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


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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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.

Author information




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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The authors declare no competing financial interests.

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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).

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