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Please use this identifier to cite or link to this item: http://repository.li.mahidol.ac.th/dspace/handle/123456789/27198
Title: Snapshots of dynamics in synthesizing N<sup>6</sup>-isopentenyladenosine at the tRNA anticodon
Authors: Sarin Chimnaronk
Farhad Forouhar
Junichi Sakai
Min Yao
Cecile M. Tron
Mohamed Atta
Marc Fontecave
John F. Hunt
Isao Tanaka
Hokkaido University
Columbia University in the City of New York
Universite Grenoble Alpes
Mahidol University
Keywords: Biochemistry, Genetics and Molecular Biology
Issue Date: 16-Jun-2009
Citation: Biochemistry. Vol.48, No.23 (2009), 5057-5065
Abstract: Bacterial and eukaryotic tRNAs that decode codons starting with uridine have a hydrophobically hypermodified adenosine at position 37 (A37) adjacent to the 3′-end of the anticodon, which is essential for efficient and highly accurate protein translation by the ribosome. However, it remains unclear as to how the corresponding tRNAs are selected to be modified by alkylation at the correct position of the adenosine base. We have determined a series of crystal structures of bacterial tRNA isopentenyltransferase (MiaA) in apo- and tRNA-bound forms, which completely render snapshots of substrate selections during the modification of RNA. A compact evolutionary inserted domain (herein swinging domain) in MiaA that exhibits as a highly mobile entity moves around the catalytic domain as likely to reach and trap the tRNA substrate. Thereby, MiaA clamps the anticodon stem loop of the tRNA substrate between the catalytic and swinging domains, where the two conserved elongated residues from the swinging domain pinch the two flanking A36and A38together to squeeze out A37into the reaction tunnel. The site-specific isopentenylation of RNA is thus ensured by a characteristic pinch-and-flip mechanism and by a reaction tunnel to confine the substrate selection. Furthermore, combining information from soaking experiments with structural comparisons, we propose a mechanism for the ordered substrate binding of MiaA. © 2009 American Chemical Society.
URI: https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=67049154309&origin=inward
http://repository.li.mahidol.ac.th/dspace/handle/123456789/27198
ISSN: 00062960
Appears in Collections:Scopus 2006-2010

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