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Nucleic Acids Research 2005 33(19):6418-6425; doi:10.1093/nar/gki927
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Published online 10 November 2005

© The Author 2005. 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

Invariant amino acids essential for decoding function of polypeptide release factor eRF1

Petr Kolosov, Ludmila Frolova, Alim Seit-Nebi, Vera Dubovaya, Artem Kononenko, Nina Oparina, Just Justesen1, Alexandr Efimov2 and Lev Kisselev*

Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences 119991 Moscow, Russia 1Institute of Molecular Biology, Aarhus University Denmark 2Institute of Protein Research Pustchino, 142290 Moscow Region, Russia

*To whom correspondence should be addressed. Tel: +7 095 1356009; Fax: +7 095 1351405; Email: kissel{at}eimb.relarn.ru

Received August 22, 2005. Revised October 8, 2005. Accepted October 8, 2005.

In eukaryotic ribosome, the N domain of polypeptide release factor eRF1 is involved in decoding stop signals in mRNAs. However, structure of the decoding site remains obscure. Here, we specifically altered the stop codon recognition pattern of human eRF1 by point mutagenesis of the invariant Glu55 and Tyr125 residues in the N domain. The 3D structure of generated eRF1 mutants was not destabilized as demonstrated by calorimetric measurements and calculated free energy perturbations. In mutants, the UAG response was most profoundly and selectively affected. Surprisingly, Glu55Arg mutant completely retained its release activity. Substitution of the aromatic ring in position 125 reduced response toward all stop codons. This result demonstrates the critical importance of Tyr125 for maintenance of the intact structure of the eRF1 decoding site. The results also suggest that Tyr125 is implicated in recognition of the 3d stop codon position and probably forms an H-bond with Glu55. The data point to a pivotal role played by the YxCxxxF motif (positions 125–131) in purine discrimination of the stop codons. We speculate that eRF1 decoding site is formed by a 3D network of amino acids side chains.

Present address: Alim Seit-Nebi, The Scripps Research Institute, La Jolla, USA

The authors dedicate this paper to the memory of Jens Nyborg to acknowledge his significant contribution to the structural biology of translation factors. We cordially thank Jens for his friendship and kindness


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