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

Abstract

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.

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Figure 1: The overall structure of the TS ribozyme.
Figure 2: Close view of special features of the TS ribozyme structure.
Figure 3: Loop L1 is quasihelical and coaxial with P1 and P2.
Figure 4: The effect of metal ions on cleavage rates by the TS ribozyme.
Figure 5: The hydrated metal ion M1 is bound to C54 in proximity to the nucleophile of the cleavage reaction.

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Acknowledgements

We thank S. Ashraf for expert synthesis of RNA, the CRUK for program support A18604 (to D.M.J.L.), the Wellcome Trust for the in-house diffractometer and ESRF for synchrotron beam time.

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Y.L. performed crystallography, T.J.W. performed mechanistic investigations and Y.L., T.J.W. and D.M.J.L. designed the research, analyzed data and wrote the manuscript.

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Correspondence to David M J Lilley.

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Supplementary Results, Supplementary Tables 1–3 and Supplementary Figures 1–12 (PDF 10052 kb)

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Liu, Y., Wilson, T. & Lilley, D. The structure of a nucleolytic ribozyme that employs a catalytic metal ion. Nat Chem Biol 13, 508–513 (2017). https://doi.org/10.1038/nchembio.2333

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