Structure of the A Site of Escherichia coli 16S Ribosomal RNA Complexed with an Aminoglycoside Antibiotic

Aminoglycoside antibiotics that bind to 30S ribosomal A-site RNA cause misreading of the genetic code and inhibit translocation. The aminoglycoside antibiotic paromomycin binds specifically to an RNA oligonucleotide that contains the 30S subunit A site, and the solution structure of the RNA-paromomycin complex was determined by nuclear magnetic resonance spectroscopy. The antibiotic binds in the major groove of the model A-site RNA within a pocket created by an A-A base pair and a single bulged adenine. Specific interactions occur between aminoglycoside chemical groups important for antibiotic activity and conserved nucleotides in the RNA. The structure explains binding of diverse aminoglycosides to the ribosome, their specific activity against prokaryotic organisms, and various resistance mechanisms, and provides insight into ribosome function.

[1]  J. Ninio.  Kinetic amplification of enzyme discrimination. , 1975, Biochimie.

[2]  D A Meyers,et al.  Major Susceptibility Locus for Prostate Cancer on Chromosome 1 Suggested by a Genome-Wide Search , 1996, Science.

[3]  S. Holbrook,et al.  Structure of an RNA double helix including uracil-uracil base pairs in an internal loop , 1995, Nature Structural Biology.

[4]  Dieter Söll,et al.  Trna: Structure, Biosynthesis, and Function , 1995 .

[5]  J. Santoro,et al.  A constant-time 2D overbodenhausen experiment for inverse correlation of isotopically enriched species , 1992 .

[6]  T. Cech,et al.  RNA substrate binding site in the catalytic core of the Tetrahymena ribozyme , 1992, Nature.

[7]  K. Muniyappa,et al.  Unwinding of heterologous DNA by RecA protein during the search for homologous sequences. , 1992, Journal of molecular biology.

[8]  Ernest Frederick Gale,et al.  The Molecular basis of antibiotic action , 1972 .

[9]  G. Varani,et al.  Structure of the P1 helix from group I self-splicing introns. , 1995, Journal of molecular biology.

[10]  L. Mueller,et al.  Improved RNA Structure Determination by Detection of NOE Contacts to Exchange-Broadened Amino Protons , 1995 .

[11]  J. Davies,et al.  Misreading of ribonucleic acid code words induced by aminoglycoside antibiotics. The effect of drug concentration. , 1968, The Journal of biological chemistry.

[12]  D. Crothers,et al.  Three-Dimensional Triple-Resonance 1H, 13C, 31P Experiment: Sequential Through-Bond Correlation of Ribose Protons and Intervening Phosphorus along the RNA Oligonucleotide Backbone , 1994 .

[13]  J. Wilhelm,et al.  Aminoglycoside antibiotics and eukaryotic protein synthesis: structure--function relationships in the stimulation of misreading with a wheat embryo system. , 1978, Biochemistry.

[14]  Harry F. Noller,et al.  Interaction of antibiotics with functional sites in 16S ribosomal RNA , 1987, Nature.

[15]  H. Noller,et al.  Interaction of antibiotics with A‐ and P‐site‐specific bases in 16S ribosomal RNA. , 1991, The EMBO journal.

[16]  J. Puglisi,et al.  Biochemical and NMR studies of RNA conformation with an emphasis on RNA pseudoknots. , 1995, Methods in enzymology.

[17]  L. Mueller,et al.  TRIPLE-RESONANCE EXPERIMENTS FOR ASSIGNMENT OF ADENINE BASE RESONANCES IN 13C/15N-LABELED RNA , 1996 .

[18]  Walter E. Hill,et al.  The Ribosome : structure, function, and evolution , 1990 .

[19]  M. Takanami.  Analysis of the 5'-terminal nucleotide sequences of ribonucleic acids. II. , 1967 .

[20]  D. Crothers,et al.  Correlation of adenine H2/H8 resonances in uniformly 13C labeled RNAs by 2D HCCH-TOCSY : a new tool for 1H assignment , 1994 .

[21]  J. Hopfield.  Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. , 1974, Proceedings of the National Academy of Sciences of the United States of America.

[22]  A. Gronenborn,et al.  Assignment of the side-chain proton and carbon-13 resonances of interleukin-1.beta. using double- and triple-resonance heteronuclear three-dimensional NMR spectroscopy , 1990 .

[23]  L. Kay,et al.  A pulsed field gradient isotope‐filtered 3D 13C HMQC‐NOESY experiment for extracting intermolecular NOE contacts in molecular complexes , 1994, FEBS letters.

[24]  T. Pape,et al.  Initial Binding of the Elongation Factor Tu·GTP·Aminoacyl-tRNA Complex Preceding Codon Recognition on the Ribosome (*) , 1996, The Journal of Biological Chemistry.

[25]  J. Gallant,et al.  Mistranslation in E. coli , 1977, Cell.

[26]  H. Noller,et al.  Binding of tRNA to the ribosomal A and P sites protects two distinct sets of nucleotides in 16 S rRNA. , 1990, Journal of molecular biology.

[27]  D. Reid,et al.  A proton and carbon 13 nuclear magnetic resonance study of neomycin B and its interactions with phosphatidylinositol 4,5-bisphosphate. , 1987, The Journal of biological chemistry.

[28]  S. Stern,et al.  Interactions of a small RNA with antibiotic and RNA ligands of the 30S subunit , 1994, Nature.

[29]  A. Dahlberg,et al.  Effects of mutagenesis of a conserved base-paired site near the decoding region of Escherichia coli 16 S ribosomal RNA. , 1990, Journal of molecular biology.

[30]  J. Davies,et al.  Structure-Activity Relationships Among the Aminoglycoside Antibiotics: Role of Hydroxyl and Amino Groups , 1973, Antimicrobial Agents and Chemotherapy.