Nature Chemical Biology
Nature Chemical Biology
5 years ago

The structure of a nucleolytic ribozyme that employs a catalytic metal ion

The structure of a nucleolytic ribozyme that employs a catalytic metal ion
David M J Lilley, Yijin Liu, Timothy J Wilson
The TS ribozyme (originally called “twister sister”) is a catalytic RNA. We present a crystal structure of the ribozyme in a pre-reactive conformation. Two co-axial helical stacks are organized by a three-way junction and two tertiary contacts. Five divalent metal ions are directly coordinated to RNA ligands, making important contributions to the RNA architecture. The scissile phosphate lies in a quasihelical loop region that is organized by a network of hydrogen bonding. A divalent metal ion is directly bound to the nucleobase 5′ to the scissile phosphate, with an inner-sphere water molecule positioned to interact with the O2′ nucleophile. The rate of ribozyme cleavage correlated in a log-linear manner with divalent metal ion pKa, consistent with proton transfer in the transition state, and we propose that the bound metal ion is a likely general base for the cleavage reaction. Our data indicate that the TS ribozyme functions predominantly as a metalloenzyme.

Publisher URL: http://dx.doi.org/10.1038/nchembio.2333

DOI: 10.1038/nchembio.2333

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