1I9V

CRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEX

Summary for 1I9V

• Entry DOI: 10.2210/pdb1i9v/pdb
• Descriptor: PHENYLALANINE TRANSFER RNA, NEOMYCIN, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: amino-acid transport, yeast, phe-trna, phenylalanine, transfer rna, aminoglycoside, neomycin b, rna
• Biological source: Saccharomyces cerevisiae (baker's yeast)
• Total number of polymer chains: 1
• Total formula weight: 25445.40

Authors

Mikkelsen, N.E.,Johansson, K.,Virtanen, A.,Kirsebom, L.A. (deposition date: 2001-03-21, release date: 2001-06-04, Last modification date: 2023-09-20)

Primary citation

Mikkelsen, N.E.,Johansson, K.,Virtanen, A.,Kirsebom, L.A.
Aminoglycoside binding displaces a divalent metal ion in a tRNA-neomycin B complex.
Nat.Struct.Biol., 8:510-514, 2001

PubMed 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'.

PubMed: 11373618
DOI: 10.1038/88569

Experimental method

X-RAY DIFFRACTION (2.6 Å)