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Information on EC 3.1.1.29 - aminoacyl-tRNA hydrolase and Organism(s) Saccharolobus solfataricus and UniProt Accession Q980V1

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EC Tree
     3 Hydrolases
         3.1 Acting on ester bonds
             3.1.1 Carboxylic-ester hydrolases
                3.1.1.29 aminoacyl-tRNA hydrolase
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This record set is specific for:
Saccharolobus solfataricus
UNIPROT: Q980V1 not found.
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The taxonomic range for the selected organisms is: Saccharolobus solfataricus
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, cdc48 adaptor, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
peptidyl-tRNA hydrolase
-
aminoacyl-transfer ribonucleate hydrolase
-
-
-
-
hydrolase, aminoacyl-transfer ribonucleate
-
-
-
-
N-substituted aminoacyl transfer RNA hydrolase
-
-
-
-
peptidyl-tRNA hydrolase
SSO0175
-
locus name
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
N-substituted aminoacyl-tRNA + H2O = N-substituted amino acid + tRNA
show the reaction diagram
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
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of carboxylic ester
-
-
-
-
PATHWAY SOURCE
PATHWAYS
-
-
SYSTEMATIC NAME
IUBMB Comments
aminoacyl-tRNA aminoacylhydrolase
-
CAS REGISTRY NUMBER
COMMENTARY hide
9054-98-2
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
5'-dephosphorylated N,N-diacetyl-L-lysyl-tRNALys + H2O
N,N-diacetyl-L-lysine + 5'-dephosphorylated tRNALys
show the reaction diagram
-
-
-
?
5'-dephosphorylated N-formyl-L-methionyl-tRNA + H2O
N-formyl-L-methionine + 5'-dephosphorylated tRNA
show the reaction diagram
-
-
-
?
acetyl-histidine-tRNA + H2O
acetyl-histidine + tRNA
show the reaction diagram
-
-
-
?
acetyl-histidyl-tRNAHis + H2O
acetyl-histidine + tRNAHis
show the reaction diagram
-
-
-
-
?
D-tyrosine-tRNA + H2O
D-tyrosine + tRNA
show the reaction diagram
-
-
-
?
dephosphorylated diacyl-lysine-tRNA + H2O
diacyl-lysine + dephosphorylated tRNA
show the reaction diagram
-
-
-
-
?
dephosphorylated formyl-Met-tRNAfMet + H2O
formyl-Met + dephosphorylated tRNAfMet
show the reaction diagram
-
-
-
-
?
dephosphorylated formyl-methioninyl-tRNA + H2O
formyl-methionine + dephosphorylated tRNA
show the reaction diagram
-
-
-
-
?
diacetyl-Lys-tRNALys + H2O
diacetyl-Lys + tRNA
show the reaction diagram
-
diacetyl-Lys-tRNALys from E. coli
-
-
?
diacetyl-lysine-tRNA + H2O
diacetyl-lysine + tRNA
show the reaction diagram
diacetyl-lysyl-tRNALys
diacetyl-Lys + tRNALys
show the reaction diagram
-
-
-
-
?
diacetyl-lysyl-tRNALys + H2O
diacetyl-lysine + tRNALys
show the reaction diagram
formyl-Met-tRNAfMet + H2O
formyl-Met + tRNAfMet
show the reaction diagram
-
-
-
-
?
formyl-methionine-tRNA + H2O
formyl-methionine + tRNA
show the reaction diagram
-
-
-
?
formyl-methioninyl-tRNA + H2O
formyl-methionine + tRNA
show the reaction diagram
-
-
-
-
?
formyl-methionyl-tRNAfMet + H2O
formyl-methionine + tRNAfMet
show the reaction diagram
-
Escherichia coli formyl-methionyltRNAfMet, phosphorylated and dephosphorylated substrate
-
-
?
N-acetyl-His-tRNA + H2O
N-acetyl-His + tRNA
show the reaction diagram
-
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
diacetyl-lysyl-tRNALys + H2O
diacetyl-lysine + tRNALys
show the reaction diagram
-
-
-
-
?
N-substituted aminoacyl-tRNA + H2O
N-substituted amino acid + tRNA
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K+
-
0.3 mM, 77fold activation
MgCl2
-
40 mM, approx. 88fold activation
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
non-esterified tRNALys
-
-
-
tRNA-formyl-methionine
-
from Escherichia coli
-
tRNA-lysine
-
from Escherichia coli
-
tRNAfMet
tRNALys
-
tRNALys from Escherichia coli
Uncharged tRNA
-
e.g. from Escherichia coli, at concentrations of 0.01 mM or above
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
spermidine
-
0.1 mM spermidine HCl, 73fold activation
spermidine-HCl
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.000016
acetyl-His-tRNAHis
-
pH 7.5, 50°C
0.000016
acetyl-histidyl-tRNA
-
50°C, pH 7.5
0.000016
acetyl-histidyl-tRNAHis
-
pH 7.5, 50°C, recombinant enzyme
0.000003
dephosphorylated diacyl-lysine-tRNA
-
50°C, pH 7.5
-
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 - 0.000011
diacetyl-Lys-tRNALys
-
0.000011
diacetyl-lysine-tRNA
-
0.0000028 - 12.8
diacetyl-lysyl-tRNALys
0.000012
formyl-Met-tRNAfMet
-
pH 7.5, 50°C
0.000012
formyl-methionyl-tRNA
-
50°C, pH 7.5
0.000012 - 0.00003
formyl-methionyl-tRNAfMet
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3.4
acetyl-His-tRNA
-
pH 7.5, 50°C
3.4
acetyl-histidyl-tRNA
-
50°C, pH 7.5
3.4
acetyl-histidyl-tRNAHis
-
pH 7.5, 50°C, recombinant enzyme
0.86 - 6.08
dephosphorylated diacyl-lysine-tRNA
-
3
dephosphorylated formyl-methioninyl-tRNA
-
50°C, pH 7.5
-
0.86 - 1.8
diacetyl-Lys-tRNALys
-
1.8
diacetyl-lysine-tRNA
-
0.002 - 2.2
diacetyl-lysyl-tRNALys
3
formyl-Met-tRNAfMet
-
pH 7.5, 50°C
3
formyl-methioninyl-tRNA
-
50°C, pH 7.5
-
3
formyl-methionyl-tRNA
-
50°C, pH 7.5
3
formyl-methionyl-tRNAfMet
-
phosphorylated and dephosphorylated substrate, pH 7.5, 50°C, recombinant enzyme
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00005
non-esterified tRNALys
-
pH 7.5, 50°C, recombinant enzyme
-
0.000095
tRNA
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
tRNAfMet
-
pH 7.5, 50°C, recombinant enzyme
0.00011
tRNAformylMet
-
pH 7.5, 50°C, tRNAformylMet from Escherichia coli
-
0.00005
tRNALys
-
pH 7.5, 50°C, tRNALys from Escherichia coli
0.0001
Uncharged tRNA
-
pH 7.5, 50°C, recombinant enzyme
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.078
-
substrate D-tyrosyl-tRNA, 37°C, pH 7.5
31.8
-
substrate diacetyl-lysine tRNA, 37°C, pH 7.5
additional information
-
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
gene pth2
Uniprot
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
13100
-
2 * 13100, deduced from nucleotide sequence
15000
25000
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
?
-
x * 15000, SDS-PAGE
dimer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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 vapour diffusion method, 1.8 A resolution
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant PTH, heat, ammonium sulfate, Superdex 75, HI-Propyl, SP-Sepharose
-
recomninant PTH from Escherichia coli strain XL 1-Blue 8500fold by ultracentrifugation, heat treatment, ammonium sulfate fractionation, gel filtration, hydrophobic interaction chromatography, and ion exchange chromatography to homogeneity
-
wild-type and mutant enzymes
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
pth2 gene, expression in Escherichia coli
expression in Escherichia coli
-
gene SS00175, DNA and amino acid sequence determination and analysis, complementation of an enzyme-deficient Escherichia coli mutant strain, and of two Saccharomyces cerevisiae gene YHR189w or YBL057c disruption mutants, overview, expression of PTH in Escherichia coli strain XL 1-Blue
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
Fromant, M.; Scvhmitt, E.; Mechulam, Y.; Lazennec, C.; Plateau, P.; Blanquet, S.
Crystal structure at 1.8 A resolution and identification of active site residues of Sulfolobus solfataricus peptidyl-tRNA hydrolase
Biochemistry
44
4292-4301
2005
Saccharolobus solfataricus
-
Manually annotated by BRENDA team
Fromant, M.; Schmitt, E.; Mechulam, Y.; Lazennec, C.; Plateau, P.; Blanquet, S.
Crystal structure at 1.8 A resolution and identification of active site residues of Sulfolobus solfataricus peptidyl-tRNA hydrolase
Biochemistry
44
4294-4301
2005
Saccharolobus solfataricus (Q980V1), Saccharolobus solfataricus
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team