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P0A6M4

- DTD_ECOLI

UniProt

P0A6M4 - DTD_ECOLI

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Protein
D-tyrosyl-tRNA(Tyr) deacylase
Gene
dtd, yihZ, b3887, JW3858
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 4 out of 5 - Experimental evidence at protein leveli

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).UniRule annotation

Sites

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

GO - Molecular functioni

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

GO - Biological processi

  1. D-amino acid catabolic process Source: UniProtKB-HAMAP
  2. regulation of translational fidelity Source: GOC
  3. 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.

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 Inferred UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 145145D-tyrosyl-tRNA(Tyr) deacylaseUniRule annotation
PRO_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

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.

Miscellaneous databases

EvolutionaryTraceiP0A6M4.

Family & Domainsi

Sequence similaritiesi

Belongs to the DTD family.

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

« 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(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: July 9, 2014
This is version 81 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

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