PAROMOMYCIN BINDING INDUCES A LOCAL CONFORMATIONAL CHANGE IN THE A-SITE OF 16-S RIBOSOMAL-RNA

Aminoglycoside antibiotics that bind to ribosomal RNA in the aminoacyl -tRNA site (A-site) cause misreading of the genetic code and inhibit t ranslocation. An A-site RNA oligonucleotide specifically binds to amin oglycoside antibiotics and the structure of the RNA-paromomycin comple x was previously determined by nuclear magnetic resonance (NMR) spectr oscopy. Here, the A-site RNA structure in its free form has been deter mined using heteronuclear NMR and compared to the structure of the par omomycin-RNA complex. As in the complex with paromomycin, the asymmetr ic internal loop is closed by a Watson-Crick base-pair (C1407.G1494) a nd by two non-canonical base-pairs (U1406.U1495, A1408.A1493). A1492 s tacks below A1493 and is intercalated between the upper and lower stem s. The comparison of the free and bound conformations of the RNA shows that two universally conserved residues of the A site of 16 S rRNA, A 1492 and A1493, are displaced towards the minor groove of the RNA heli x in presence of antibiotic. These changes in the RNA conformation pla ce the N1 positions of A1492 and A1493 on the minor groove side of the A-site RNA and suggest a mechanism of action of aminoglycosides on tr anslation. (C) 1998 Academic Press Limited.