title: Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions.
abstract: 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.
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Wasserman
authors.affiliation: 1] Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA [2] Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, USA.
authors.forename: Arto
authors.initials: A
authors.lastname: Pulk
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA.
authors.forename: Zhou
authors.initials: Z
authors.lastname: Zhou
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA.
authors.forename: Roger B
authors.initials: RB
authors.lastname: Altman
authors.affiliation: Tri-Institutional Training Program in Chemical Biology, Weill Cornell Medical College, Rockefeller University, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.
authors.forename: John C
authors.initials: JC
authors.lastname: Zinder
authors.affiliation: Department of Pharmaceutical Sciences, University of Kentucky College of Pharmacy, Lexington, Kentucky 40536, USA.
authors.forename: Keith D
authors.initials: KD
authors.lastname: Green
authors.affiliation: Department of Pharmaceutical Sciences, University of Kentucky College of Pharmacy, Lexington, Kentucky 40536, USA.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Garneau-Tsodikova
authors.affiliation: 1] Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA [2] Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, USA.
authors.forename: Jamie H Doudna
authors.initials: JH
authors.lastname: Cate
authors.affiliation: 1] Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA [2] Tri-Institutional Training Program in Chemical Biology, Weill Cornell Medical College, Rockefeller University, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.
authors.forename: Scott C
authors.initials: SC
authors.lastname: Blanchard
mesh_terms: D000617:Aminoglycosides / Q000378:metabolism / Q000494:pharmacology*; D000900:Anti-Bacterial Agents / Q000378:metabolism / Q000494:pharmacology*; D001665:Binding Sites; D004926:Escherichia coli; D029968:Escherichia coli Proteins / Q000187:drug effects / Q000378:metabolism; D005601:Framycetin / Q000378:metabolism / Q000494:pharmacology; D009355:Neomycin / Q000378:metabolism / Q000494:pharmacology; D010303:Paromomycin / Q000378:metabolism / Q000494:pharmacology; D012329:RNA, Bacterial / Q000187:drug effects* / Q000378:metabolism; D054681:Ribosome Subunits, Large, Bacterial / Q000187:drug effects* / Q000378:metabolism; D054680:Ribosome Subunits, Small, Bacterial / Q000187:drug effects* / Q000378:metabolism; D012270:Ribosomes / Q000187:drug effects / Q000378:metabolism; D012271:Ribostamycin / Q000378:metabolism / Q000494:pharmacology; D012399:Rotation
chemical_list: D000617:Aminoglycosides; D000900:Anti-Bacterial Agents; D029968:Escherichia coli Proteins; D012329:RNA, Bacterial; D012271:Ribostamycin; D005601:Framycetin; C488396:neamine; D010303:Paromomycin; D009355:Neomycin