锤头形核酶存在于多种植物RNA病毒的卫星病毒中，它具有高度专一的核酸内切酶活性，能够催化自身发生RNA剪切反应，是核酶中应用最广泛、研究最深入的一类，被认为是了解RNA催化机制的模式核酶。但是，科学家目前还不清楚二价阳离子和其它可溶性物质在其催化过程中的作用。
来自美国加利福尼亚大学的Martick等人用X射线晶体衍射的技术得到了在10mM Mn2+和1M NH4+条件下锤头形核酶的全长结构，其分辨率可达2.0 ?，结果检测到5个Mn2+结合位点，以及200多个可溶性分子（主要是H2O，部分可能是NH4+）的结合。其中一个Mn2+直接结合位于活性部位的A9磷酸基团，而活性部位中G12的N1位点和G8的2′-O位点与水分子之间形成氢键网络，以往研究已经表明G8位点在酸性催化（将质子转移给离去基团）过程中起重要作用。用分子动态模拟的方法，研究人员推断上述结构能够促进剪切过程中的质子转移。
该研究结果表明，结合晶体衍射技术和分子动态模拟，有助于更详细阐释核酶催化作用的分子和化学机制。该项研究以封面论文形式发表于2008年4月21日的《化学与生物》（Chemistry & Biology）上。（科学网 穆宏平/编译）
生物谷推荐原始出处：
（Chemistry & Biology），Vol 15, 332-342, 21 April 2008，Monika Martick, William G. Scott
Solvent Structure and Hammerhead Ribozyme Catalysis
Monika Martick,1,2 Tai-Sung Lee,3,4 Darrin M. York,4 and William G. Scott4,5,
1 Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
2 The Center for the Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
3 Consortium for Bioinformatics and Computational Biology, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, MN 55455, USA
4 Department of Chemistry, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, MN 55455, USA
5 Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
Summary
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 Å structure of the full-length hammerhead 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.
