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Nucleic Acids Research 2006 34(2):676-685; doi:10.1093/nar/gkj467
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Published online 1 February 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site

Jiro Kondo, Alexandre Urzhumtsev1 and Eric Westhof*

Institut de Biologie Moléculaire et Cellulaire, UPR9002 CNRS, Université Louis Pasteur 15 rue René Descartes, 67084 Strasbourg, France 1Faculté des Sciences, Université Henri Poincaré Vandoeuvre-lès-Nancy, 54506 Nancy, France

*To whom correspondence should be addressed. Tel: 33 3 88 41 70 46; Fax: 33 3 88 60 18 22; Email: E.Westhof{at}ibmc.u-strasbg.fr

Received December 19, 2005. Revised January 9, 2006. Accepted January 9, 2006.

The decoding A site of the small ribosomal subunit is an RNA molecular switch, which monitors codon–anticodon interactions to guarantee translation fidelity. We have solved the crystal structure of an RNA fragment containing two Homo sapiens cytoplasmic A sites. Each of the two A sites presents a different conformational state. In one state, adenines A1492 and A1493 are fully bulged-out with C1409 forming a wobble-like pair to A1491. In the second state, adenines A1492 and A1493 form non-Watson–Crick pairs with C1409 and G1408, respectively while A1491 bulges out. The first state of the eukaryotic A site is, thus, basically the same as in the bacterial A site with bulging A1492 and A1493. It is the state used for recognition of the codon/anticodon complex. On the contrary, the second state of the H.sapiens cytoplasmic A site is drastically different from any of those observed for the bacterial A site without bulging A1492 and A1493.


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