Dynamic remodelling of intersubunit bridge B2, a conserved RNA domain of the bacterial ribosome connecting helices 44 (h44) and 69 (H69) of the small and large subunit, respectively, impacts translation by controlling intersubunit rotation. Here we show that aminoglycosides chemically related to neomycin-paromomycin, ribostamycin and neamine-each bind to sites within h44 and H69 to perturb bridge B2 and affect subunit rotation. Neomycin and paromomycin, which only differ by their ring-I 6'-polar group, drive subunit rotation in opposite directions. This suggests that their distinct actions hinge on the 6'-substituent and the drug's net positive charge. By solving the crystal structure of the paromomycin-ribosome complex, we observe specific contacts between the apical tip of H69 and the 6'-hydroxyl on paromomycin from within the drug's canonical h44-binding site. These results indicate that aminoglycoside actions must be framed in the context of bridge B2 and their regulation of subunit rotation.

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Published in Nature Communications, v. 6, article 7896, p. 1-12.

© 2015 Macmillan Publishers Limited. All rights reserved.

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This work was supported by the US National Institutes of Health (2R01GM079238 to S.C.B., 1R01GM65050 to J.H.D.C., 1R01AI090048 to S.G.-T. and National Cancer Institute grant CA92584 for the SIBYLS and 8.3.1 beamlines at the Advanced Light Source (ALS), Lawrence Berkeley National Laboratory), the Human Frontiers in Science Program (RGY0088), the National Science Foundation (0644129) and the US Department of Energy (DE-AC0376SF00098 for the SIBYLS and 8.3.1 beamlines at the ALS, Lawrence Berkeley National Laboratory).

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Supplementary Figures 1-14, Supplementary Table 1 and Supplementary References