Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions

Michael R. Wasserman, Arto Pulk, Zhou Zhou, Roger B. Altman, John C. Zinder, Keith D. Green, Sylvie Garneau-Tsodikova, Jamie H. Doudna Cate, Scott C. Blanchard

Research output: Contribution to journalArticlepeer-review

47 Scopus citations


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 drugâ €™ 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 drugâ €™ 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.

Original languageEnglish
Article number7896
JournalNature Communications
StatePublished - Jul 30 2015

Bibliographical note

Funding Information:
We thank R. Green (Johns Hopkins University) for providing the S13 knockout strain, P. Schultz for providing the L5 knockout strain (Scripps Research Institute), T. Suzuki (University of Tokyo) for providing the pKK3535 ribosome plasmids, D. Crish (Wayne State University) for providing 6′-deoxy-paromomycin and M. O’Connor (University of Missouri-Kansas City) for helpful discussions throughout the course of this work. We also acknowledge helpful discussions and insights provided by all members of the Blanchard and Cate laboratories and J. Headd (Lawrence Berkeley National Laboratory) for help with PHENIX refinement. 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).

ASJC Scopus subject areas

  • General Chemistry
  • General Biochemistry, Genetics and Molecular Biology
  • General Physics and Astronomy


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