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Information on EC 3.1.1.29 - aminoacyl-tRNA hydrolase and Organism(s) Escherichia coli and UniProt Accession P0A7D1
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3.1.1.29 aminoacyl-tRNA hydrolaseSpecify your search results
Word Map
- 3.1.1.29
- peptidyl-trnas
- aminoacyl-trnas
-
drop-off
- trnalys
-
infantile-onset
- drug development
The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
peptidyl-trna hydrolase, ankzf1, ptrhd1, spovc, mspth, bacterial peptidyl-trna hydrolase, peptidyl-trna hydrolase 2, yhr189w, abpth, aminoacyl-trna hydrolase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
aminoacyl-transfer ribonucleate hydrolase
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-
-
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hydrolase, aminoacyl-transfer ribonucleate
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-
-
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N-substituted aminoacyl transfer RNA hydrolase
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peptidyl-tRNA hydrolase
PTH
peptidyl-tRNA hydrolase
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-
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PTH
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-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
N-substituted aminoacyl-tRNA + H2O = N-substituted amino acid + tRNA
reaction mechanism, active-site residues N10, H20 and D93 are crucial for catalysis
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of carboxylic ester
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-
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
aminoacyl-tRNA aminoacylhydrolase
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CAS REGISTRY NUMBER
COMMENTARY
9054-98-2
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
2'(3')-O-L-(N,N-diacetyl-lysinyl)adenosine + H2O
?
minimalist substrate
-
-
?
diacetyl-lysyl-tRNALys + H2O
diacetyl-lysine + tRNALys
diacetyl-lysyl-tRNALys is hydrolyzed by the wild type enzyme 360fold more efficiently than Lys-tRNALys
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
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-
-
?
N-acetyl-Phe-tRNA + H2O
N-acetyl-Phe + tRNA
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enzyme with broad specificity
-
-
?
N-formyl-Val-tRNA + H2O
N-formyl-Val + tRNA
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reaction at a lower rate than with the N-acetyl derivative
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-
?
Oregon Green-methionine-tRNA + H2O
Oregon Green-methionine + tRNA
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-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
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-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
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-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
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-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
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-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
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-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
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the enzyme or an element directly controlled by the enzyme, is the target for the lethal effect by bacterophage lambda
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-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
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Pth recycles N-acetyl-aminoacyl tRNAs and peptidyl-tRNAs by cleaving the ester bond between tRNA and peptide
-
?
peptidyl-tRNAL + H2O
peptide + tRNA
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Pth is a key protein at the crossroads to the function of several translational factors, accumulation of peptidyl-tRNA in the cells leads to depletion of aminoacyl-tRNA pools and halts protein biosynthesis, it is vital for cells to maintain Pth activity to deal with the pollution of peptidyl-tRNAs generated during the initiation, elongation and termination steps of protein biosynthesis, overview
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-
?
peptidyl-tRNAL + H2O
peptide + tRNA
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Pth prefers substrates with two or more peptide bonds compared to those with a single peptide bond
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-
?
peptidyl-tRNALys + H2O
peptide + tRNALys
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accumulation of peptidyl-tRNA due to enzyme misfunction is toxic to the cells, overproduction of tRNALys suppresses the effects of pthTs mutation at 41°C but not at 43°C, and increases the levels of aminoacyl-tRNA
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-
?
additional information
?
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very slow hydrolysis of denatured N-acetyl-aminoacyl-tRNA, no hydrolysis of partly deaminated N-acetyl-Val-tRNA
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-
?
additional information
?
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derivatives of tRNAMetf with various combinations of bases at position 1 and 72 in the acceptor stem have been produced, aminoacylated and chemically acetylated. TrNAmetd derivatives with either C1A72, c1C72, U1G72, U1C72 or A1C72 behave as poor substrates of the enzyme compared to those with C1G72, U1A72, G1C72, A1U72 or G1U72
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-
?
additional information
?
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the enzyme plays a central role and is indispensable in Escherichia coli
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-
?
additional information
?
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genetic interactions and the mechanism of peptidyl-tRNA drop-off of translating ribosomes leading to accumutaion of peptidyl-tRNA, overview
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-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
?
peptidyl-tRNAL + H2O
peptide + tRNA
-
Pth is a key protein at the crossroads to the function of several translational factors, accumulation of peptidyl-tRNA in the cells leads to depletion of aminoacyl-tRNA pools and halts protein biosynthesis, it is vital for cells to maintain Pth activity to deal with the pollution of peptidyl-tRNAs generated during the initiation, elongation and termination steps of protein biosynthesis, overview
-
-
?
peptidyl-tRNALys + H2O
peptide + tRNALys
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accumulation of peptidyl-tRNA due to enzyme misfunction is toxic to the cells, overproduction of tRNALys suppresses the effects of pthTs mutation at 41°C but not at 43°C, and increases the levels of aminoacyl-tRNA
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
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-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
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-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
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-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
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-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
the enzyme or an element directly controlled by the enzyme, is the target for the lethal effect by bacterophage lambda
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
Pth recycles N-acetyl-aminoacyl tRNAs and peptidyl-tRNAs by cleaving the ester bond between tRNA and peptide
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?
additional information
?
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-
the enzyme plays a central role and is indispensable in Escherichia coli
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-
?
additional information
?
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genetic interactions and the mechanism of peptidyl-tRNA drop-off of translating ribosomes leading to accumutaion of peptidyl-tRNA, overview
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?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mn2+
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the enzyme almost completely inactive in absence of divalent cations. Mn2+ is partly effective, optimal concentration is about 0.2-0.5 mM
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
70 S ribosome
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free N-carbobenzyloxy-Phe-tRNA is rapidly cleaved by the enzyme. When bound to a 30 S ribosome in the presence of poly(U), the substrate is hydrolyzed rapidly as when free. The addition of 50 S ribosomal subunits to form the 70S ribosomal binding complex protects the bound substrate from the enzyme
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diethyldicarbonate
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0.5 mM, 90% inactivation after 10 min, activity can be recovered to 41% of initial activity by treatment wit 200 mM hydroxylamine
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
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effect of mutations altering the 1-72 pair of E. coli tRNAMetf on the Km-value
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0.024
diacetyl-Lys-tRNALys
pH 7.5, 28°C, 5'-dephosphoylated diacetyl-Lys-tRNALys, wild-type enzyme
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0.00471
N-acetyl-Ala-tRNA(Ala)
wild type enzyme, in 20 mM HEPES-KOH (pH 7.6), 10 mM MgCl2, at 28°C
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0.0134
N-acetyl-Ala-tRNA(Ala)
mutant enzyme N185A, in 20 mM HEPES-KOH (pH 7.6), 10 mM MgCl2, at 28°C
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0.0171
N-acetyl-Ala-tRNA(Ala)
mutant enzyme H188A, in 20 mM HEPES-KOH (pH 7.6), 10 mM MgCl2, at 28°C
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0.0269
N-acetyl-Ala-tRNA(Ala)
mutant enzyme N185A/H188A, in 20 mM HEPES-KOH (pH 7.6), 10 mM MgCl2, at 28°C
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
effect of mutations altering the 1-72 pair of E. coli tRNAMetf on the turnover-number
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0.85
diacetyl-Lys-tRNALys
pH 7.5, 28°C, 5'-dephosphoylated diacetyl-Lys-tRNALys, wild-type enzyme
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5.8
N-acetyl-Ala-tRNA(Ala)
mutant enzyme N185A, in 20 mM HEPES-KOH (pH 7.6), 10 mM MgCl2, at 28°C
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7.93
N-acetyl-Ala-tRNA(Ala)
mutant enzyme H188A, in 20 mM HEPES-KOH (pH 7.6), 10 mM MgCl2, at 28°C
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8.7
N-acetyl-Ala-tRNA(Ala)
mutant enzyme N185A/H188A, in 20 mM HEPES-KOH (pH 7.6), 10 mM MgCl2, at 28°C
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11.7
N-acetyl-Ala-tRNA(Ala)
wild type enzyme, in 20 mM HEPES-KOH (pH 7.6), 10 mM MgCl2, at 28°C
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.51
2'(3')-O-L-(N,N-diacetyl-lysinyl)adenosine
wild type enzyme, 28°C, 20 mM Tris-HCl (pH 7.5), 10 mM MgCl2, 0.1 mM EDTA, 0.1 mM dithiothreitol
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
12
3'-L-(N,N-diacetyl-lysinyl)amino-3'-deoxyadenosine
at pH 6.0, with 50 mM sodium acetate and 200 mM NaCl, at 28°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
wild-type and mutant enzymes N10A, H20A, M67A, F66A, D93A, H113A, K142A
UniProt
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
-
mutant strain AA7852 with temperature-sensitive Pth grown at 32°C and at 41°C
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
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since build-up of peptidyl-tRNAs is toxic, defects in enzyme function result in cell death
physiological function
physiological function
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peptidyl-tRNA hydrolase is an essential enzyme which acts as one of the rescue factors of the stalled ribosomes. This enzyme is required for rapid clearing of the peptidyl-tRNAs, the accumulation of which in the cell leads to cell death
physiological function
-
the enzyme removes the peptide portion from peptidyl-tRNA, returning free tRNAs to participate in translation
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystallization using polyethylene glycol as precipitant and isopropanol as additive, crystal structure at 1.2 A
in complex with the tRNA CCA-acceptor-TpsiC domain of tRNAAla, sitting drop vapor diffusion method, using 100 mM sodium acetate buffer (pH 5.2), 20% (w/v) 1,4-butanediol and 30 mM glycyl-glycylglycine, at 20°C
crystallization by using polyethylene glycol as precipitant, recombinant enzyme
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D93A
turnover-number is 0.1% of the turnover-number for wild-type enzyme, Km-value for diacetyl-Lys-tRNALys is 1.67fold higher than the Km-value for the wild-type enzyme
F66A
turnover-number is 26% of the turnover-number for wild-type enzyme, Km-value for diacetyl-Lys-tRNALys is 1.15fold higher than the Km-value for the wild-type enzyme
H113A
turnover-number is 33% of the turnover-number for wild-type enzyme, Km-value for diacetyl-Lys-tRNALys is 1.46fold higher than the Km-value for the wild-type enzyme
H188A
the mutation results in a 5.4fold decrease in the kcat/Km value compared to the wild type enzyme
H20A
K142A
turnover-number is 24% of the turnover-number for wild-type enzyme, Km-value for diacetyl-Lys-tRNALys is 4fold higher than the Km-value for the wild-type enzyme
M67A
turnover-number is 4.7% of the turnover-number for wild-type enzyme, Km-value for diacetyl-Lys-tRNALys is 70% of the Km-value for the wild-type enzyme
N10A
N10D
the mutant shows strongly reduced activity with diacetyl-lysyl-tRNALys and L-Lys-tRNALys compared to the wild type enzyme
N185A
the mutation results in a 5.7fold decrease in the kcat/Km value compared to the wild type enzyme
N185A/H188A
the mutation results in a 7.7fold decrease in the kcat/Km value compared to the wild type enzyme
additional information
-
excess of charged tRNALys maintains low levels of peptidyl-tRNA hydrolase in pth mutants at a non-permissive temperature, strain AA7852 phenotype and levels of aminoacyl- and peptidyl-tRNAs, overproduction of tRNALys suppresses the effects of pthTs mutation at 41°C but not at 43°C, and increases the levels of aminoacyl-tRNA, overview
H20A
the mutant is unable to hydrolyze 2'(3')-O-L-(N,N-diacetyl-lysinyl)adenosine
N10A
turnover-number is 0.7% of the turnover-number for wild-type enzyme, Km-value for diacetyl-Lys-tRNALys is 1.1fold higher than the Km-value for the wild-type enzyme
N10A
the mutant shows strongly reduced activity with diacetyl-lysyl-tRNALys and L-Lys-tRNALys compared to the wild type enzyme
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
wild-type and mutant enzymes N10A, H20A, M67A, F66A, D93A, H113A, K142A
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
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Pth is a potential drug target to control eubacterial infections
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Paulin, D.; Yot, P.; Chapeville, F.
Enzymatic hydrolysis of N-substituted aminoacyl-tRNA
FEBS Lett.
1
163-165
1968
Escherichia coli, Escherichia coli MRE 600
Vogel, Z.; Vogel, T.; Zamir, A.; Elson, D.
The protection by 70 S ribosomes of N-acyl-aminoacyl-tRNA against cleavage by peptidyl-tRNA hydrolase and its use to assay ribosomal association
Eur. J. Biochem.
21
582-592
1971
Escherichia coli
de Pereda, J.M.; Waas, W.F.; Jan, Y.; Ruoslathi, E.; Schimmel, P.; Pascual, J.
Crystral structure of a human peptidyl-tRNA hydrolase eveals a new fold and suggests basis for a bifunctional activity
J. Biol. Chem.
279
8111-8115
2003
Escherichia coli, Homo sapiens (Q9Y3E5), Homo sapiens, Saccharolobus solfataricus
Fromant, M.; Ferri-Fioni, M.L.; Plateau, P.; Blanquet, S.
Peptidyl-tRNA hydrolase from Sulfolobus solfataricus
Nucleic Acids Res.
31
3227-3235
2003
Escherichia coli, Saccharolobus solfataricus, Saccharomyces cerevisiae
Refugio Garcia-Villegas, M.; De La Vega, F.; Galindo, J.M.; Segura, M.; Buckingham, R.H.; Guarneros, G.
Peptidyl-tRNA hydrolase is involved in lambda inhibition of host protein synthesis
EMBO J.
10
3549-3555
1991
Escherichia coli
Dutka, S.; Meinnel, T.; Lazennec, C.; Mechulam, Y.; Blanquet, S.
Role of the 1-72 base pair in tRNAs for the activity of Escherichia coli peptidyl-tRNA hydrolase
Nucleic Acids Res.
21
4025-4030
1993
Escherichia coli
Schmitt, E.; Mechulam, Y.; Fromant, M.; Plateau, P.; Blanquet, S.
Crystal structure at 1.2 A resolution and active site mapping of Escherichia coli peptidyl-tRNA hydrolase
EMBO J.
16
4760-4769
1997
Escherichia coli (P0A7D1), Escherichia coli
Schmitt, E.; Fromant, M.; Plateau, P.; Mechulam, Y.; Blanquet, S.
Crystallization and preliminary X-ray analysis of Escherichia coli peptidyl-tRNA hydrolase
Proteins Struct. Funct. Genet.
28
135-136
1997
Escherichia coli
Goodall, J.J.; Chen, G.J.; Page, M.G.
Essential role of histidine 20 in the catalytic mechanism of Escherichia coli peptidyl-tRNA hydrolase
Biochemistry
43
4583-4591
2004
Escherichia coli
Menez, J.; Remy, E.; Buckingham, R.H.
Suppression of thermosensitive peptidyl-tRNA hydrolase mutation in Escherichia coli by gene duplication
Microbiology
147
1581-1589
2001
Escherichia coli
Singh, N.S.; Varshney, U.
A physiological connection between tmRNA and peptidyl-tRNA hydrolase functions in Escherichia coli
Nucleic Acids REs.
32
6028-2037
2004
Escherichia coli
Das, G.; Varshney, U.
Peptidyl-tRNA hydrolase and its critical role in protein biosynthesis
Microbiology
152
2191-2195
2006
Escherichia coli
Vivanco-Dominguez, S.; Cruz-Vera, L.R.; Guarneros, G.
Excess of charged tRNALys maintains low levels of peptidyl-tRNA hydrolase in pth(Ts) mutants at a non-permissive temperature
Nucleic Acids Res.
34
1564-1570
2006
Escherichia coli
Giorgi, L.; Plateau, P.; O'Mahony, G.; Aubard, C.; Fromant, M.; Thureau, A.; Grotli, M.; Blanquet, S.; Bontems, F.
NMR-based substrate analog docking to Escherichia coli peptidyl-tRNA hydrolase
J. Mol. Biol.
412
619-633
2011
Escherichia coli (P0A7D1), Escherichia coli
Sharma, S.; Kaushik, S.; Sinha, M.; Kushwaha, G.S.; Singh, A.; Sikarwar, J.; Chaudhary, A.; Gupta, A.; Kaur, P.; Singh, T.P.
Structural and functional insights into peptidyl-tRNA hydrolase
Biochim. Biophys. Acta
1844
1279-1288
2014
Acinetobacter baumannii, Escherichia coli, Francisella tularensis, Methanocaldococcus jannaschii (Q60363), Mycobacterium tuberculosis, Mycolicibacterium smegmatis, Pseudomonas aeruginosa, Pyrococcus horikoshii (O74017), Pyrococcus horikoshii OT-3 (O74017), Saccharolobus solfataricus, Saccharolobus solfataricus P2
McFeeters, H.; Gilbert, M.J.; Thompson, R.M.; Setzer, W.N.; Cruz-Vera, L.R.; McFeeters, R.L.
Inhibition of essential bacterial peptidyl-tRNA hydrolase activity by tropical plant extracts
Nat. Prod. Commun.
7
1107-1110
2012
Escherichia coli
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