Solvent structure and hammerhead ribozyme catalysis
Solvent structure and hammerhead ribozyme catalysis
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DOI：
10.1016/j.chembiol.2008.03.010
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发表时间：
2008-04-01
影响因子：
--
通讯作者：
Scott, William G.
中科院分区：
文献类型：
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作者：
Martick, Monika;Lee, Tai-Sung;Scott, William G.
尽管锤头状核酶被认为是理解RNA催化的原型，但相关金属离子和水分子在切割反应中的机械作用仍然存在争议。我们已经研究了所观察到的二价金属离子和水分子结合到2埃结构的全长锤头状核酶通过使用X射线晶体学结合分子动力学模拟的催化潜力。一个单一的Mn 2+被观察到直接结合到A9磷酸盐的活性位点，伴随着一个氢键网络，涉及一个有序的水分子跨越N1的G12（一般的碱）和2 '-O的G8（以前牵连在一般的酸催化），我们建议，基于分子动力学计算，促进质子转移的裂解反应。磷酸盐桥金属相互作用和其他机制的假设也用这种方法进行了测试。
Although the hammerhead ribozyme is regarded as a prototype for understanding RNA catalysis, the mechanistic roles of associated metal ions and water molecules in the cleavage reaction remain controversial. We have investigated the catalytic potential of observed divalent metal ions and water molecules bound to a 2 angstrom structure of the full-length hammer head ribozyme by using X-ray crystallography in combination with molecular dynamics simulations. A single Mn2+ is observed to bind directly to the A9 phosphate in the active site, accompanying a hydrogen-bond network involving a well-ordered water molecule spanning N1 of G12 (the general base) and 2'-O of G8 (previously implicated in general acid catalysis) that we propose, based on molecular dynamics calculations, facilitates proton transfer in the cleavage reaction. Phosphate-bridging metal interactions and other mechanistic hypotheses are also tested with this approach.