錘頭形核酶存在于多種植物RNA病毒的衛(wèi)星病毒中,，它具有高度專(zhuān)一的核酸內(nèi)切酶活性,，能夠催化自身發(fā)生RNA剪切反應(yīng),，是核酶中應(yīng)用最廣泛,、研究最深入的一類(lèi),，被認(rèn)為是了解RNA催化機(jī)制的模式核酶,。但是,，科學(xué)家目前還不清楚二價(jià)陽(yáng)離子和其它可溶性物質(zhì)在其催化過(guò)程中的作用。
來(lái)自美國(guó)加利福尼亞大學(xué)的Martick等人用X射線(xiàn)晶體衍射的技術(shù)得到了在10mM Mn2+和1M NH4+條件下錘頭形核酶的全長(zhǎng)結(jié)構(gòu),，其分辨率可達(dá)2.0 ?,，結(jié)果檢測(cè)到5個(gè)Mn2+結(jié)合位點(diǎn)，以及200多個(gè)可溶性分子（主要是H2O,，部分可能是NH4+）的結(jié)合,。其中一個(gè)Mn2+直接結(jié)合位于活性部位的A9磷酸基團(tuán)，而活性部位中G12的N1位點(diǎn)和G8的2′-O位點(diǎn)與水分子之間形成氫鍵網(wǎng)絡(luò),，以往研究已經(jīng)表明G8位點(diǎn)在酸性催化（將質(zhì)子轉(zhuǎn)移給離去基團(tuán)）過(guò)程中起重要作用,。用分子動(dòng)態(tài)模擬的方法，研究人員推斷上述結(jié)構(gòu)能夠促進(jìn)剪切過(guò)程中的質(zhì)子轉(zhuǎn)移,。
該研究結(jié)果表明,，結(jié)合晶體衍射技術(shù)和分子動(dòng)態(tài)模擬，有助于更詳細(xì)闡釋核酶催化作用的分子和化學(xué)機(jī)制,。該項(xiàng)研究以封面論文形式發(fā)表于2008年4月21日的《化學(xué)與生物》（Chemistry & Biology）上,。（科學(xué)網(wǎng) 穆宏平/編譯）
生物谷推薦原始出處：
（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.
