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Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif

Nature Structural & Molecular Biology volume 11, pages 187192 (2004) | Download Citation

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Abstract

Domain 5 (D5) is the central core of group II intron ribozymes. Many base and backbone substituents of this highly conserved hairpin participate in catalysis and are crucial for binding to other intron domains. We report the solution structures of the 34-nucleotide D5 hairpin from the group II intron ai5γ in the absence and presence of divalent metal ions. The bulge region of D5 adopts a novel fold, where G26 adopts a syn conformation and flips down into the major groove of helix 1, close to the major groove face of the catalytic AGC triad. The backbone near G26 is kinked, exposing the base plane of the adjacent A-U pair to the solvent and causing bases of the bulge to stack intercalatively. Metal ion titrations reveal strong Mg2+ binding to a minor groove shelf in the D5 bulge. Another distinct metal ion–binding site is observed along the minor groove side of the catalytic triad, in a manner consistent with metal ion binding in the ribozyme active site.

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Acknowledgements

We thank L. Nikstad for helping with structure determination and P. Pang, C. Duarte and L. Wadley for many helpful discussions. NMR studies carried out at the National Magnetic Resonance Facility at Madison were supported by the US National Institutes of Health (NIH) Biomedical Technology Program with additional equipment funding from the University of Wisconsin, US National Science Foundation (NSF) Academic Infrastructure Program, NIH Shared Instrumentation Program, NSF Biological Instrumentation Program, and the US Department of Agriculture. We are grateful for financial support from the Swiss Academy of Natural Sciences and the Swiss National Science Foundation (Grant for Young Scientists for R.K.O.S.), the NSF (A.G.P.) and the NIH (S.E.B. and A.M.P.). A.M.P. is a Howard Hughes Medical Institute investigator.

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Affiliations

  1. Department of Chemistry, Winterthurerstrasse 190, University of Zürich, CH-8057 Zürich, Switzerland.

    • Roland K O Sigel
  2. Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA.

    • Dipali G Sashital
    •  & Samuel E Butcher
  3. Department of Biochemistry and Molecular Biophysics, 650 W. 168th Street, Columbia University, New York, New York 10032, USA.

    • Dana L Abramovitz
    •  & Arthur G Palmer III
  4. Department of Molecular Biophysics and Biochemistry and the Howard Hughes Medical Institute, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520, USA.

    • Anna Marie Pyle

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The authors declare no competing financial interests.

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Correspondence to Samuel E Butcher or Anna Marie Pyle.

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https://doi.org/10.1038/nsmb717

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