A pH Controlled Conformational Switch In the Cleavage Site of the VS Ribozyme Substrate RNA

Author： Flinders J.   Dieckmann T.  

Publisher： Academic Press

ISSN： 0022-2836

Source： Journal of Molecular Biology, Vol.308, Iss.4, 2001-05, pp. : 665-679

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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.

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