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Crystal structure and mechanistic investigation of the twister ribozyme

Nature Chemical Biology volume 10, pages 739–744 (2014)Cite this article

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Abstract

We present a crystal structure at 2.3-Å resolution of the recently described nucleolytic ribozyme twister. The RNA adopts a previously uncharacterized compact fold based on a double-pseudoknot structure, with the active site at its center. Eight highly conserved nucleobases stabilize the core of the ribozyme through the formation of one Watson-Crick and three noncanonical base pairs, and the highly conserved adenine 3′ of the scissile phosphate is bound in the major groove of an adjacent pseudoknot. A strongly conserved guanine nucleobase directs its Watson-Crick edge toward the scissile phosphate in the crystal structure, and mechanistic evidence supports a role for this guanine as either a general base or acid in a concerted, general acid-base–catalyzed cleavage reaction.

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Figure 1: The sequence and structure of the twister ribozyme.
Figure 2: The structural role of conserved nucleotides in the twister ribozyme.
Figure 3: The active center of the twister ribozyme.
Figure 4: The catalytic mechanism of the twister ribozyme.

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Acknowledgements

We are extremely grateful to R. Breaker for early communication of his data on the twister ribozyme and B. Hunter and L. Huang for valuable advice and discussion. The work was funded by Cancer Research UK (program grant A11722).

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Authors and Affiliations

  1. Cancer Research UK Nucleic Acid Structure Research Group, Medical Sciences Institute/Wellcome Trust Building (MSI/WTB) Complex, University of Dundee, Dundee, UK

    Yijin Liu, Timothy J Wilson, Scott A McPhee & David M J Lilley

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  1. Yijin Liu
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  2. Timothy J Wilson
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  4. David M J Lilley
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Contributions

Y.L. performed crystallography; T.J.W. performed mechanistic investigations; S.A.M. synthesized RNA; 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 Figures 1–15 and Supplementary Tables 1 and 2. (PDF 8919 kb)

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Liu, Y., Wilson, T., McPhee, S. et al. Crystal structure and mechanistic investigation of the twister ribozyme. Nat Chem Biol 10, 739–744 (2014). https://doi.org/10.1038/nchembio.1587

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