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Information on EC 3.1.1.96 - D-aminoacyl-tRNA deacylase and Organism(s) Escherichia coli and UniProt Accession P0A6M4

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EC Tree
     3 Hydrolases
         3.1 Acting on ester bonds
             3.1.1 Carboxylic-ester hydrolases
                3.1.1.96 D-aminoacyl-tRNA deacylase
IUBMB Comments
The enzyme, found in all domains of life, can cleave mischarged glycyl-tRNAAla . The enzyme from Escherichia coli can cleave D-tyrosyl-tRNATyr, D-aspartyl-tRNAAsp and D-tryptophanyl-tRNATrp . Whereas the enzyme from the archaeon Pyrococcus abyssi is a zinc protein, the enzyme from Escherichia coli does not carry any zinc .
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Escherichia coli
UNIPROT: P0A6M4
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Word Map
The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
a D-aminoacyl-tRNA
+
=
+
glycyl-tRNAAla
+
=
+
Synonyms
d-aminoacyl-trna deacylase, d-tyr-trna(tyr) deacylase, h-dtd, d-tyr-trnatyr deacylase, ss02234, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D-Tyr-tRNA(Tyr) deacylase
-
D-Tyr-tRNATyr deacylase
-
D-Tyr-tRNATyr deacylase
-
-
SYSTEMATIC NAME
IUBMB Comments
D-aminoacyl-tRNA aminoacylhydrolase
The enzyme, found in all domains of life, can cleave mischarged glycyl-tRNAAla [5]. The enzyme from Escherichia coli can cleave D-tyrosyl-tRNATyr, D-aspartyl-tRNAAsp and D-tryptophanyl-tRNATrp [1]. Whereas the enzyme from the archaeon Pyrococcus abyssi is a zinc protein, the enzyme from Escherichia coli does not carry any zinc [2].
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
D-aminoacyl-tRNA + H2O
D-amino acid + tRNA
show the reaction diagram
the enzyme recognize almost all D-aminoacyl-tRNAs instead of only D-Tyr-tRNATyr
-
-
?
D-aspartyl-tRNAAsp + H2O
D-aspartate + tRNAAsp
show the reaction diagram
no activity with L-aspartyl-tRNAAsp
-
-
?
D-tryptophanyl-tRNATrp + H2O
D-tryptophan + tRNATrp
show the reaction diagram
-
-
-
?
D-tyrosyl-tRNATyr + H2O
D-tyrosine + tRNATyr
show the reaction diagram
D-aminoacyl-tRNA + H2O
D-amino acid + tRNA
show the reaction diagram
-
-
-
-
?
D-Tyr-tRNA + H2O
D-Tyr + tRNA
show the reaction diagram
-
-
-
-
?
Gly-tRNAAla + H2O
Gly + tRNAAla
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
D-aminoacyl-tRNA + H2O
D-amino acid + tRNA
show the reaction diagram
the enzyme recognize almost all D-aminoacyl-tRNAs instead of only D-Tyr-tRNATyr
-
-
?
D-tyrosyl-tRNATyr + H2O
D-tyrosine + tRNATyr
show the reaction diagram
-
-
-
?
D-aminoacyl-tRNA + H2O
D-amino acid + tRNA
show the reaction diagram
-
-
-
-
?
D-Tyr-tRNA + H2O
D-Tyr + tRNA
show the reaction diagram
-
-
-
-
?
Gly-tRNAAla + H2O
Gly + tRNAAla
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
KCl
the initial rate of D-Tyr-tRNATyr hydrolysis, in a 20 mM Tris-HCl buffer (pH 7.8) containing 0.1 mM EDTA, is increased 3–4-fold upon the addition of 50 mM KCl
MgCl2
the initial rate of D-Tyr-tRNATyr hydrolysis, in a 20 mM Tris-HCl buffer (pH 7.8) containing 0.1 mM EDTA, is increased 3–4-fold upon the addition of 50 mM MgCl2
additional information
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.001
D-tyrosyl-tRNATyr
pH 7.8, 28°C
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
6
D-tyrosyl-tRNATyr
pH 7.8, 28°C
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
12000
D-aspartyl-tRNAAsp
pH 7.8, 28°C
2800 - 6000
D-tyrosyl-tRNATyr
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
metabolism
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
vapor diffusion method in hanging drops at 6°C. Crystallographic structure at 1.55 A. The structure corresponds to a beta-barrel closed on one side by a beta-sheet lid. This barrel results from the assembly of the two subunits. Analysis of the structure in relation with sequence homologies in the orthologous family suggests the location of the active sites at the carboxy end of the beta-strands
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Rigden, D.J.
Archaea recruited D-Tyr-tRNATyr deacylase for editing in Thr-tRNA synthetase
RNA
10
1845-1851
2004
Azotobacter vinelandii, Escherichia coli, Haemophilus influenzae (P44814)
Manually annotated by BRENDA team
Soutourina, J.; Plateau, P.; Delort, F.; Peirotes, A.; Blanquet, S.
Functional characterization of the D-Tyr-tRNATyr deacylase from Escherichia coli
J. Biol. Chem.
274
19109-19114
1999
Escherichia coli (P0A6M4), Escherichia coli
Manually annotated by BRENDA team
Soutourina, J.; Plateau, P.; Blanquet, S.
Metabolism of D-aminoacyl-tRNAs in Escherichia coli and Saccharomyces cerevisiae cells
J. Biol. Chem.
275
32535-32542
2000
Escherichia coli (P0A6M4), Escherichia coli, Saccharomyces cerevisiae (Q07648), Saccharomyces cerevisiae
Manually annotated by BRENDA team
Ferri-Fioni, M.L.; Schmitt, E.; Soutourina, J.; Plateau, P.; Mechulam, Y.; Blanquet, S.
Structure of crystalline D-Tyr-tRNA(Tyr) deacylase. A representative of a new class of tRNA-dependent hydrolases
J. Biol. Chem.
276
47285-47290
2001
Escherichia coli (P0A6M4), Escherichia coli
Manually annotated by BRENDA team
Yang, H.; Zheng, G.; Peng, X.; Qiang, B.; Yuan, J.
D-Amino acids and D-Tyr-tRNA(Tyr) deacylase: stereospecificity of the translation machine revisited
FEBS Lett.
552
95-98
2003
Escherichia coli (P0A6M4)
Manually annotated by BRENDA team
Soutourina, O.; Soutourina, J.; Blanquet, S.; Plateau, P.
Formation of D-tyrosyl-tRNATyr accounts for the toxicity of D-tyrosine toward Escherichia coli
J. Biol. Chem.
279
42560-42565
2004
Escherichia coli, Escherichia coli K-37
Manually annotated by BRENDA team
Pawar, K.I.; Suma, K.; Seenivasan, A.; Kuncha, S.K.; Routh, S.B.; Kruparani, S.P.; Sankaranarayanan, R.
Role of D-aminoacyl-tRNA deacylase beyond chiral proofreading as a cellular defense against glycine mischarging by AlaRS
eLife
6
e24001
2017
Escherichia coli
Manually annotated by BRENDA team
Calendar, R.
D-Tyrosyl-tRNA deacylase A new function
Trends Biochem. Sci.
42
684-686
2017
Escherichia coli
Manually annotated by BRENDA team