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Literature summary for 3.1.1.29 extracted from

  • Kabra, A.; Shahid, S.; Pal, R.K.; Yadav, R.; Pulavarti, S.V.; Jain, A.; Tripathi, S.; Arora, A.
    Unraveling the stereochemical and dynamic aspects of the catalytic site of bacterial peptidyl-tRNA hydrolase (2017), RNA, 23, 202-216 .
    View publication on PubMedView publication on EuropePMC

Crystallization (Commentary)

Crystallization (Comment) Organism
analysis of VcPth crystal structure, PDB ID 4ZXP Vibrio cholerae serotype O1

Protein Variants

Protein Variants Comment Organism
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 Vibrio cholerae serotype O1
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 Vibrio cholerae serotype O1
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 Vibrio cholerae serotype O1
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 Vibrio cholerae serotype O1
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 Vibrio cholerae serotype O1

Localization

Localization Comment Organism GeneOntology No. Textmining
cytoplasm
-
Vibrio cholerae serotype O1 5737
-

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
peptidyl-tRNA + H2O Vibrio cholerae serotype O1
-
peptide + tRNA
-
?

Organism

Organism UniProt Comment Textmining
Vibrio cholerae serotype O1 Q9KQ21
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
peptidyl-tRNA + H2O
-
Vibrio cholerae serotype O1 peptide + tRNA
-
?

Synonyms

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

Temperature Stability [°C]

Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
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 Vibrio cholerae serotype O1

General Information

General Information Comment Organism
malfunction backbone dynamics of VcPth and its mutants, NMR and molecular dynamics simulation, overview Vibrio cholerae serotype O1
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 Vibrio cholerae serotype O1
physiological function bacterial peptidyl-tRNA hydrolase hydrolyzes the peptidyl-tRNAs accumulated in the cytoplasm and thereby preventing cell death by alleviating tRNA starvation Vibrio cholerae serotype O1