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Crystal structure of a self-splicing group I intron with both exons

Nature volume 430, pages 45–50 (2004)Cite this article

Abstract

The discovery of the RNA self-splicing group I intron provided the first demonstration that not all enzymes are proteins. Here we report the X-ray crystal structure (3.1-Å resolution) of a complete group I bacterial intron in complex with both the 5′- and the 3′-exons. This complex corresponds to the splicing intermediate before the exon ligation step. It reveals how the intron uses structurally unprecedented RNA motifs to select the 5′- and 3′-splice sites. The 5′-exon's 3′-OH is positioned for inline nucleophilic attack on the conformationally constrained scissile phosphate at the intron–3′-exon junction. Six phosphates from three disparate RNA strands converge to coordinate two metal ions that are asymmetrically positioned on opposing sides of the reactive phosphate. This structure represents the first splicing complex to include a complete intron, both exons and an organized active site occupied with metal ions.

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Figure 1: Overall secondary and tertiary structure of the Azoarcus pre-2S intron splicing complex.
Figure 2: The G binding motif and the structure of the pre-2S active site.
Figure 3: Recognition of the P1 substrate helix by the active site.
Figure 4: Active-site metal ions and their ligands.

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Acknowledgements

We thank J. Steitz, T. Steitz, J. Piccirilli, A. Pyle, S. Woodson, L. Szewczak, J. Cochrane, M. Gill, R. Anderson and A. Seila for discussion and comments on the manuscript; C. Höbartner and R. Micura for the gift of a 2′-seleno-methyl substituted dCIRC oligonucleotide (Supplementary Information); L. Wadley for assistance with PRIMOS analysis; M. Becker and the staff of the X-25 beamline at Brookhaven NSLS for assistance with data collection; and the staff in the Yale Center for Structural Biology for extensive technical assistance. This project was supported by grants from the NSF and the NIH.

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  1. Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, Connecticut, 06520-8114, New Haven, USA

    Peter L. Adams, Mary R. Stahley, Anne B. Kosek, Jimin Wang & Scott A. Strobel

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Correspondence to Jimin Wang or Scott A. Strobel.

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Supplementary information

Supplementary Information

These supplementary data demonstrate that the pre-2S complex assembles, and that it is active with a ribose at ΩG206 and inactive when 2'-deoxy is substituted at this position. It shows the positions of heavy atoms used to confirm the register of the RNA within the electron density, and it shows the sites of Tl+ binding in complexes with 2'-deoxy ribose or ribose at ΩG206. (PDF 2211 kb)

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Adams, P., Stahley, M., Kosek, A. et al. Crystal structure of a self-splicing group I intron with both exons. Nature 430, 45–50 (2004). https://doi.org/10.1038/nature02642

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