SNAP annotations: PDB entry 1vy7

PDB-id

1vy7; DSSR-derived features in text and JSON formats; DNAproDB

Class

ribosome

Method

X-ray (2.8 Å)

Summary

Crystal structure of the thermus thermophilus 70s ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic cytidine-cytidine-puromycin in the a site and acylated trna in the p site.

Reference

Polikanov YS, Steitz TA, Innis CA (2014): "A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome." Nat.Struct.Mol.Biol., 21, 787-793. doi: 10.1038/nsmb.2871.

Abstract

During peptide-bond formation on the ribosome, the α-amine of an aminoacyl-tRNA attacks the ester carbonyl carbon of a peptidyl-tRNA to yield a peptide lengthened by one amino acid. Although the ribosome's contribution to catalysis is predominantly entropic, the lack of high-resolution structural data for the complete active site in complex with full-length ligands has made it difficult to assess how the ribosome might influence the pathway of the reaction. Here, we present crystal structures of preattack and postcatalysis complexes of the Thermus thermophilus 70S ribosome at ~2.6-Å resolution. These structures reveal a network of hydrogen bonds along which proton transfer could take place to ensure the concerted, rate-limiting formation of a tetrahedral intermediate. We propose that, unlike earlier models, the ribosome and the A-site tRNA facilitate the deprotonation of the nucleophile through the activation of a water molecule.