1VY4

Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing acylated tRNA-substrates in the A and P sites.

This is a non-PDB format compatible entry.

Summary for 1VY4

• Entry DOI: 10.2210/pdb1vy4/pdb
• Descriptor: 16S Ribosomal RNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... (61 entities in total)
• Functional Keywords: 70s, ribosome, translation, peptydil transfer reaction, proton transfer mechanism, acylated trna
• Biological source: Escherichia coli; More
• Total number of polymer chains: 112
• Total formula weight: 4551990.81

Authors

Polikanov, Y.S.,Steitz, T.A.,Innis, C.A. (deposition date: 2014-05-13, release date: 2014-08-20, Last modification date: 2023-12-27)

Primary citation

Polikanov, Y.S.,Steitz, T.A.,Innis, C.A.
A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.
Nat.Struct.Mol.Biol., 21:787-793, 2014

PubMed 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.

PubMed: 25132179
DOI: 10.1038/nsmb.2871

Experimental method

X-RAY DIFFRACTION (2.6 Å)