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Metal ion binding sites in a group II intron core

Nature Structural Biology volume 7, pages 1111–1116 (2000)Cite this article

Abstract

Group II introns are catalytic RNA molecules that require divalent metal ions for folding, substrate binding, and chemical catalysis. Metal ion binding sites in the group II core have now been elucidated by monitoring the site-specific RNA hydrolysis patterns of bound ions such as Tb3+ and Mg2+. Major sites are localized near active site elements such as domain 5 and its surrounding tertiary interaction partners. Numerous sites are also observed at intron substructures that are involved in binding and potentially activating the splice sites. These results highlight the locations of specific metal ions that are likely to play a role in ribozyme catalysis.

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Figure 1: Tb3+ and Mg2+ cleavage sites in domain 5.
Figure 2: Tb3+ cleavage sites throughout the D135 ribozyme.
Figure 3: Sites of Tb3+ and Mg2+ cleavage superimposed on a secondary structural representation of the ai5γ intron.
Figure 4: Effects of competing Mg2+ and exon binding on Tb3+ cleavage.

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Acknowledgements

We are grateful to C. Duarte, J. Swisher and O. Fedorova for helpful discussions, to Q. Liu for preparation of plasmids, and to the Swiss Academy of Natural Sciences, the Swiss National Science Foundation (fellowship to R.K.O.S.) and the Howard Hughes Medical Institute (A.V. and A.M.P.) for financial support.

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Biophysics, 630 W. 168th Street, Box 36

    Roland K. O. Sigel & Anna Marie Pyle

  2. Columbia University, New York, 10032, New York, USA

    Roland K. O. Sigel & Anna Marie Pyle

  3. Howard Hughes Medical Institute, 630 W. 168th Street, Box 36

    Anand Vaidya & Anna Marie Pyle

  4. Columbia University, New York, 10032, New York, USA

    Anand Vaidya & Anna Marie Pyle

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  1. Roland K. O. Sigel
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Correspondence to Anna Marie Pyle.

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Sigel, R., Vaidya, A. & Pyle, A. Metal ion binding sites in a group II intron core. Nat Struct Mol Biol 7, 1111–1116 (2000). https://doi.org/10.1038/81958

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