title: A pH controlled conformational switch in the cleavage site of the VS ribozyme substrate RNA.
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.
authors.affiliation: Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA.
authors.forename: J
authors.initials: J
authors.lastname: Flinders
authors.forename: T
authors.initials: T
authors.lastname: Dieckmann
mesh_terms: D000225:Adenine / Q000378:metabolism; D020029:Base Pairing / Q000187:drug effects; D001483:Base Sequence; D001665:Binding Sites; D002384:Catalysis / Q000187:drug effects; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D008274:Magnesium / Q000494:pharmacology; D008958:Models, Molecular; D009491:Neurospora / Q000235:genetics*; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation / Q000187:drug effects; D011522:Protons; D012313:RNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D016337:RNA, Catalytic / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: D011522:Protons; D016337:RNA, Catalytic; D012313:RNA; D008274:Magnesium; D000225:Adenine