SNAP output for PDB entry 1vq7 [SNAP web server]

PDB-id

1vq7; SNAP-derived features in text and JSON formats; DNAproDB

Class

ribosome

Method

X-ray (2.5 Å)

Summary

The structure of the transition state analogue "dca" bound to the large ribosomal subunit of haloarcula marismortui

Reference

Schmeing TM, Huang KS, Strobel SA, Steitz TA (2005): "An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA." Nature, 438, 520-524. doi: 10.1038/nature04152.

Abstract

The large ribosomal subunit catalyses the reaction between the alpha-amino group of the aminoacyl-tRNA bound to the A site and the ester carbon of the peptidyl-tRNA bound to the P site, while preventing the nucleophilic attack of water on the ester, which would lead to unprogrammed deacylation of the peptidyl-tRNA. Here we describe three new structures of the large ribosomal subunit of Haloarcula marismortui (Hma) complexed with peptidyl transferase substrate analogues that reveal an induced-fit mechanism in which substrates and active-site residues reposition to allow the peptidyl transferase reaction. Proper binding of an aminoacyl-tRNA analogue to the A site induces specific movements of 23S rRNA nucleotides 2618-2620 (Escherichia coli numbering 2583-2585) and 2541(2506), thereby reorienting the ester group of the peptidyl-tRNA and making it accessible for attack. In the absence of the appropriate A-site substrate, the peptidyl transferase centre positions the ester link of the peptidyl-tRNA in a conformation that precludes the catalysed nucleophilic attack by water. Protein release factors may also function, in part, by inducing an active-site rearrangement similar to that produced by the A-site aminoacyl-tRNA, allowing the carbonyl group and water to be positioned for hydrolysis.