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Information on EC 3.1.1.29 - aminoacyl-tRNA hydrolase and Organism(s) Vibrio cholerae serotype O1 and UniProt Accession Q9KQ21
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3.1.1.29 aminoacyl-tRNA hydrolaseSpecify your search results
Word Map
- 3.1.1.29
- peptidyl-trnas
- aminoacyl-trnas
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drop-off
- trnalys
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infantile-onset
- drug development
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, 
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topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
aminoacyl-transfer ribonucleate hydrolase
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hydrolase, aminoacyl-transfer ribonucleate
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N-substituted aminoacyl transfer RNA hydrolase
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peptidyl-tRNA hydrolase
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PTH
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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
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
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
backbone dynamics of VcPth and its mutants, NMR and molecular dynamics simulation, overview
physiological function
additional information
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
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
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
42.9 - 55.6
thermal stabilities of wild-type VcPth and its mutants, overview. Melting temperatures (Tm) for wild-type VcPth, and mutants N14D, H24N, N72D, D97N, and N118D are 52.08°C, 46.18°C, 48.62°C, 52.06°C, 42.93°C, and 55.56°C, respectively
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by two steps of nickel affinity chromatography, followed by gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene pth, recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Shahid, S.; Kabra, A.; Mundra, S.; Pal, R.K.; Tripathi, S.; Jain, A.; Arora, A.
Role of methionine 71 in substrate recognition and structural integrity of bacterial peptidyl-tRNA hydrolase
Biochim. Biophys. Acta
1866
865-874
2018
Vibrio cholerae serotype O1 (Q9KQ21), Vibrio cholerae serotype O1 El Tor Inaba N16961 (Q9KQ21), Vibrio cholerae serotype O1 ATCC 39315 (Q9KQ21)
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Release 2023.1 (January 2023)
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