1A3M

PAROMOMYCIN BINDING INDUCES A LOCAL CONFORMATIONAL CHANGE IN THE A SITE OF 16S RRNA, NMR, 20 STRUCTURES

Summary for 1A3M

• Entry DOI: 10.2210/pdb1a3m/pdb
• Descriptor: 16S RRNA (5'-R(*GP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*UP*UP*C)-3'), 16S RRNA (5'-R(*GP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*C)-3') (2 entities in total)
• Functional Keywords: ribosomal rna complex, decoding region, rna-ligand interaction, rna
• Total number of polymer chains: 2
• Total formula weight: 8611.22

Authors

Fourmy, D.,Yoshizawa, S.,Puglisi, J.D. (deposition date: 1998-01-22, release date: 1998-04-29, Last modification date: 2024-05-22)

Primary citation

Fourmy, D.,Yoshizawa, S.,Puglisi, J.D.
Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA.
J.Mol.Biol., 277:333-345, 1998

PubMed Abstract: Aminoglycoside antibiotics that bind to ribosomal RNA in the aminoacyl-tRNA site (A-site) cause misreading of the genetic code and inhibit translocation. An A-site RNA oligonucleotide specifically binds to aminoglycoside antibiotics and the structure of the RNA-paromomycin complex was previously determined by nuclear magnetic resonance (NMR) spectroscopy. Here, the A-site RNA structure in its free form has been determined using heteronuclear NMR and compared to the structure of the paromomycin-RNA complex. As in the complex with paromomycin, the asymmetric internal loop is closed by a Watson-Crick base-pair (C1407.G1494) and by two non-canonical base-pairs (U1406.U1495, A1408.A1493). A1492 stacks below A1493 and is intercalated between the upper and lower stems. 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, A1492 and A1493, are displaced towards the minor groove of the RNA helix in presence of antibiotic. These changes in the RNA conformation place 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 translation.

PubMed: 9514734
DOI: 10.1006/jmbi.1997.1551

Experimental method

SOLUTION NMR