Flinders J, Dieckmann T
Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA.
J Mol Biol. 2001 May 11;308(4):665-79. doi: 10.1006/jmbi.2001.4627.
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.
VS核酶是在某些自然的脉孢菌菌株中发现的一段154个核苷酸的序列。该RNA可分为底物和催化结构域。在此，我们展示了在Mg2+存在下，被催化结构域在反式反应中切割的底物RNA的溶液结构。30个核苷酸的底物RNA形成了一个由柔性环封端的紧密螺旋。切割位点凸起包含三个非经典碱基对，包括一个带有质子化腺嘌呤的A+.C对。这个腺嘌呤（A622）是一个受pH控制的构象开关，在较高pH下会打开内部环。讨论了这种开关对底物识别和切割的可能意义。
