A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.

Publication Type:

Journal Article

Source:

Nat Struct Mol Biol, Volume 21, Issue 9, p.787-93 (2014)

Keywords:

Crystallography, X-Ray, Hydrogen Bonding, Models, Molecular, Peptides, Protons, Ribosomes, RNA, Transfer, Amino Acyl, Thermus thermophilus, Water

Abstract:

<p>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.</p>

PDB: 
4QCM 4QCN 4QCO 4QCP 4QCQ 4QCR 4QCS 4QCT 4QCU 4QCV 4QCW 4QCX 4QCY 4QCZ 4QD0 4QD1
Detector: 
Q315
Beamline: 
24-ID-C