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Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome

Nature Structural & Molecular Biology volume 16, pages 528–533 (2009)Cite this article

Abstract

Protein synthesis is catalyzed in the peptidyl transferase center (PTC), located in the large (50S) subunit of the ribosome. No high-resolution structure of the intact ribosome has contained a complete active site including both A- and P-site tRNAs. In addition, although past structures of the 50S subunit have found no ordered proteins at the PTC, biochemical evidence suggests that specific proteins are capable of interacting with the 3′ ends of tRNA ligands. Here we present structures, at 3.6-Å and 3.5-Å resolution respectively, of the 70S ribosome in complex with A- and P-site tRNAs that mimic pre- and post-peptidyl-transfer states. These structures demonstrate that the PTC is very similar between the 50S subunit and the intact ribosome. They also reveal interactions between the ribosomal proteins L16 and L27 and the tRNA substrates, helping to elucidate the role of these proteins in peptidyl transfer.

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Figure 1: Ribosomal substrates in the peptidyl transferase center.
Figure 2: Interactions of the ribosomal substrates with the 23S RNA in the peptidyl transferase center.
Figure 3: Interactions of the ribosomal proteins L27 and L16 with the ribosomal substrates.

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Acknowledgements

We thank M. Schmeing for guidance with refinement and interpretation of the data, E. Stephens for mass spectrometry work, J.C. Cochrane for critical review of the manuscript, and M. Fuchs and C. Schulze-Briese for their advice and help with data collection at the Swiss Light Source. This work was supported by the Medical Research Council UK, the Wellcome Trust, the Agouron Institute and the Louis-Jeantet Foundation. R.M.V. is the recipient of a Gates-Cambridge scholarship.

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  1. Medical Research Council Laboratory of Molecular Biology, Cambridge, UK

    Rebecca M Voorhees, Albert Weixlbaumer, David Loakes, Ann C Kelley & V Ramakrishnan

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Correspondence to V Ramakrishnan.

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V.R. is on the Scientific Advisory Board of Rib-X Pharmaceuticals, a company involved in developing new antibiotics that target the ribosome.

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Supplementary Text and Figures

Supplementary Figures 1–3 (PDF 3253 kb)

Supplementary Video 1

Accommodation of the A-site tRNA. This movie models the conformational changes that occur within the 23S RNA upon A-site tRNA binding. The movie was made using coordinates from Selmer et al.1, which did not contain an A-site substrate within the PTC, and the pre-peptidyl transfer structure reported here, containing an ordered A-site tRNA within the PTC. 23S RNA is represented in cyan, A- and P-site tRNAs are modeled in green and red, respectively, and the A- and P-site amino acids are shown in yellow. (MOV 1224 kb)

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Voorhees, R., Weixlbaumer, A., Loakes, D. et al. Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome. Nat Struct Mol Biol 16, 528–533 (2009). https://doi.org/10.1038/nsmb.1577

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