PDBsum entry 5b6j

Hydrolase

PDB id: 5b6j

Contents

Protein chains

196 a.a.

Waters ×107

PDB id:

5b6j

Name:

Hydrolase

Title:

Crystal structure of peptidyl-tRNA hydrolase mutant -h24n from vibrio cholerae

Structure:

Peptidyl-tRNA hydrolase. Chain: a, b. Synonym: pth. Engineered: yes. Mutation: yes

Source:

Vibrio cholerae. Organism_taxid: 345073. Strain: atcc 39541 / classical ogawa 395 / o395. Gene: pth, vc0395_a1761, vc395_2298. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.43Å R-factor: 0.188 R-free: 0.250

Authors:

S.Shahid,A.Kabra,R.K.Pal,A.Arora

Key ref:

A.Kabra et al. (2017). Unraveling the stereochemical and dynamic aspects of the catalytic site of bacterial peptidyl-tRNA hydrolase. Rna, 23, 202-216. PubMed id: 28096445

Date:

30-May-16 Release date: 12-Apr-17

Supersedes:

4y2z

Protein chains

A5F686  (PTH_VIBC3) -  Peptidyl-tRNA hydrolase from Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)

Seq: 196 a.a.

Struc: 196 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.1.29 - peptidyl-tRNA hydrolase.
• Reaction: an N-acyl-L-alpha-aminoacyl-tRNA + H2O = an N-acyl-L-amino acid + a tRNA + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

Rna 23:202-216 (2017)

PubMed id: 28096445

Unraveling the stereochemical and dynamic aspects of the catalytic site of bacterial peptidyl-tRNA hydrolase.

A.Kabra, S.Shahid, R.K.Pal, R.Yadav, S.V.Pulavarti, A.Jain, S.Tripathi, A.Arora.

ABSTRACT

Bacterial peptidyl-tRNA hydrolase (Pth; EC 3.1.1.29) hydrolyzes the peptidyl-tRNAs accumulated in the cytoplasm and thereby prevents cell death by alleviating tRNA starvation. X-ray and NMR studies of Vibrio cholerae Pth (VcPth) and mutants of its key residues involved in catalysis show that 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 α3 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. Overall, the dynamics of interactions between the side chains of N14, H24, D97, and N118, control the catalysis of substrate by this enzyme.