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Information on EC 3.1.1.29 - aminoacyl-tRNA hydrolase
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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 enzyme appears in viruses and cellular organisms
Synonyms
AbPth, alanyl-tRNA editing protein AlaX-M, AlaX-M trans-editing enzyme, aminoacyl-transfer ribonucleate hydrolase, Ankzf1, bacterial peptidyl-tRNA hydrolase, Cdc48 adaptor, hydrolase, aminoacyl-transfer ribonucleate, ICT1, MJ0051, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
AbPth
aminoacyl-transfer ribonucleate hydrolase
-
-
-
-
Cdc48 adaptor
hydrolase, aminoacyl-transfer ribonucleate
-
-
-
-
MsPth
N-substituted aminoacyl transfer RNA hydrolase
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-
-
-
peptidyl-tRNA hydrolase
peptidyl-tRNA hydrolase 1
peptidyl-tRNA hydrolase 2
peptidyl-tRNA hydrolases
PH1539
PTH
Pth1
Pth2
SaPth
SSO0175
VcPth
VC_2184
Vms1
peptidyl-tRNA hydrolase
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-
-
-
peptidyl-tRNA hydrolase
-
-
PTH
-
-
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-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
N-substituted aminoacyl-tRNA + H2O = N-substituted amino acid + tRNA
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-
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N-substituted aminoacyl-tRNA + H2O = N-substituted amino acid + tRNA
reaction mechanism, active-site residues N10, H20 and D93 are crucial for catalysis
-
N-substituted aminoacyl-tRNA + H2O = N-substituted amino acid + tRNA
residues K18, D86, and T90 are essential for catalytic activity, they are located in the N-part of alpha1 and in the beta3-beta4 loop. K18 and D86, which form a salt bridge, might play a role in the catalysis thanks to their acid and basic functions, whereas the OH group of T90 could act as a nucleophile
N-substituted aminoacyl-tRNA + H2O = N-substituted amino acid + tRNA
structure-function relationship, residues Asp95 and His115 are involved in catalysis, overview
N-substituted aminoacyl-tRNA + H2O = N-substituted amino acid + tRNA
structure-function relationship, residues Asp95 and His115 are involved in catalysis, overview
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of carboxylic ester
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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
-
-
?
5'-dephosphorylated N,N-diacetyl-L-lysyl-tRNALys + H2O
N,N-diacetyl-L-lysine + 5'-dephosphorylated tRNALys
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-
-
?
5'-dephosporylated N-formyl-L-methionyl-tRNA + H2O
N-formyl-L-methionine + 5'-dephosphorylated tRNA
-
-
-
?
acetyl-histidine-tRNA + H2O
acetyl-histidine + tRNA
-
-
-
?
acetyl-histidyl-tRNAHis + H2O
acetyl-histidine + tRNAHis
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-
-
-
?
dephosphorylated diacyl-lysine-tRNA + H2O
diacyl-lysine + dephosphorylated tRNA
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-
-
-
?
dephosphorylated formyl-Met-tRNAfMet + H2O
formyl-Met + dephosphorylated tRNAfMet
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-
-
-
?
dephosphorylated formyl-methioninyl-tRNA + H2O
formyl-methionine + dephosphorylated tRNA
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-
-
-
?
formyl-methionine-tRNA + H2O
formyl-methionine + tRNA
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-
-
?
formyl-methionyl-tRNAfMet + H2O
formyl-methionine + tRNAfMet
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Escherichia coli formyl-methionyltRNAfMet, phosphorylated and dephosphorylated substrate
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?
N-benzoyl-Gly-Gly-Phe-tRNA + H2O
N-benzoyl-Gly-Gly-Phe + tRNA
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-
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-
?
N-benzoyl-Gly-GlyGly-Phe-tRNA + H2O
N-benzoyl-Gly-Gly-Gly-Phe + tRNA
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-
-
-
?
Oregon Green-methionine-tRNA + H2O
Oregon Green-methionine + tRNA
-
-
-
?
diacetyl-Lys-tRNALys + H2O
diacetyl-Lys + tRNA
-
diacetyl-Lys-tRNALys from E. coli
-
-
?
diacetyl-lysine-tRNA + H2O
diacetyl-lysine + tRNA
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-
-
?
diacetyl-lysyl-tRNALys + H2O
diacetyl-lysine + tRNALys
diacetyl-lysyl-tRNALys is hydrolyzed by the wild type enzyme 360fold more efficiently than Lys-tRNALys
-
-
?
diacetyl-lysyl-tRNALys + H2O
diacetyl-lysine + tRNALys
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-
-
-
?
diacetyl-lysyl-tRNALys + H2O
diacetyl-lysine + tRNALys
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Escherichia coli diacetyl-lysyl-tRNALys, phosphorylated and dephosphorylated substrate
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-
?
Flag-tagged CRPNSKn-tRNA + H2O
Flag-tagged CRPNSKn + tRNA
purified recombinant Ankzf1 catalyzes deacylation
-
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?
Flag-tagged CRPNSKn-tRNA + H2O
Flag-tagged CRPNSKn + tRNA
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-
-
?
Flag-tagged CRPNSKn-tRNA + H2O
Flag-tagged CRPNSKn + tRNA
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-
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?
N-acetyl-Phe-tRNA + H2O
N-acetyl-Phe + tRNA
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enzyme from encysted embryos is specific for acetyl-Phe-tRNA
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?
N-acetyl-Phe-tRNA + H2O
N-acetyl-Phe + tRNA
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enzyme with broad specificity
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-
?
N-acetyl-Phe-tRNA + H2O
N-acetyl-Phe + tRNA
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enzyme with broad specificity
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?
N-acetyl-Phe-tRNA + H2O
N-acetyl-Phe + tRNA
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enzyme with broad specificity
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-
?
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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-
?
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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?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
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-
-
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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
-
-
-
-
?
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
-
-
-
?
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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-
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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
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?
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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?
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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?
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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?
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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-
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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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-
-
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?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
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?
peptidyl-tRNA + H2O
?
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?
peptidyl-tRNA + H2O
?
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?
peptidyl-tRNA + H2O
peptide + tRNA
peptidyl-tRNA hydrolase cleaves the ester bond between tRNA and the attached peptide in peptidyl-tRNA in order to avoid the toxicity resulting from its accumulation and to free the tRNA available for further rounds in protein synthesis
-
-
?
peptidyl-tRNA + H2O
peptide + tRNA
peptidyl-tRNA hydrolase cleaves the ester bond between tRNA and the attached peptide in peptidyl-tRNA in order to avoid the toxicity resulting from its accumulation and to free the tRNA available for further rounds in protein synthesis
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?
peptidyl-tRNA + H2O
peptide + tRNA
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?
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-tRNAL + H2O
peptide + tRNA
cleavage of the ester bond between tRNA and the attached peptide in peptidyl-tRNA, substrate binding channel structure, overview
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?
peptidyl-tRNAL + H2O
peptide + tRNA
cleavage of the ester bond between tRNA and the attached peptide in peptidyl-tRNA, substrate binding channel structure, overview
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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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no activity with N-formyl-methionyl-tRNA
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-
?
additional information
?
-
the cytarabine-binding site is formed with residues: Gln19, Trp27, Glu30, Gln31, Lys152, Gln158 and Asp162, binding structure of the enzyme with cytosine arabinoside (cytarabine), overview
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-
?
additional information
?
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the cytarabine-binding site is formed with residues: Gln19, Trp27, Glu30, Gln31, Lys152, Gln158 and Asp162, binding structure of the enzyme with cytosine arabinoside (cytarabine), overview
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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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?
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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no activity with N-formyl-methionyl-tRNA
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-
?
additional information
?
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enzyme shows species specificity. Aminoacyl-tRNAs in which the tRNA comes from eucaryotes are equally efficient as substrates of the enzyme, when tRNA comes from procaryotic organisms it is hydrolyzed 40% less efficiently
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?
additional information
?
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weak binding to peptidyl-tRNA for PTRHD1, binding to tRNA is detected but also the absence of peptidyl-tRNA hydrolase activity. Thus, PTRHD1 is not a Pth and the functional consequence of nucleotide binding remains undefined
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?
additional information
?
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weak binding to peptidyl-tRNA for PTRHD1, binding to tRNA is detected but also the absence of peptidyl-tRNA hydrolase activity. Thus, PTRHD1 is not a Pth and the functional consequence of nucleotide binding remains undefined
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?
additional information
?
-
no activity with N-formyl-methionyl-tRNA
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?
additional information
?
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-
the enzyme and its conserved active-site residues N12, H22 and D95 are essential for the viability of the bacteria
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-
?
additional information
?
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the enzyme salvages tRNA from peptidyl-tRNA by hydrolyzing the ester link between the peptide and the 2'-or 3'-OH of the sugar at the end of tRNA, since accumulation of peptidyl-tRNA, due to drop-off of translating ribosomes, is toxic to the cell, overview
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-
?
additional information
?
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-
no activity with N-formyl-methionyl-tRNA
-
-
?
additional information
?
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-
the enzyme salvages tRNA from peptidyl-tRNA by hydrolyzing the ester link between the peptide and the 2'-or 3'-OH of the sugar at the end of tRNA, since accumulation of peptidyl-tRNA, due to drop-off of translating ribosomes, is toxic to the cell, overview
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-
?
additional information
?
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the enzyme and its conserved active-site residues N12, H22 and D95 are essential for the viability of the bacteria
-
-
?
additional information
?
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-
no activity with N-formyl-methionyl-tRNA
-
-
?
additional information
?
-
-
no activity with N-formyl-methionyl-tRNA
-
-
?
additional information
?
-
no activity with N-formyl-methionyl-tRNA
-
-
?
additional information
?
-
no activity with N-formyl-methionyl-tRNA
-
-
?
additional information
?
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-
the enzyme is involved in the recycling of peptidyl-tRNA, it shows poor D-aminoacyl-tRNA hydrolysis
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-
?
additional information
?
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-
no activity with N-formyl-methionyl-tRNA
-
-
?
additional information
?
-
-
no activity with N-formyl-methionyl-tRNA
-
-
?
additional information
?
-
-
N-acetyl-Val-adenosine is not a substrate, N-acetyl-Val-oligonucleotide is hydrolyzed very slowly. The specificity for the tRNA moiety does not seem to be directed towards a particular species of organism
-
-
?
additional information
?
-
substrate-binding cleft pattern of SaPth, the cleft is conservatively composed of three segments, namely, a base loop (Gly106-Gly113 in SaPth), a gate loop (Leu89-Val100 in SaPth), and a lid loop (Gly134-Gln148 in SaPth). The base loop constitutes one side of the cleft, and the gate loop and lid loop form the other side of the cleft. A structural comparison among all of the substrate-free structures in Pths reveals three different states of substrate-binding clefts; one state is the closed state (the substrate-binding cleft is closed at both the lid and gate loops, such as in SpPth), the second is the semi-closure state (the substrate-binding cleft is closed at the gate loop but wide-open at the lid loop, such as in MtPth and MsPth), and the third is the open state (the substrate-binding cleft is wide-open when both the lid and gate loops are away from the base loop)
-
-
?
additional information
?
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substrate-binding cleft pattern of SaPth, the cleft is conservatively composed of three segments, namely, a base loop (Gly106-Gly113 in SaPth), a gate loop (Leu89-Val100 in SaPth), and a lid loop (Gly134-Gln148 in SaPth). The base loop constitutes one side of the cleft, and the gate loop and lid loop form the other side of the cleft. A structural comparison among all of the substrate-free structures in Pths reveals three different states of substrate-binding clefts; one state is the closed state (the substrate-binding cleft is closed at both the lid and gate loops, such as in SpPth), the second is the semi-closure state (the substrate-binding cleft is closed at the gate loop but wide-open at the lid loop, such as in MtPth and MsPth), and the third is the open state (the substrate-binding cleft is wide-open when both the lid and gate loops are away from the base loop)
-
-
?
additional information
?
-
substrate-binding cleft pattern of SaPth, the cleft is conservatively composed of three segments, namely, a base loop (Gly106-Gly113 in SaPth), a gate loop (Leu89-Val100 in SaPth), and a lid loop (Gly134-Gln148 in SaPth). The base loop constitutes one side of the cleft, and the gate loop and lid loop form the other side of the cleft. A structural comparison among all of the substrate-free structures in Pths reveals three different states of substrate-binding clefts; one state is the closed state (the substrate-binding cleft is closed at both the lid and gate loops, such as in SpPth), the second is the semi-closure state (the substrate-binding cleft is closed at the gate loop but wide-open at the lid loop, such as in MtPth and MsPth), and the third is the open state (the substrate-binding cleft is wide-open when both the lid and gate loops are away from the base loop)
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?
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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
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
-
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
-
-
?
diacetyl-lysyl-tRNALys + H2O
diacetyl-lysine + tRNALys
-
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
?
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
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
-
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
-
-
-
?
peptidyl-tRNA + H2O
peptide + tRNA
peptidyl-tRNA hydrolase cleaves the ester bond between tRNA and the attached peptide in peptidyl-tRNA in order to avoid the toxicity resulting from its accumulation and to free the tRNA available for further rounds in protein synthesis
-
-
?
peptidyl-tRNA + H2O
peptide + tRNA
peptidyl-tRNA hydrolase cleaves the ester bond between tRNA and the attached peptide in peptidyl-tRNA in order to avoid the toxicity resulting from its accumulation and to free the tRNA available for further rounds in protein synthesis
-
-
?
peptidyl-tRNA + H2O
peptide + tRNA
-
-
-
?
additional information
?
-
-
the enzyme plays a central role and is indispensable in Escherichia coli
-
-
?
additional information
?
-
-
genetic interactions and the mechanism of peptidyl-tRNA drop-off of translating ribosomes leading to accumutaion of peptidyl-tRNA, overview
-
-
?
additional information
?
-
-
the enzyme and its conserved active-site residues N12, H22 and D95 are essential for the viability of the bacteria
-
-
?
additional information
?
-
-
the enzyme salvages tRNA from peptidyl-tRNA by hydrolyzing the ester link between the peptide and the 2'-or 3'-OH of the sugar at the end of tRNA, since accumulation of peptidyl-tRNA, due to drop-off of translating ribosomes, is toxic to the cell, overview
-
-
?
additional information
?
-
-
the enzyme salvages tRNA from peptidyl-tRNA by hydrolyzing the ester link between the peptide and the 2'-or 3'-OH of the sugar at the end of tRNA, since accumulation of peptidyl-tRNA, due to drop-off of translating ribosomes, is toxic to the cell, overview
-
-
?
additional information
?
-
-
the enzyme and its conserved active-site residues N12, H22 and D95 are essential for the viability of the bacteria
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
KCl
Mg2+
Mn2+
Zn2+
a zinc ion is coordinated by the conserved zinc-binding cluster in the C-domain, which is expected to be the enzymatic active site
Mg2+
-
the enzyme is maximally active in presence of divalent cations, Mg2+ or Mn2+. Maximal activity with 20 mM Mg2+
Mn2+
-
the enzyme is maximally active in presence of divalent cations, Mg2+ or Mn2+. Maximal activity with 2.5 mM, 50% of the activation with Mg2+
Mn2+
-
the enzyme almost completely inactive in absence of divalent cations. Mn2+ is partly effective, optimal concentration is about 0.2-0.5 mM
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
70 S ribosome
-
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
-
diethyldicarbonate
-
0.5 mM, 90% inactivation after 10 min, activity can be recovered to 41% of initial activity by treatment wit 200 mM hydroxylamine
Uncharged tRNA
-
e.g. from Escherichia coli, at concentrations of 0.01 mM or above
-
additional information
cytarabine-enzyme binding and enzyme immobilization analysis using tryptophan fluorescence and surface plasmon resonance, binding complex structure analysis, overview. Strong binding affinity of cytarabine with Pth. This compound successfully kills bacteria in both sensitive and in resistant isolates of bacteria, antibacterial potential of cytrabine is determined by agar diffusion assay
-
tRNA
-
unfractionated Escherichia coli tRNA; unfractionated from Escherichia coli
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Bacterial Infections
Crystal structure of peptidyl-tRNA hydrolase from mycobacterium smegmatis reveals novel features related to enzyme dynamics.
Carcinoma
Knockdown of immature colon carcinoma transcript 1 induces suppression of proliferation, S-phase arrest and apoptosis in leukemia cells.
Colonic Neoplasms
High ANKZF1 expression is associated with poor overall survival and recurrence-free survival in colon cancer.
Colorectal Neoplasms
High ANKZF1 expression is associated with poor overall survival and recurrence-free survival in colon cancer.
Intellectual Disability
Lack of PTRHD1 mutation in patients with young-onset and familial Parkinson's disease in a Taiwanese population.
Intellectual Disability
PTRHD1 (C2orf79) mutations lead to autosomal-recessive intellectual disability and parkinsonism.
Intellectual Disability
PTRHD1 and possibly ADORA1 mutations contribute to Parkinsonism with intellectual disability.
Intellectual Disability
PTRHD1 Loss-of-function mutation in an african family with juvenile-onset Parkinsonism and intellectual disability.
Lyme Disease
Microbial genes homologous to the peptidyl-tRNA hydrolase-encoding gene of Escherichia coli.
Movement Disorders
PTRHD1 (C2orf79) mutations lead to autosomal-recessive intellectual disability and parkinsonism.
Movement Disorders
PTRHD1 Loss-of-function mutation in an african family with juvenile-onset Parkinsonism and intellectual disability.
Neoplasms
High ANKZF1 expression is associated with poor overall survival and recurrence-free survival in colon cancer.
Pancreatic Diseases
Infantile-Onset Multisystem Neurologic, Endocrine, and Pancreatic Disease: Case and Review.
Pancreatic Diseases
Phenotype variability of infantile-onset multisystem neurologic, endocrine, and pancreatic disease IMNEPD.
Parkinson Disease
Analysis of PTRHD1 common and rare variants in European patients with Parkinson's disease.
Parkinson Disease
Lack of PTRHD1 mutation in patients with young-onset and familial Parkinson's disease in a Taiwanese population.
Parkinsonian Disorders
Analysis of PTRHD1 common and rare variants in European patients with Parkinson's disease.
Parkinsonian Disorders
Lack of PTRHD1 mutation in patients with young-onset and familial Parkinson's disease in a Taiwanese population.
Parkinsonian Disorders
PTRHD1 (C2orf79) mutations lead to autosomal-recessive intellectual disability and parkinsonism.
Parkinsonian Disorders
PTRHD1 and possibly ADORA1 mutations contribute to Parkinsonism with intellectual disability.
Parkinsonian Disorders
PTRHD1 Loss-of-function mutation in an african family with juvenile-onset Parkinsonism and intellectual disability.
Pulmonary Disease, Chronic Obstructive
Mining novel cell glycolysis related gene markers that can predict the survival of colon adenocarcinoma patients.
Starvation
Protein Synthesis Factors (RF1, RF2, RF3, RRF, and tmRNA) and Peptidyl-tRNA Hydrolase Rescue Stalled Ribosomes at Sense Codons.
Starvation
Role of methionine 71 in substrate recognition and structural integrity of bacterial peptidyl-tRNA hydrolase.
Starvation
The growth defect in Escherichia coli deficient in peptidyl-tRNA hydrolase is due to starvation for Lys-tRNA(Lys).
Starvation
Unraveling the stereochemical and dynamic aspects of the catalytic site of bacterial peptidyl-tRNA hydrolase.
Tuberculosis
Characterization of peptidyl-tRNA hydrolase encoded by open reading frame Rv1014c of Mycobacterium tuberculosis H37Rv.
Tuberculosis
Cloning, expression, purification, crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Mycobacterium tuberculosis.
Tuberculosis
Crowding, molecular volume and plasticity: an assessment involving crystallography, NMR and simulations.
Tuberculosis
NMR assignment of peptidyl-tRNA hydrolase from Mycobacterium tuberculosis H37Rv.
Tuberculosis
Solution structure and dynamics of peptidyl-tRNA hydrolase from Mycobacterium tuberculosis H37Rv.
Tuberculosis
Structural plasticity and enzyme action: crystal structures of mycobacterium tuberculosis peptidyl-tRNA hydrolase.
Tuberculosis
Structures of new crystal forms of Mycobacterium tuberculosis peptidyl-tRNA hydrolase and functionally important plasticity of the molecule.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.000016
acetyl-histidyl-tRNAHis
-
pH 7.5, 50°C, recombinant enzyme
0.00003
dephosphorylated formyl-Met-tRNAfMet
-
pH 7.5, 50°C, dephosphorylated formyl-Met-tRNAfMet
-
0.00003
dephosphorylated formyl-methioninyl-tRNA
-
50°C, pH 7.5
-
0.0000028
diacetyl-Lys-tRNALys
-
pH 7.5, 50°C, dephosphorylated diacetyl-Lys-tRNALys
-
0.024
diacetyl-Lys-tRNALys
pH 7.5, 28°C, 5'-dephosphoylated diacetyl-Lys-tRNALys, wild-type enzyme
-
0.0000028
diacetyl-lysyl-tRNALys
-
dephosphorylated substrate, pH 7.5, 50°C, recombinant enzyme
0.000011
diacetyl-lysyl-tRNALys
-
pH 7.5, 50°C, recombinant enzyme
6.7
diacetyl-lysyl-tRNALys
-
pH 7.5, 50°C, mutant enzyme D86A/K18A
0.000012
formyl-methionyl-tRNAfMet
-
pH 7.5, 50°C, recombinant enzyme
0.00003
formyl-methionyl-tRNAfMet
-
dephosphorylated substrate, pH 7.5, 50°C, recombinant enzyme
0.00471
N-acetyl-Ala-tRNA(Ala)
wild type enzyme, in 20 mM HEPES-KOH (pH 7.6), 10 mM MgCl2, at 28°C
-
0.0134
N-acetyl-Ala-tRNA(Ala)
mutant enzyme N185A, in 20 mM HEPES-KOH (pH 7.6), 10 mM MgCl2, at 28°C
-
0.0171
N-acetyl-Ala-tRNA(Ala)
mutant enzyme H188A, in 20 mM HEPES-KOH (pH 7.6), 10 mM MgCl2, at 28°C
-
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
-
additional information
additional information
-
effect of mutations altering the 1-72 pair of E. coli tRNAMetf on the Km-value
-
additional information
additional information
-
Michaelis-Menten kinetics
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
3
formyl-methionyl-tRNAfMet
-
phosphorylated and dephosphorylated substrate, pH 7.5, 50°C, recombinant enzyme
additional information
additional information
-
effect of mutations altering the 1-72 pair of E. coli tRNAMetf on the turnover-number
-
0.85
diacetyl-Lys-tRNALys
pH 7.5, 28°C, 5'-dephosphoylated diacetyl-Lys-tRNALys, wild-type enzyme
-
0.86
diacetyl-Lys-tRNALys
-
pH 7.5, 50°C, dephosphorylated diacetyl-Lys-tRNALys
-
0.002
diacetyl-lysyl-tRNALys
-
pH 7.5, 50°C, mutant enzyme D86A/K18A
0.86
diacetyl-lysyl-tRNALys
-
dephosphorylated substrate, pH 7.5, 50°C, recombinant enzyme
5.8
N-acetyl-Ala-tRNA(Ala)
mutant enzyme N185A, in 20 mM HEPES-KOH (pH 7.6), 10 mM MgCl2, at 28°C
-
7.93
N-acetyl-Ala-tRNA(Ala)
mutant enzyme H188A, in 20 mM HEPES-KOH (pH 7.6), 10 mM MgCl2, at 28°C
-
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
-
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
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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
0.00005
non-esterified tRNALys
-
pH 7.5, 50°C, recombinant enzyme
-
0.0001
tRNA-formyl-methionine
-
tRNA-ormyl-methionine from Escherichia coli, 50°C, pH 7.5
-
0.00005
tRNA-lysine
-
tRNA-lysine from Escherichia coli, 50°C, pH 7.5
-
0.00011
tRNAformylMet
-
pH 7.5, 50°C, tRNAformylMet from Escherichia coli
-
0.000095
tRNA
-
pH 7.5, 50°C, unfractionated Escherichia coli tRNA
0.000095
tRNA
-
unfractionated tRNA from Escherichia coli, 50°C, pH 7.5
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
4.14
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6 - 8.5
approx. 38% at pH 6.0, approx. 20% of maximal activity at pH 8.5
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
essential gene required for both vegetative growth and sporulation
-
-
brenda
wild-type and mutant enzymes N10A, H20A, M67A, F66A, D93A, H113A, K142A
UniProt
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
enzyme from encysted embryos is specific for acetyl-Phe-tRNA. An unspecific hydrolase active on several N-substituted amiinoacyl-tRNAs is practically absent in the encysted embryos and during embryogenesis and appears abruptly during larval development
brenda
additional information
-
mutant strain AA7852 with temperature-sensitive Pth grown at 32°C and at 41°C
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
firmly bound, not an integral part of the ribosomal subunit
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
metabolism
physiological function
additional information
evolution
performing the essential function of recycling peptidyl-tRNAs, peptidyl-tRNA hydrolases are ubiquitous in all domains of life. The multicomponent eukaryotic Pth system differs greatly from the bacterial system composed predominantly of a single Pth1 enzyme
evolution
Vms1 is a member of a clade of eRF1 homologues that is designated the Vms1-like RF1 clade (VLRF1)
evolution
-
Vms1 is a member of a clade of eRF1 homologues that is designated the Vms1-like RF1 clade (VLRF1)
-
malfunction
-
since build-up of peptidyl-tRNAs is toxic, defects in enzyme function result in cell death
malfunction
backbone dynamics of VcPth and its mutants, NMR and molecular dynamics simulation, overview
metabolism
enzyme Vms1, which contains a Cdc48-binding VIM motif, is implicated in the ribosome quality control (RQC) pathway. The 60S subunits retain the peptidyl-tRNA nascent chains, which recruit the RQC complex comprised of Rqc1-Rqc2-Ltn1-Cdc48-Ufd1-Npl4. Nascent chains ubiquitylated by the E3/ubiquitin ligase Ltn1 are extracted from the 60S by the ATPase Cdc48-Ufd1-Npl4 and presented to the 26S proteasome for degradation. The Vms1-dependent reaction does not display strong dependence on substrate ubiquitylation
metabolism
-
enzyme Vms1, which contains a Cdc48-binding VIM motif, is implicated in the ribosome quality control (RQC) pathway. The 60S subunits retain the peptidyl-tRNA nascent chains, which recruit the RQC complex comprised of Rqc1-Rqc2-Ltn1-Cdc48-Ufd1-Npl4. Nascent chains ubiquitylated by the E3/ubiquitin ligase Ltn1 are extracted from the 60S by the ATPase Cdc48-Ufd1-Npl4 and presented to the 26S proteasome for degradation. The Vms1-dependent reaction does not display strong dependence on substrate ubiquitylation
-
physiological function
ICT1 is a member of the large mitoribosomal subunit: it behaves as an integral member of the 39S mt-LSU and a component of the intact 55S monosome
physiological function
-
azithromycin stationary-phase killing is decreased in enzyme-overexpressing Pseudomonas aeruginosa cells. Overexpressing the enzyme counteracts the azithromycin-mediated effect on rhamnolipid production and partially restores swarming activity
physiological function
-
isoform Pth4 can help recycling stalled ribosomes. High dosage of isoform Pth4 can compensate for the absence of the ribosomal release factor Mrf1
physiological function
-
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
-
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
-
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
-
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
-
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
-
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
-
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
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
peptidyl-tRNA hydrolase is an essential enzymewhich 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
physiological function
bacterial peptidyl-tRNA hydrolase (Pth) is an essential enzyme that alleviates tRNA starvation by recycling prematurely dissociated peptidyl-tRNAs. Pth performs the essential function of hydrolyzing the peptidyl-tRNAs released in the cytoplasm because of premature termination of translation. Hydrolysis of the substrate is achieved by the coordinated action of highly conserved residues N14, H24, D97, and N118
physiological function
bacterial peptidyl-tRNA hydrolase hydrolyzes the peptidyl-tRNAs accumulated in the cytoplasm and thereby preventing cell death by alleviating tRNA starvation
physiological function
peptidyl-tRNA hydrolase (Pth) catalyzes the breakdown of peptidyl-tRNA into peptide and tRNA components. Pth is an esterase and cleaves the peptidyl-tRNA molecules at the ester bond between the tRNA and the peptide and generates tRNA and peptide components to ensure continuous supply of the required raw material in terms of tRNA and amino acids. This allows the continuity of the essential protein biosynthetic process. Thus, Pth plays a crucial role in the regulation of protein synthesis in the cell
physiological function
peptidyl-tRNA hydrolase (Pth) catalyzes the release of tRNA to relieve peptidyl-tRNA accumulation. The enzyme activity is essential for the viability of bacteria
physiological function
the Cdc48 adaptor Vms1 is a peptidyl-tRNA hydrolase. Yeast Cdc48, a AAA+ ATPase that is conserved across eukaryotes and archaea, is a protein unfoldase that engages in myriad cellular functions through binding of adaptors such as Ufd1-Npl4 (UN), which bind both Cdc48 and ubiquitylated substrate proteins
physiological function
the enzyme is unable to complement a Pth1-deficient Salmonella typhimurium mutant strain. PTRHD1 does bind RNA but is not a peptidyl-tRNA hydrolase and its function needs to be determined for reclassification
physiological function
-
peptidyl-tRNA hydrolase (Pth) catalyzes the release of tRNA to relieve peptidyl-tRNA accumulation. The enzyme activity is essential for the viability of bacteria
-
physiological function
-
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
-
peptidyl-tRNA hydrolase (Pth) catalyzes the breakdown of peptidyl-tRNA into peptide and tRNA components. Pth is an esterase and cleaves the peptidyl-tRNA molecules at the ester bond between the tRNA and the peptide and generates tRNA and peptide components to ensure continuous supply of the required raw material in terms of tRNA and amino acids. This allows the continuity of the essential protein biosynthetic process. Thus, Pth plays a crucial role in the regulation of protein synthesis in the cell
-
physiological function
-
the Cdc48 adaptor Vms1 is a peptidyl-tRNA hydrolase. Yeast Cdc48, a AAA+ ATPase that is conserved across eukaryotes and archaea, is a protein unfoldase that engages in myriad cellular functions through binding of adaptors such as Ufd1-Npl4 (UN), which bind both Cdc48 and ubiquitylated substrate proteins
-
physiological function
-
bacterial peptidyl-tRNA hydrolase (Pth) is an essential enzyme that alleviates tRNA starvation by recycling prematurely dissociated peptidyl-tRNAs. Pth performs the essential function of hydrolyzing the peptidyl-tRNAs released in the cytoplasm because of premature termination of translation. Hydrolysis of the substrate is achieved by the coordinated action of highly conserved residues N14, H24, D97, and N118
-
physiological function
-
peptidyl-tRNA hydrolase is an essential enzymewhich 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
-
bacterial peptidyl-tRNA hydrolase (Pth) is an essential enzyme that alleviates tRNA starvation by recycling prematurely dissociated peptidyl-tRNAs. Pth performs the essential function of hydrolyzing the peptidyl-tRNAs released in the cytoplasm because of premature termination of translation. Hydrolysis of the substrate is achieved by the coordinated action of highly conserved residues N14, H24, D97, and N118
-
additional information
enzyme structure and dynamics by NMR spectroscopy and molecular dynamics simulations. Of the substrate binding segments, the gate loop is rigid, the base loop displays slow motions, while the lid loop displays fast timescale motions. The NMR structure of Mycobacterium smegmatis MsPth shares the canonical Pth fold with theNMR structure of Mycobacterium tuberculosis MtPth
additional information
-
enzyme structure and dynamics by NMR spectroscopy and molecular dynamics simulations. Of the substrate binding segments, the gate loop is rigid, the base loop displays slow motions, while the lid loop displays fast timescale motions. The NMR structure of Mycobacterium smegmatis MsPth shares the canonical Pth fold with theNMR structure of Mycobacterium tuberculosis MtPth
additional information
enzyme Vms1 activity is dependent on a conserved catalytic glutamine. The putative catalytic region of Vms1 and other VLRF1 proteins is flanked by additional N- and C-terminal domains. The N-terminal C2H2-zinc finger of Vms1 is specifically related to those of Rei1 and certain SBDS paralogues, which function at late steps in 60S subunit maturation
additional information
-
enzyme Vms1 activity is dependent on a conserved catalytic glutamine. The putative catalytic region of Vms1 and other VLRF1 proteins is flanked by additional N- and C-terminal domains. The N-terminal C2H2-zinc finger of Vms1 is specifically related to those of Rei1 and certain SBDS paralogues, which function at late steps in 60S subunit maturation
additional information
PTRHD1 lacks the conserved, catalytically essential His20
additional information
-
PTRHD1 lacks the conserved, catalytically essential His20
additional information
role of Met71 in substrate recognition and structural integrity of bacterial peptidyl-tRNA hydrolase. The interactions of M71 with N14 and H24 play an important role in optimal positioning of their side-chains relative to the peptidyl-tRNA substrate. These interactions of M71 are important for the activity, stability, and compactness of the protein. Molecular dynamics simulation of M71A mutant in comparison to wild-type, overview
additional information
the activity and selectivity of the protein depends on the stereochemistry and dynamics of residues H24, D97, N118, and N14. D97-H24 interaction is critical for activity because it increases the nucleophilicity of H24. The N118 and N14 have orthogonally competing interactions with H24, both of which reduce the nucleophilicity of H24 and are likely to be offset by positioning of a peptidyl-tRNA substrate. The region proximal to H24 and the lid region exhibit slow motions that may assist in accommodating the substrate. Helix alpha3 exhibits a slow wobble with intermediate time scale motions of its N-cap residue N118, which may work as a flypaper to position the scissile ester bond of the substrate. The dynamics of interactions between the side chains of N14, H24, D97, and N118, control the catalysis of substrate by this enzyme, structure-function analysis, overview. The catalytic site resides in a crevice on the surface of the protein, active site structure analysis, NMR and molecular dynamics simulation study for structure modelling
additional information
-
enzyme structure and dynamics by NMR spectroscopy and molecular dynamics simulations. Of the substrate binding segments, the gate loop is rigid, the base loop displays slow motions, while the lid loop displays fast timescale motions. The NMR structure of Mycobacterium smegmatis MsPth shares the canonical Pth fold with theNMR structure of Mycobacterium tuberculosis MtPth
-
additional information
-
enzyme Vms1 activity is dependent on a conserved catalytic glutamine. The putative catalytic region of Vms1 and other VLRF1 proteins is flanked by additional N- and C-terminal domains. The N-terminal C2H2-zinc finger of Vms1 is specifically related to those of Rei1 and certain SBDS paralogues, which function at late steps in 60S subunit maturation
-
additional information
-
role of Met71 in substrate recognition and structural integrity of bacterial peptidyl-tRNA hydrolase. The interactions of M71 with N14 and H24 play an important role in optimal positioning of their side-chains relative to the peptidyl-tRNA substrate. These interactions of M71 are important for the activity, stability, and compactness of the protein. Molecular dynamics simulation of M71A mutant in comparison to wild-type, overview
-
additional information
-
enzyme structure and dynamics by NMR spectroscopy and molecular dynamics simulations. Of the substrate binding segments, the gate loop is rigid, the base loop displays slow motions, while the lid loop displays fast timescale motions. The NMR structure of Mycobacterium smegmatis MsPth shares the canonical Pth fold with theNMR structure of Mycobacterium tuberculosis MtPth
-
additional information
-
role of Met71 in substrate recognition and structural integrity of bacterial peptidyl-tRNA hydrolase. The interactions of M71 with N14 and H24 play an important role in optimal positioning of their side-chains relative to the peptidyl-tRNA substrate. These interactions of M71 are important for the activity, stability, and compactness of the protein. Molecular dynamics simulation of M71A mutant in comparison to wild-type, overview
-
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
12700
15000
20455
23000
25000
25300
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
monomer
additional information
dimer
crystal structure analysis, three-dimensional structure, each protomer is made of a mixed five-stranded beta-sheet surrounded by two groups of two alpha-helices, the dimer interface is mainly formed by van der Waals interactions between hydrophobic residues belonging to the two N-terminal R1 helices contributed by two protomers, overview
monomer
analysis and comparisons of the overall NMR solution structure of enzyme MsPth, secondary structure comparisons. In solution, enzyme MsPth exists as a monomeric protein consisting of an alpha/beta globular domain with seven beta-strands and six alpha-helices
monomer
-
analysis and comparisons of the overall NMR solution structure of enzyme MsPth, secondary structure comparisons. In solution, enzyme MsPth exists as a monomeric protein consisting of an alpha/beta globular domain with seven beta-strands and six alpha-helices
-
monomer
-
analysis and comparisons of the overall NMR solution structure of enzyme MsPth, secondary structure comparisons. In solution, enzyme MsPth exists as a monomeric protein consisting of an alpha/beta globular domain with seven beta-strands and six alpha-helices
-
monomer
gel-filtration followed by a combination of static light scattering and refractive index
monomer
1 * 21700, about, sequence calculation, 1 * 24000, recombinant His6-tagged enzyme, SDS-PAGE
monomer
-
1 * 21700, about, sequence calculation, 1 * 24000, recombinant His6-tagged enzyme, SDS-PAGE
-
additional information
-
3D fold based on NMR and a structural model based on the Escherichia coli Pth crystal structure are generated for Mycobacterium tuberculosis Pth, structure comparison, molecular modeling, construction of a model of structural changes associated with enzyme action on the basis of the plasticity of the molecule, overview
additional information
-
3D fold based on NMR and a structural model based on the Escherichia coli Pth crystal structure are generated for Mycobacterium tuberculosis Pth, structure comparison, molecular modeling, construction of a model of structural changes associated with enzyme action on the basis of the plasticity of the molecule, overview
-
additional information
enzyme SaPth was a monomer in solution, the dimerization of SaPth in the crystal may be related to the crystal-packing environment. Four parallel beta-strands (beta1, beta4, beta5, and beta7) form a twisted beta-sheet in the center of the molecule, two beta-strands (beta2 and beta3) are antiparallel to the beta-sheet and are located at one side of the center beta-sheet, and the third antiparallel beta-strand (beta6) is located at the other side. The beta-structure is surrounded at both sides by helices, overview
additional information
-
enzyme SaPth was a monomer in solution, the dimerization of SaPth in the crystal may be related to the crystal-packing environment. Four parallel beta-strands (beta1, beta4, beta5, and beta7) form a twisted beta-sheet in the center of the molecule, two beta-strands (beta2 and beta3) are antiparallel to the beta-sheet and are located at one side of the center beta-sheet, and the third antiparallel beta-strand (beta6) is located at the other side. The beta-structure is surrounded at both sides by helices, overview
additional information
-
enzyme SaPth was a monomer in solution, the dimerization of SaPth in the crystal may be related to the crystal-packing environment. Four parallel beta-strands (beta1, beta4, beta5, and beta7) form a twisted beta-sheet in the center of the molecule, two beta-strands (beta2 and beta3) are antiparallel to the beta-sheet and are located at one side of the center beta-sheet, and the third antiparallel beta-strand (beta6) is located at the other side. The beta-structure is surrounded at both sides by helices, overview
-
additional information
in the M71A mutant structure, chain A residues N14, P15, E18, Y19, H24, P46, T68-L73, K76, N118, V149, A150, V153, L154 are involved in interfacial interaction. While for chain B, the interfacial residues are L101-V105, K107-K109, R137, H142-G144, C164, and H192-E197. This indicates that the interface is formed between the active site of chain A and the C-terminal of chain B. The intermolecular bonding network for the M71A mutant is completely different from wild-type enzyme VcPth. In the M71A mutant structure, the interface has 8 hydrogen bonds, 2 salt bridges and 6 hydrophobic interactions. The three hydrogen bonds that stabilize the interface are formed by strictly conserved residues involved in the enzyme catalysis, i.e. N and ND2 atoms of N72 with the O atoms of K195 and E197, respectively
additional information
-
in the M71A mutant structure, chain A residues N14, P15, E18, Y19, H24, P46, T68-L73, K76, N118, V149, A150, V153, L154 are involved in interfacial interaction. While for chain B, the interfacial residues are L101-V105, K107-K109, R137, H142-G144, C164, and H192-E197. This indicates that the interface is formed between the active site of chain A and the C-terminal of chain B. The intermolecular bonding network for the M71A mutant is completely different from wild-type enzyme VcPth. In the M71A mutant structure, the interface has 8 hydrogen bonds, 2 salt bridges and 6 hydrophobic interactions. The three hydrogen bonds that stabilize the interface are formed by strictly conserved residues involved in the enzyme catalysis, i.e. N and ND2 atoms of N72 with the O atoms of K195 and E197, respectively
-
additional information
-
in the M71A mutant structure, chain A residues N14, P15, E18, Y19, H24, P46, T68-L73, K76, N118, V149, A150, V153, L154 are involved in interfacial interaction. While for chain B, the interfacial residues are L101-V105, K107-K109, R137, H142-G144, C164, and H192-E197. This indicates that the interface is formed between the active site of chain A and the C-terminal of chain B. The intermolecular bonding network for the M71A mutant is completely different from wild-type enzyme VcPth. In the M71A mutant structure, the interface has 8 hydrogen bonds, 2 salt bridges and 6 hydrophobic interactions. The three hydrogen bonds that stabilize the interface are formed by strictly conserved residues involved in the enzyme catalysis, i.e. N and ND2 atoms of N72 with the O atoms of K195 and E197, respectively
-
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
native enzyme and in complex with cytidine or uridine, hanging drop vapor diffusion method, using 25% (w/v) PEG 10000, 0.3 M MgCl2 and 0.1 M HEPES buffer at pH 6.0
purified recombinant Pth from Acinetobacter baumannii (AbPth) in a native unbound (AbPth-N) state and in a bound state with the phosphate ion and cytosine arabinoside (cytarabine) (AbPth-C), hanging drop vapour diffusion method, mixing of 15 mg/ml protein in 20 mM Tris-HCl, pH 7.5, 50 mM NaCl, 1.0 mM EDTA, and 5 mM of 2-mercaptoethanol, with reservoir solution containing 15% PEG 1500 in 0.3 M HEPES, pH of 7.0, 2 weeks, the crystals are soaked in reservoir solution containing 50 mg/ml cytosine arabinoside (cytarabine), X-ray diffraction structure determination and analysis 1.10-1.36 A, modelling
crystallization by using polyethylene glycol as precipitant, recombinant enzyme
-
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
sitting-drop vapor diffusion at room temperature, 10 mg/ml protein in 100 mM HEPES, pH 7.5 and 20% polyethylene glycol 10000 is equilibrated against a reservoir of the same solution, crystals diffract to 2.0 A
microbatch-under-oil method, using 0.1 M HEPES pH 7.5, 15% (w/v) PEG 8000, 5% (v/v) isopropanol or 0.1 M HEPES pH 7.5 and 5% (v/v) dioxane with 25% (w/v) PEG 8000
purified recombinant enzyme, X-ray diffraction structure determination and analysis at 1.98 A, 2.35 A, and 2.49 A resolution, molecular replacement
purified recombinant His-tagged enzyme, microbatch method, 0.002 ml each of the protein solution, containing 6 mg/ml protein, 20 mM Tris-HCl, pH 7.5, 100 mM NaCl and 2 mM 2-mercaptoethanol, and the precipitant solution, containing 20% w/v PEG 8000 in 0.1 M HEPES, pH 7.5, and 5% v/v 2-propanol or dioxane or 25% w/v PEG 8000, 100 mM sodium cacodylate, pH 6.6, and 5% v/v 2-propanol, are mixed, 5 days to 2 weeks, X-ray diffraction structure determination and analysis at 1.97-2.49 A resolution
-
hanging drop vapor diffusion method, using 30% (w/v) PEG-1500 and 10% (v/v) isopropanol in 100 mM HEPES buffer, pH 6.5
-
native enzyme and in complex with 3'-deoxy-N[(O-methyl-L-tyrosyl)amino]adenosine or 5-azacytidine, hanging drop vapor diffusion method, using 25% (w/v) PEG 4000, 5% (v/v) propan-2-ol and 0.1 M HEPES buffer, pH 7.5
hanging-drop vapour-diffusion method at 20°C, crystal structure is determined at 2.7 A resolution
purified recombinant enzyme, hanging drop vapour diffusion method, 24°C, 0.0027 ml of 1.3 mg/ml protein in 20 mM Tris-HCl, pH 7.0, 0.1 mM EDTA, and 10 mM 2-mercaptoethanol are mixed with 0.0007 ml of 11 mg/ml tRNAfMet solution and 0.002 ml of reservoir solution containing 0.8 M LiSO4 and 1.6% PEG 8000, crystallization of tRNA free crystals within a few days, X-ray diffraction structure determination and analysis of native and HgBr2-containing crystals at 1.8-3.0 A resolution, modeling
hanging drop vapor diffusion method, using 0.03 M citric acid, 0.05 M Bis-Tris propane, 1% (v/v) glycerol, 3% (w/v) sucrose, 25% (w/v) PEG 6000 pH 7.6
purified recombinant His6-tagged enzyme, hanging drop vapor diffusion method, mixing of 2 mg/ml protein in 20 mM Tris-HCl, pH 8.5, and 200 mM NaC with reservoir solution containing 25% PEG 3350, 0.2 M ammonium sulfate, and 0.1 M HEPES, pH 7.5, in a 1:1 ratio, at 16°C for 3 days, X-ray diffraction structure determination and analysis at 2.25 A resolution, molecular replacement using the structure of Pth from Mycobacterium tuberculosis (PDB ID 2Z2I) as the search model
sitting drop vapor diffusion method, using 100 mM phosphate-citrate buffer pH 4.2, and 50% (w/v) 2-methyl-2,4-pentanediol
-
purified recombinant His-tagged mutant M17A enzyme, hanging drop vapor diffusion method, 8 mg/ml protein, X-ray diffraction structure determination and analysis at 2.55 A resolution. The mutant enzyme M71A mutant does not crystallize in the dimeric form observed for the wild-type and all other mutants. Rather, the dimer interface involved the active site of one molecule into which the C-terminal region of the other molecule is inserted
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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
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
C166A
-
site-directed mutagenesis, the mutant effectively complements the enzyme-defective thermosensitive Escherichia coli mutant strain AA7852 for growth at 42°C
C67S
-
site-directed mutagenesis, the mutant effectively complements the enzyme-defective thermosensitive Escherichia coli mutant strain AA7852 for growth at 42°C
D95N
-
site-directed mutagenesis, the catalytic residue mutant is not able to complement the enzyme-defective thermosensitive Escherichia coli mutant strain AA7852 for growth at 42°C
H22N
N12D
-
site-directed mutagenesis, the catalytic residue mutant is not able to complement the enzyme-defective thermosensitive Escherichia coli mutant strain AA7852 for growth at 42°C
C166A
-
site-directed mutagenesis, the mutant effectively complements the enzyme-defective thermosensitive Escherichia coli mutant strain AA7852 for growth at 42°C
-
C67S
-
site-directed mutagenesis, the mutant effectively complements the enzyme-defective thermosensitive Escherichia coli mutant strain AA7852 for growth at 42°C
-
D95N
-
site-directed mutagenesis, the catalytic residue mutant is not able to complement the enzyme-defective thermosensitive Escherichia coli mutant strain AA7852 for growth at 42°C
-
H22N
D86A
-
kcat/Km for diacetyl-lysyl-tRNALys is 0.22% of wild-type value
D86A/K18A
-
kcat/Km for diacetyl-lysyl-tRNALys is 0.17% of wild-type value
H25A
-
kcat/Km for diacetyl-lysyl-tRNALys is 13% of wild-type value
K118A
-
kcat/Km for diacetyl-lysyl-tRNALys is 87% of wild-type value
K18A
-
kcat/Km for diacetyl-lysyl-tRNALys is 0.2% of wild-type value
K56A
-
kcat/Km for diacetyl-lysyl-tRNALys is 12% of wild-type value
Q22A
-
kcat/Km for diacetyl-lysyl-tRNALys is 20% of wild-type value
Q54A
-
kcat/Km for diacetyl-lysyl-tRNALys is 47% of wild-type value
T90A
-
kcat/Km for diacetyl-lysyl-tRNALys is 1.4% of wild-type value
T98A
-
kcat/Km for diacetyl-lysyl-tRNALys is 34% of wild-type value
Q295L
D97N
site-directed mutagenesis, the catalytically important hydrogen bond between D97 and H24 is lost after the mutation and a new H-bond is formed between H24 and N118
H24N
site-directed mutagenesis, the amide group of N24 partially occupies the site of the original histidine ring. The salt bridge between H24 and D97, which is conserved in all other canonical Pth structures, is lost in the H24N mutant structure of VcPth. N24 forms a hydrogen bond with D97, and a new hydrogen bond is also formed between N14 and N24. Hydrophobic interactions of H24 with M71 and V153 are lost upon H24N mutation
M71A
site-directed mutagenesis, molecular dynamics (MD) simulation of M71A mutant in comparison to wild-type. In the M71A mutant structure, chain A residues N14, P15, E18, Y19, H24, P46, T68-L73, K76, N118, V149, A150, V153, L154 are involved in interfacial interaction. While for chain B, the interfacial residues are L101-V105, K107-K109, R137, H142-G144, C164, and H192-E197. This indicates that the interface is formed between the active site of chain A and the C-terminal of chain B. The intermolecular bonding network for the M71A mutant is completely different from wild-type enzyme VcPth. In the M71A mutant structure, the interface has 8 hydrogen bonds, 2 salt bridges and 6 hydrophobic interactions
N118D
site-directed mutagenesis, the N118D crystal structure shows a change in the side-chain orientation of D118, which results in the formation of a new hydrogen bond between NE2 of H24 and OD1 of D118 after the mutation
N14D
site-directed mutagenesis, backbone amide resonances for D14 and D147 cannot be assigned for the N14D mutant, loss of the conserved hydrogen bond between OD1 of N14 and N of M71, but the reciprocatory hydrogen bonding between N14 and N25, which is observed in wild-type VcPth, is conserved in the N14D mutant
N72D
site-directed mutagenesis, for the N72D mutant, crystal structure cannot be determined under similar conditions but NMR backbone assignments can be achieved. In the N72D mutant, the perturbations are much less in comparison to other mutants
M71A
additional information
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
N10D
the mutant shows strongly reduced activity with diacetyl-lysyl-tRNALys and L-Lys-tRNALys compared to the wild type enzyme
H22N
-
site-directed mutagenesis, the catalytic residue mutant is not able to complement the enzyme-defective thermosensitive Escherichia coli mutant strain AA7852 for growth at 42°C
H22N
-
site-directed mutagenesis, the mutation affects the enzyme structure, overview
H22N
-
site-directed mutagenesis, the catalytic residue mutant is not able to complement the enzyme-defective thermosensitive Escherichia coli mutant strain AA7852 for growth at 42°C
-
H22N
-
site-directed mutagenesis, the mutation affects the enzyme structure, overview
-
M71A
-
site-directed mutagenesis, molecular dynamics (MD) simulation of M71A mutant in comparison to wild-type. In the M71A mutant structure, chain A residues N14, P15, E18, Y19, H24, P46, T68-L73, K76, N118, V149, A150, V153, L154 are involved in interfacial interaction. While for chain B, the interfacial residues are L101-V105, K107-K109, R137, H142-G144, C164, and H192-E197. This indicates that the interface is formed between the active site of chain A and the C-terminal of chain B. The intermolecular bonding network for the M71A mutant is completely different from wild-type enzyme VcPth. In the M71A mutant structure, the interface has 8 hydrogen bonds, 2 salt bridges and 6 hydrophobic interactions
-
M71A
-
site-directed mutagenesis, molecular dynamics (MD) simulation of M71A mutant in comparison to wild-type. In the M71A mutant structure, chain A residues N14, P15, E18, Y19, H24, P46, T68-L73, K76, N118, V149, A150, V153, L154 are involved in interfacial interaction. While for chain B, the interfacial residues are L101-V105, K107-K109, R137, H142-G144, C164, and H192-E197. This indicates that the interface is formed between the active site of chain A and the C-terminal of chain B. The intermolecular bonding network for the M71A mutant is completely different from wild-type enzyme VcPth. In the M71A mutant structure, the interface has 8 hydrogen bonds, 2 salt bridges and 6 hydrophobic interactions
-
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
additional information
truncated ICT1 form lacking the N-terminal 29 residues leads to reduction in mitochondrial protein synthesis, a mutation of the GGQ domain of ICT1 by site-directed mutagenesis causes loss of cell viability
additional information
-
truncated ICT1 form lacking the N-terminal 29 residues leads to reduction in mitochondrial protein synthesis, a mutation of the GGQ domain of ICT1 by site-directed mutagenesis causes loss of cell viability
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE