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This Article OPEN ACCESS ARTICLE Full Text (PDF) All Versions of this Article: rna.942308v1 14/6/1048    most recent Alert me when this article is cited Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Google Scholar Articles by Fedorova, O. Articles by Pyle, A. M. PubMed PubMed Citation Articles by Fedorova, O. Articles by Pyle, A. M. Social Bookmarking                   What's this?

A conserved element that stabilizes the group II intron active site

¹ Howard Hughes Medical Institute at Yale, Yale University, New Haven, Connecticut 06520, USA
² Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA

The internal loop at the base of domain 3 (D3) is one of the most conserved and catalytically important elements of a group II intron. However, the location and molecular nature of its tertiary interaction partners has remained unknown. By employing a combination of site-directed photo-cross-linking and nucleotide analog interference suppression (NAIS), we show that the domain 3 internal loop (D3IL) interacts with the -' duplex, which is an active-site element located near the 5'-splice site in D1. Our data also suggest that the D3IL may interact with the bulge of D5, which is a critical active site component. The results of this and other recent studies indicate that the D3IL participates in a complex network of tertiary interactions involving -', the bulge of D5 and J23, and that it helps to optimize active site architecture by supporting interactions among these catalytic motifs. Our results are consistent with the role of D3 as a catalytic effector that enhances intron reactivity through active site stabilization.

Keywords: ribozyme; splicing; catalysis; tertiary structure

Reprint requests to: Anna Marie Pyle, Department of Molecular Biophysics and Biochemistry, 266 Whitney Avenue, Box 208114, Yale University, New Haven, CT 06520, USA; e-mail: anna.pyle{at}yale.edu; fax: (203) 432-5316.

Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.942308.

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