title: Structures of the orthosomycin antibiotics avilamycin and evernimicin in complex with the bacterial 70S ribosome.
abstract: The ribosome is one of the major targets for therapeutic antibiotics; however, the rise in multidrug resistance is a growing threat to the utility of our current arsenal. The orthosomycin antibiotics evernimicin (EVN) and avilamycin (AVI) target the ribosome and do not display cross-resistance with any other classes of antibiotics, suggesting that they bind to a unique site on the ribosome and may therefore represent an avenue for development of new antimicrobial agents. Here we present cryo-EM structures of EVN and AVI in complex with the Escherichia coli ribosome at 3.6- to 3.9-Å resolution. The structures reveal that EVN and AVI bind to a single site on the large subunit that is distinct from other known antibiotic binding sites on the ribosome. Both antibiotics adopt an extended conformation spanning the minor grooves of helices 89 and 91 of the 23S rRNA and interacting with arginine residues of ribosomal protein L16. This binding site overlaps with the elbow region of A-site bound tRNA. Consistent with this finding, single-molecule FRET (smFRET) experiments show that both antibiotics interfere with late steps in the accommodation process, wherein aminoacyl-tRNA enters the peptidyltransferase center of the large ribosomal subunit. These data provide a structural and mechanistic rationale for how these antibiotics inhibit the elongation phase of protein synthesis.
authors.affiliation: Gene Center and Department for Biochemistry, University of Munich, 81377 Munich, Germany;
authors.forename: Stefan
authors.initials: S
authors.lastname: Arenz
authors.affiliation: Department of Physiology and Biophysics, Weill Medical College, Cornell University, New York, NY 10065;
authors.forename: Manuel F
authors.identifier: 0000-0002-8760-8080
authors.initials: MF
authors.lastname: Juette
authors.affiliation: Gene Center and Department for Biochemistry, University of Munich, 81377 Munich, Germany;
authors.forename: Michael
authors.initials: M
authors.lastname: Graf
authors.affiliation: Gene Center and Department for Biochemistry, University of Munich, 81377 Munich, Germany;
authors.forename: Fabian
authors.initials: F
authors.lastname: Nguyen
authors.affiliation: Gene Center and Department for Biochemistry, University of Munich, 81377 Munich, Germany;
authors.forename: Paul
authors.initials: P
authors.lastname: Huter
authors.affiliation: Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607; wilson@lmb.uni-muenchen.de yuryp@uic.edu scb2005@med.cornell.edu.
authors.forename: Yury S
authors.initials: YS
authors.lastname: Polikanov
authors.affiliation: Department of Physiology and Biophysics, Weill Medical College, Cornell University, New York, NY 10065; wilson@lmb.uni-muenchen.de yuryp@uic.edu scb2005@med.cornell.edu.
authors.forename: Scott C
authors.initials: SC
authors.lastname: Blanchard
authors.affiliation: Gene Center and Department for Biochemistry, University of Munich, 81377 Munich, Germany; Center for Integrated Protein Science Munich, University of Munich, 81377 Munich, Germany wilson@lmb.uni-muenchen.de yuryp@uic.edu scb2005@med.cornell.edu.
authors.forename: Daniel N
authors.initials: DN
authors.lastname: Wilson
mesh_terms: D000595:Amino Acid Sequence; D000617:Aminoglycosides / Q000494:pharmacology*; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001665:Binding Sites; D020285:Cryoelectron Microscopy; D004926:Escherichia coli; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009844:Oligosaccharides / Q000494:pharmacology*; D010441:Peptide Chain Elongation, Translational / Q000187:drug effects*; D054681:Ribosome Subunits, Large, Bacterial / Q000187:drug effects* / Q000648:ultrastructure; D000072760:Single Molecule Imaging
chemical_list: D000617:Aminoglycosides; D000900:Anti-Bacterial Agents; D009844:Oligosaccharides; C001202:evernimicin; C006653:avilamycin
keywords: Ziracin; antimicrobial; cryo-EM; everninomicin; rRNA