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Aminoglycoside binding displaces a divalent metal ion in a tRNA–neomycin B complex

Nature Structural Biology volume 8, pages 510–514 (2001)Cite this article

Abstract

Aminoglycosides bind to RNA and interfere with its function, and it has been suggested that aminoglycoside binding to RNA displaces essential divalent metal ions. Here we demonstrate that addition of various aminoglycosides inhibited Pb2+-induced cleavage of yeast tRNAPhe. Cocrystallization of yeast tRNAPhe and an aminoglycoside, neomycin B, resulted in crystals that diffracted to 2.6 Å and the structure of the complex was solved by molecular replacement. The structure shows that the neomycin B binding site overlaps with known divalent metal ion binding sites in yeast tRNAPhe, providing direct evidence for the hypothesis that aminoglycosides displace metal ions. Additionally, the neomycin B binding site overlaps with major determinants for Escherichia coli phenylalanyl-tRNA-synthetase. Here we present data demonstrating that addition of neomycin B inhibited aminoacylation of E. coli tRNAPhe in the mid μM range. Given that aminoglycoside and metal ion binding sites overlap, we discuss that aminoglycosides can be considered as 'metal mimics'.

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Figure 1: Structures of aminoglycosides and yeast tRNAPhe.
Figure 2: Aminoglycoside inhibition of Pb2+ cleavage and aminoacylation of tRNA.
Figure 3: Three dimensional structure of yeast tRNAPhe in complex with neomycin B.
Figure 4: Structural comparison of neomycin B bound to various RNA.

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Acknowledgements

We thank H. Eklund and D. Hughes for discussions and critical reading of the manuscript. We are also grateful to J. Davis for the generous gift of 5-epi-sisomicin. This work was supported by the Strategic Research Foundation and the Swedish Natural Science Research Council.

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Authors and Affiliations

  1. Department of Cell and Molecular Biology, Uppsala University, Box 596, Biomedical Center, Uppsala, SE-751 24, Sweden

    Nils E. Mikkelsen, Anders Virtanen & Leif A. Kirsebom

  2. Department of Molecular Biology, The Swedish Agricultural University, Box 580, Biomedical Center, Uppsala, SE-751 24, Sweden

    Kenth Johansson

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  1. Nils E. Mikkelsen
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Correspondence to Leif A. Kirsebom.

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Mikkelsen, N., Johansson, K., Virtanen, A. et al. Aminoglycoside binding displaces a divalent metal ion in a tRNA–neomycin B complex. Nat Struct Mol Biol 8, 510–514 (2001). https://doi.org/10.1038/88569

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