Literature summary for 3.1.1.29 extracted from

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 (2018), Biochim. Biophys. Acta, 1866, 865-874 .

Cloned(Commentary)

Cloned (Comment)	Organism
gene pth, recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)	Vibrio cholerae serotype O1

Crystallization (Commentary)

Crystallization (Comment)	Organism
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	Vibrio cholerae serotype O1

Crystallization (Comment)

Organism

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

Vibrio cholerae serotype O1

Protein Variants

Protein Variants	Comment	Organism
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	Vibrio cholerae serotype O1

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
peptidyl-tRNA + H2O	Vibrio cholerae serotype O1	-	peptide + tRNA	-	?
peptidyl-tRNA + H2O	Vibrio cholerae serotype O1 El Tor Inaba N16961	-	peptide + tRNA	-	?
peptidyl-tRNA + H2O	Vibrio cholerae serotype O1 ATCC 39315	-	peptide + tRNA	-	?

Organism

Organism	UniProt	Comment	Textmining
Vibrio cholerae serotype O1	Q9KQ21	-	-
Vibrio cholerae serotype O1 ATCC 39315	Q9KQ21	-	-
Vibrio cholerae serotype O1 El Tor Inaba N16961	Q9KQ21	-	-

Purification (Commentary)

Purification (Comment)	Organism
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	Vibrio cholerae serotype O1

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
peptidyl-tRNA + H2O	-	Vibrio cholerae serotype O1	peptide + tRNA	-	?
peptidyl-tRNA + H2O	-	Vibrio cholerae serotype O1 El Tor Inaba N16961	peptide + tRNA	-	?
peptidyl-tRNA + H2O	-	Vibrio cholerae serotype O1 ATCC 39315	peptide + tRNA	-	?

Subunits

Subunits	Comment	Organism
More	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	Vibrio cholerae serotype O1

Synonyms

Synonyms	Comment	Organism
peptidyl-tRNA hydrolase	-	Vibrio cholerae serotype O1
PTH	-	Vibrio cholerae serotype O1
VcPth	-	Vibrio cholerae serotype O1
VC_2184	-	Vibrio cholerae serotype O1

General Information

General Information	Comment	Organism
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	Vibrio cholerae serotype O1
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	Vibrio cholerae serotype O1