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

  title={Structure of the A Site of Escherichia coli 16S Ribosomal RNA Complexed with an Aminoglycoside Antibiotic},
  author={Dominique Fourmy and Michael I. Recht and Scott C. Blanchard and Joseph D. Puglisi},
  pages={1367 - 1371}
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… 
Structural origins of gentamicin antibiotic action
The structure of gentamicin leads to a general model for specific ribosome recognition by aminoglycoside antibiotics and a possible mechanism for translational inhibition and miscoding, and provides a structural rationale for chemical synthesis of novel am inoglycosides.
Structural origins of aminoglycoside specificity for prokaryotic ribosomes.
It is suggested that eukaryotic ribosomal RNA has a shallow binding pocket for aminoglycosides, which accommodates only certain antibiotics.
Binding of neomycin-class aminoglycoside antibiotics to the A-site of 16 S rRNA.
NMR data show that rings I and II of neomycin-class aminoglycosides are sufficient to confer specificity to the binding of the antibiotics to the model A-site RNA.
Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA.
Two universally conserved residues of the A site of 16 S rRNA, A1492 and A1493, are displaced towards the minor groove of the RNA helix in presence of antibiotic and changes in the RNA conformation suggest a mechanism of action of aminoglycosides on translation.
Basis for prokaryotic specificity of action of aminoglycoside antibiotics
The results indicate that the identity of the nucleotide at position 1408 is a major determinant of specificity of aminoglycoside action, and agree with prior structural studies of am inoglycosides–rRNA complexes.
Recognition of Cognate Transfer RNA by the 30S Ribosomal Subunit
Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved


Interactions of a small RNA with antibiotic and RNA ligands of the 30S subunit
It is reported here that an oligo-ribonucleotide analogue of the decoding region interacts with both antibiotic and RNA ligands of the 30S subunit in a manner that correlates with normal subunit function, suggesting that the intimidating structural complexity of the ribosome can be circumvented.
Interaction of antibiotics with functional sites in 16S ribosomal RNA
Chemical footprinting shows that several classes of antibiotics protect concise sets of highly conserved nucleotides in 16S ribosomal RNA when bound to ribosomes, having strong implications for the mechanism of action of these antibiotics and for the assignment of functions to specific structural features of 16S rRNA.
Interaction of antibiotics with A‐ and P‐site‐specific bases in 16S ribosomal RNA.
Surprisingly, myomycin fails to give strong protection of any bases in 16S rRNA, in spite of having an apparently identical target site and mode of action to streptomycin, which protects several bases in the 915 region, and these results suggest that the binding site(s) of strePTomycin andmyomycin have yet to be identified.
Structure of an RNA double helix including uracil-uracil base pairs in an internal loop
The crystal structure of the RNA dodecamer 5′-GGACUUUGGUCC-3′ has been determined from X-ray diffraction data to 2.6 Å resolution and illustrates a new form of RNA helix-helix interaction.
Structure of the P1 helix from group I self-splicing introns.
The upstream cleavage site of group I self-splicing introns is identified by an absolutely conserved U.G base-pair within a double helix, explaining the great stability of RNA UUCG loops when compared with DNA loops of identical sequence, and is one of the first NMR observations of RNA 2'-OH resonances.
RNA substrate binding site in the catalytic core of the Tetrahymena ribozyme
A conserved adenine in the catalytic core is identified that contributes to the stability of this arrangement and it is proposed that it accepts a hydrogen bond from a specific 2′-OH in P1.
Initial Binding of the Elongation Factor Tu·GTP·Aminoacyl-tRNA Complex Preceding Codon Recognition on the Ribosome (*)
It is suggested that codon-anticodon recognition, which takes place after the formation of the initial binding complex, provides a specific signal that triggers fast GTP hydrolysis by EF-Tu on the ribosome, which is strongly affected by the presence of the tRNA.