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Protein

D-aminoacyl-tRNA deacylase

Gene

dtd

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

Functioni

D-aminoacyl-tRNA deacylase with broad substrate specificity. 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. Catalyzes the hydrolysis of D-tyrosyl-tRNA(Tyr), D-aspartyl-tRNA(Asp) and D-tryptophanyl-tRNA(Trp).1 Publication

Catalytic activityi

A D-aminoacyl-tRNA + H2O = a D-amino acid + tRNA.UniRule annotation1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei80 – 801NucleophileUniRule annotationBy 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
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Enzyme and pathway databases

BioCyciEcoCyc:EG11852-MONOMER.
ECOL316407:JW3858-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 annotation1 Publication)
Alternative name(s):
D-tyrosyl-tRNA(Tyr) deacylase1 Publication
Gene namesi
Name:dtdUniRule annotation
Synonyms:yihZ
Ordered Locus Names:b3887, JW3858
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11852. dtd.

Subcellular locationi

Cytoplasm UniRule annotationCurated

GO - Cellular componenti

  1. cytoplasm Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

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

Proteomic databases

PaxDbiP0A6M4.
PRIDEiP0A6M4.

Expressioni

Gene expression databases

GenevestigatoriP0A6M4.

Interactioni

Subunit structurei

Homodimer.1 Publication

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 – 1514Combined sources
Beta strandi18 – 3215Combined sources
Helixi39 – 5113Combined sources
Beta strandi62 – 643Combined sources
Turni66 – 705Combined sources
Beta strandi72 – 776Combined sources
Helixi79 – 824Combined sources
Beta strandi86 – 905Combined sources
Beta strandi94 – 963Combined sources
Helixi99 – 11517Combined sources
Beta strandi120 – 1223Combined sources
Beta strandi129 – 14416Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.UniRule annotationCurated

Phylogenomic databases

eggNOGiCOG1490.
HOGENOMiHOG000113982.
InParanoidiP0A6M4.
KOiK07560.
OMAiENDGPFT.
OrthoDBiEOG6C2WM2.
PhylomeDBiP0A6M4.

Family and domain databases

Gene3Di3.50.80.10. 1 hit.
HAMAPiMF_00518. 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

        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 9, 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.
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:
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.
YP_491563.1. NC_007779.1.

3D structure databases

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

Protein-protein interaction databases

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

Proteomic databases

PaxDbiP0A6M4.
PRIDEiP0A6M4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EchoBASEiEB1798.
EcoGeneiEG11852. dtd.

Phylogenomic databases

eggNOGiCOG1490.
HOGENOMiHOG000113982.
InParanoidiP0A6M4.
KOiK07560.
OMAiENDGPFT.
OrthoDBiEOG6C2WM2.
PhylomeDBiP0A6M4.

Enzyme and pathway databases

BioCyciEcoCyc:EG11852-MONOMER.
ECOL316407:JW3858-MONOMER.
MetaCyc:EG11852-MONOMER.
BRENDAi3.1.1.96. 2026.

Miscellaneous databases

EvolutionaryTraceiP0A6M4.
PROiP0A6M4.

Gene expression databases

GenevestigatoriP0A6M4.

Family and domain databases

Gene3Di3.50.80.10. 1 hit.
HAMAPiMF_00518. 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.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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(1992) [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(2005) [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(1998) [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(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY.
    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(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS), SUBUNIT.
    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 9, 2005
Last sequence update: May 9, 2005
Last modified: March 31, 2015
This is version 87 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

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 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.