Download MendeleyA pH controlled conformational switch in the cleavage site of the VS ribozyme substrate RNA.
Flinders, J., Dieckmann, T.(2001) J Mol Biol 308: 665-679
- PubMed: 11350168
- DOI: https://doi.org/10.1006/jmbi.2001.4627
- Primary Citation of Related Structures:
1HWQ - PubMed Abstract:
The VS ribozyme is a 154 nucleotide sequence found in certain natural strains of Neurospora. The RNA can be divided into a substrate and a catalytic domain. Here we present the solution structure of the substrate RNA that is cleaved in a trans reaction by the catalytic domain in the presence of Mg2+. The 30 nucleotide substrate RNA forms a compact helix capped by a flexible loop. The cleavage site bulge contains three non-canonical base-pairs, including an A+.C pair with a protonated adenine. This adenine (A622) is a pH controlled conformational switch that opens up the internal loop at higher pH. The possible significance of this switch for substrate recognition and cleavage is discussed.
Organizational Affiliation:
Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA.
