title: Aminoglycoside binding displaces a divalent metal ion in a tRNA-neomycin B complex.
abstract: Aminoglycosides bind to RNA and interfere with its function, and it has been suggested that aminoglycoside binding to RNA displaces essential divalent metal ions. Here we demonstrate that addition of various aminoglycosides inhibited Pb2+-induced cleavage of yeast tRNA(Phe). Cocrystallization of yeast tRNA(Phe) and an aminoglycoside, neomycin B, resulted in crystals that diffracted to 2.6 A and the structure of the complex was solved by molecular replacement. The structure shows that the neomycin B binding site overlaps with known divalent metal ion binding sites in yeast tRNA(Phe), providing direct evidence for the hypothesis that aminoglycosides displace metal ions. Additionally, the neomycin B binding site overlaps with major determinants for Escherichia coli phenylalanyl-tRNA-synthetase. Here we present data demonstrating that addition of neomycin B inhibited aminoacylation of E. coli tRNA(Phe) in the mid microM range. Given that aminoglycoside and metal ion binding sites overlap, we discuss that aminoglycosides can be considered as 'metal mimics'.
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University, Box 596, Biomedical Center, SE-751 24, Uppsala, Sweden.
authors.forename: N E
authors.initials: NE
authors.lastname: Mikkelsen
authors.forename: K
authors.initials: K
authors.lastname: Johansson
authors.forename: A
authors.initials: A
authors.lastname: Virtanen
authors.forename: L A
authors.initials: LA
authors.lastname: Kirsebom
mesh_terms: D000215:Acylation; D000900:Anti-Bacterial Agents / Q000737:chemistry* / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites; D002413:Cations, Divalent / Q000037:antagonists & inhibitors* / Q000378:metabolism; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000201:enzymology; D005601:Framycetin / Q000737:chemistry* / Q000378:metabolism*; D006860:Hydrogen Bonding; D007854:Lead / Q000037:antagonists & inhibitors* / Q000378:metabolism; D008958:Models, Molecular; D018716:Molecular Mimicry; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010652:Phenylalanine-tRNA Ligase / Q000737:chemistry / Q000378:metabolism; D012331:RNA, Fungal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012360:RNA, Transfer, Phe / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015003:Yeasts / Q000235:genetics
chemical_list: D000900:Anti-Bacterial Agents; D002413:Cations, Divalent; D012331:RNA, Fungal; D012360:RNA, Transfer, Phe; D007854:Lead; D005601:Framycetin; D010652:Phenylalanine-tRNA Ligase