Campbell Dean O, Legault Pascale
Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA.
Biochemistry. 2005 Mar 22;44(11):4157-70. doi: 10.1021/bi047963l.
An important step in the substrate recognition of the Neurospora Varkud Satellite (VS) ribozyme is the formation of a magnesium-dependent loop/loop interaction between the terminal loops of stem-loops I and V. We have studied the structure of stem-loop V by nuclear magnetic resonance spectroscopy and shown that it adopts a U-turn conformation, a common motif found in RNA. Structural comparisons indicate that the U-turn of stem-loop V fulfills some but not all of the structural characteristics found in canonical U-turn structures. This U-turn conformation exposes the Watson-Crick faces of the bases within stem-loop V (G697, A698, and C699) and makes them accessible for interaction with stem-loop I. Using chemical-shift mapping, we show that magnesium ions interact with the loop of the isolated stem-loop V and induce a conformational change that may be important for interaction with stem-loop I. This study expands our understanding of the role of U-turn motifs in RNA structure and function and provides insights into the mechanism of substrate recognition in the VS ribozyme.
粗糙脉孢菌瓦尔库德卫星（VS）核酶底物识别过程中的一个重要步骤是在茎环I和V的末端环之间形成镁依赖性的环/环相互作用。我们通过核磁共振光谱研究了茎环V的结构，结果表明它采用了U型转折构象，这是RNA中常见的一种基序。结构比较表明，茎环V的U型转折满足了典型U型转折结构中的部分而非全部结构特征。这种U型转折构象暴露了茎环V内碱基（G697、A698和C699）的沃森-克里克面，使其可与茎环I相互作用。通过化学位移图谱，我们发现镁离子与分离的茎环V的环相互作用，并诱导一种构象变化，这可能对与茎环I的相互作用很重要。这项研究扩展了我们对U型转折基序在RNA结构和功能中作用的理解，并为VS核酶的底物识别机制提供了见解。
