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Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation

Abstract

The majority of structural efforts addressing RNA's catalytic function have focused on natural ribozymes, which catalyze phosphodiester transfer reactions. By contrast, little is known about how RNA catalyzes other types of chemical reactions. We report here the crystal structures of a ribozyme that catalyzes enantioselective carbon-carbon bond formation by the Diels-Alder reaction in the unbound state and in complex with a reaction product. The RNA adopts a λ-shaped nested pseudoknot architecture whose preformed hydrophobic pocket is precisely complementary in shape to the reaction product. RNA folding and product binding are dictated by extensive stacking and hydrogen bonding, whereas stereoselection is governed by the shape of the catalytic pocket. Catalysis is apparently achieved by a combination of proximity, complementarity and electronic effects. We observe structural parallels in the independently evolved catalytic pocket architectures for ribozyme- and antibody-catalyzed Diels-Alder carbon-carbon bond-forming reactions.

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Figure 1: Secondary and tertiary folds of the Diels-Alder ribozyme.
Figure 2: Details of the structure of the Diels-Alder ribozyme–product complex.
Figure 3: Structural elements of the Diels-Alder ribozyme–product complex.
Figure 4: Surface representation of the catalytic pocket.
Figure 5: Superposition of the Diels-Alder ribozyme structures around the catalytic pocket.
Figure 6: Comparison of the RNA and protein catalytic sites for the Diels-Alder reaction.

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Acknowledgements

We gratefully acknowledge support by the US National Institutes of Health, the DeWitt Wallace Foundation and the Abby Rockefeller Mauze Trust (D.J.P.), the Bundesministerium für Bildung und Forschung (BioFuture program), the Deutsche Forschungsgemeinschaft, HFSP and the Fonds der Chemischen Industrie (A.J.), and the Austrian Science Fund FWF (R.M.). We thank V. Kuryavyi for extensive discussions on graphic programs, A. Teplov for help with data collection, M. Becker and the staff of the X25 and X12c beamlines at National Synchrotron Light Source for assistance with data collection, and the personnel of beamlines 14-BM and 19-BM at the Advanced Photon Source for data collection support.

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Correspondence to Andres Jäschke or Dinshaw J Patel.

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Supplementary information

Supplementary Fig. 1

Structural details. (PDF 701 kb)

Supplementary Fig. 2

Folding of the ribozyme monitored by NMR. (PDF 180 kb)

Supplementary Fig. 3

Schematic drawings of RNA pseudoknot topologies. (PDF 104 kb)

Supplementary Fig. 4

Model for the catalytic mechanism. (PDF 615 kb)

Supplementary Fig. 5

Electron density maps. (PDF 552 kb)

Supplementary Methods (PDF 80 kb)

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Serganov, A., Keiper, S., Malinina, L. et al. Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation. Nat Struct Mol Biol 12, 218–224 (2005). https://doi.org/10.1038/nsmb906

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