    Phylogenomic databases

    eggNOGi COG1490.
    HOGENOMi HOG000113982.
    KOi K07560.
    OMAi GDENDKM.
    OrthoDBi EOG6C2WM2.
    PhylomeDBi P0A6M4.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG11852-MONOMER.
    ECOL316407:JW3858-MONOMER.
    MetaCyc:EG11852-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P0A6M4.
    PROi P0A6M4.

    Gene expression databases

    Genevestigatori P0A6M4.

    Family and domain databases

    Gene3Di 3.50.80.10. 1 hit.
    HAMAPi MF_00518. Tyr_Deacylase_Dtd.
    InterProi IPR023509. DTD-like_dom.
    IPR003732. DTyrtRNA_deacyls.
    [Graphical view ]
    PANTHERi PTHR10472. PTHR10472. 1 hit.
    Pfami PF02580. Tyr_Deacylase. 1 hit.
    [Graphical view ]
    SUPFAMi SSF69500. SSF69500. 1 hit.
    TIGRFAMsi TIGR00256. TIGR00256. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes."
      Plunkett G. III, Burland V., Daniels D.L., Blattner F.R.
      Nucleic Acids Res. 21:3391-3398(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. "Functional characterization of the D-Tyr-tRNATyr deacylase from Escherichia coli."
      Soutourina J., Plateau P., Delort F., Peirotes A., Blanquet S.
      J. Biol. Chem. 274:19109-19114(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION, PROTEIN SEQUENCE OF 1-10.
      Strain: K12 / K37.
    5. "Metabolism of D-aminoacyl-tRNAs in Escherichia coli and Saccharomyces cerevisiae cells."
      Soutourina J., Plateau P., Blanquet S.
      J. Biol. Chem. 275:32535-32542(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
      Strain: K12 / K37.
    6. "Structure of crystalline D-Tyr-tRNA(Tyr) deacylase. A representative of a new class of tRNA-dependent hydrolases."
      Ferri-Fioni M.-L., Schmitt E., Soutourina J., Plateau P., Mechulam Y., Blanquet S.
      J. Biol. Chem. 276:47285-47290(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS).
      Strain: K12 / K37.

    Entry informationi

    Entry nameiDTD_ECOLI
    AccessioniPrimary (citable) accession number: P0A6M4
    Secondary accession number(s): P32147, Q2M8I4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 10, 2005
    Last sequence update: May 10, 2005
    Last modified: October 1, 2014
    This is version 82 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, 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

    External Data

    Dasty 3