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Conformational switch in the decoding region of 16S rRNA during aminoacyl-tRNA selection on the ribosome

Nature Structural Biology volume 7, pages 104–107 (2000)Cite this article

Abstract

Binding of aminoglycoside antibiotics to 16S ribosomal RNA induces a particular structure of the decoding center and increases the misincorporation of near-cognate amino acids. By kinetic analysis we show that this is due to stabilization of the near-cognate codon recognition complex and the acceleration of two rearrangements that limit the rate of amino acid incorporation. The same rearrangement steps are accelerated in the cognate coding situation. We suggest that cognate codon recognition, or near-cognate codon recognition augmented by aminoglycoside binding, promote the transition of 16S rRNA from a ‘binding’ to a ‘productive’ conformation that determines the fidelity of decoding.

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Figure 1: Kinetic scheme of aa-tRNA binding to the ribosomal A site.
Figure 2: Paromomycin effect on GTP hydrolysis.
Figure 3: Kinetics of Leu 2 binding in the presence of paromomycin.

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Acknowledgements

We thank J.D. Puglisi for valuable comments on the manuscript; C. Gualerzi and R. Spurio for overproducing strains and mRNA constructs; Yu. Semenkov and V. Katunin for tRNA preparations; D. Rodnin for computer programming; P. Striebeck for expert technical assistance. The work was supported by the Deutsche Forschungsgemeinschaft, the Alfried Krupp von Bohlen und Halbach-Stiftung, and the Fonds der Chemischen Industrie. T.P. acknowledges a fellowship of the Werner Richard-Dr. Carl Dörken-Stiftung.

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  1. Institute of Molecular Biology, University of Witten/Herdecke, Witten, 58448, Germany

    Tillmann Pape, Wolfgang Wintermeyer & Marina V. Rodnina

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  1. Tillmann Pape
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  2. Wolfgang Wintermeyer
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  3. Marina V. Rodnina
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Correspondence to Marina V. Rodnina.

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Pape, T., Wintermeyer, W. & Rodnina, M. Conformational switch in the decoding region of 16S rRNA during aminoacyl-tRNA selection on the ribosome. Nat Struct Mol Biol 7, 104–107 (2000). https://doi.org/10.1038/72364

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