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（Chemistry & Biology），Vol 15, 332-342, 21 April 2008，Monika Martick, William G. Scott
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
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.
