1tob

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SACCHARIDE-RNA RECOGNITION IN AN AMINOGLYCOSIDE ANTIBIOTIC-RNA APTAMER COMPLEX, NMR, 7 STRUCTURES

Overview

BACKGROUND: Aminoglycoside antibiotics are known to target ribosomal, retroviral and catalytic RNAs with high affinity and specificity., Recently, in vitro selection experiments have identified RNA aptamers that, bind to aminoglycoside antibiotics with nanomolar affinity and stringent, specificity, allowing discrimination between closely related family, members. There has, to date, been limited structural information on the, molecular basis of such saccharide-RNA recognition. RESULTS: We describe a, solution-structure determination of the tobramycin-RNA aptamer complex, obtained using NMR and molecular dynamics. The structure gives insight, into the molecular features associated with saccharide-RNA recognition., Tobramycin adopts a defined alignment and binds to the RNA major groove, centered about a stem-loop junction site. A portion of the bound, tobramycin is encapsulated between the floor of the major groove and a, looped-out cytosine residue that forms a flap over the binding site in the, complex. CONCLUSIONS: The emergence of antibiotic-resistant pathogens and, their impact on human health continues to be a major concern in the, medical community. Rational modification of existing antibiotics aimed at, improving their efficacy requires a molecular view of their, receptor-binding sites. We have provided such a molecular view for a, member of the aminoglycoside antibiotic family that targets RNA.

About this Structure

1TOB is a Protein complex structure of sequences from [1] with TOA, TOC and TOB as ligands. Full crystallographic information is available from OCA.

Reference

Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex., Jiang L, Suri AK, Fiala R, Patel DJ, Chem Biol. 1997 Jan;4(1):35-50. PMID:9070426

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