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Nucleic Acids Research 2006 34(4):1158-1165; doi:10.1093/nar/gkj508
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Published online 22 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

Molecular localization of a ribosome-dependent ATPase on Escherichia coli ribosomes

J. Xu, M. C. Kiel1, A. Golshani2, J. G. Chosay3, H. Aoki and M. C. Ganoza*

Banting and Best Department of Medical Research, University of Toronto 112 College Street, Toronto, Ontario, Canada M5G 1L6 1Science Department, Marywood University 2300 Adams Avenue, Scranton, PA 18509, USA 2Department of Science, Carleton University 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6 3Pfizer Pharmaceuticals 5/MS-1, 2800 Plymouth Road, Ann Arbor, MI 48105, USA

*To whom correspondence should be addressed. Tel: +1 416 978 8918; Fax: +1 416 978 8528; Email: m.ganoza{at}utoronta.ca

Received October 5, 2005. Revised January 15, 2006. Accepted January 27, 2006.

We have previously isolated and described an Escherichia coli ribosome-bound ATPase, RbbA, that is required for protein synthesis in the presence of ATP, GTP and the elongation factors, EF-Tu and EF-G. The gene encoding RbbA, yhih, has been cloned and the deduced protein sequence harbors two ATP-motifs and one RNA-binding motif and is homologous to the fungal EF-3. Here, we describe the isolation and assay of a truncated form of the RbbA protein that is stable to overproduction and purification. Chemical protection results show that the truncated RbbA specifically protects nucleotide A937 on the 30S subunit of ribosomes, and the protected site occurs at the E-site where the tRNA is ejected upon A-site occupation. Other weakly protected bases in the region occur at or near the mRNA binding site. Using radiolabeled tRNAs, we study the stimulating effect of this truncated RbbA on the binding and release of different tRNAs bound to the (aminoacyl) A-, (peptidyl) P- and (exit) E-sites of 70S ribosomes. The combined data suggest plausible mechanisms for the function of RbbA in translation.


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