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The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome

Nature Structural & Molecular Biology volume 17, pages 289–293 (2010)Cite this article

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Abstract

Viomycin and capreomycin belong to the tuberactinomycin family of antibiotics, which are among the most effective antibiotics against multidrug-resistant tuberculosis. Here we present two crystal structures of the 70S ribosome in complex with three tRNAs and bound to either viomycin or capreomycin at 3.3- and 3.5-Å resolution, respectively. Both antibiotics bind to the same site on the ribosome, which lies at the interface between helix 44 of the small ribosomal subunit and helix 69 of the large ribosomal subunit. The structures of these complexes suggest that the tuberactinomycins inhibit translocation by stabilizing the tRNA in the A site in the pretranslocation state. In addition, these structures show that the tuberactinomycins bind adjacent to the binding sites for the paromomycin and hygromycin B antibiotics, which may enable the development of new derivatives of tuberactinomycins that are effective against drug-resistant strains.

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Figure 1: Chemical structure of the tuberactinomycins.
Figure 2: Binding site of viomycin and capreomycin.
Figure 3: Overlapping binding sites.

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Acknowledgements

We thank the staffs at the Advanced Photon Source beamline 24-ID and at the National Synchrotron Light Source beamline X29 for help during data collection, the staff at the Center for Structural Biology at Yale University for computational support, I. Lomakin (Yale University) for providing us with methionyl-tRNA synthetase and U.L. RajBhandary (Massachusetts Institute of Technology), K.H. Nierhaus (Max-Planck-Institut für Molekulare Genetik), P. Nissen (Aarhaus University) and M. Sprinzl (University Bayreuth) for providing us with ET-Ts for the overexpression plasmids of methionyl-tRNA formyltransferase, initiator tRNA, EF-Tu and EF-Ts, respectively. This work was supported by the US National Institutes of Health grant GM 22778 to T.A.S.

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  1. Robin E Stanley

    Present address: Present address: Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA.,

  2. Robin E Stanley and Gregor Blaha: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA

    Robin E Stanley, Gregor Blaha, Robert L Grodzicki, Michael D Strickler & Thomas A Steitz

  2. Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA

    Robert L Grodzicki, Michael D Strickler & Thomas A Steitz

  3. Department of Chemistry, Yale University, New Haven, Connecticut, USA

    Thomas A Steitz

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Contributions

R.E.S. prepared and crystallized the complexes; R.E.S. and G.B. collected data and processed and refined X-ray data; G.B. and R.L.G. purified all components of complex; M.D.S. energy-minimized the initial tuberactinomycin structures and solved all computational problems related to the large size of the datasets and complexes; T.A.S., G.B. and R.E.S. contributed to the experimental design and analysis of the structure; T.A.S., G.B. and R.E.S. wrote the manuscript, on which all authors commented.

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Correspondence to Thomas A Steitz.

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Competing interests

T.A.S. owns stock in and is on the advisory board of Rib-X Pharmaceuticals, Inc., which does structure-based drug design targeted at the ribosome.

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Stanley, R., Blaha, G., Grodzicki, R. et al. The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome. Nat Struct Mol Biol 17, 289–293 (2010). https://doi.org/10.1038/nsmb.1755

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