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Crystal structure of a phage Twort group I ribozyme–product complex

Nature Structural & Molecular Biology volume 12, pages 82–89 (2005)Cite this article

Abstract

Group I introns are catalytic RNAs capable of orchestrating two sequential phosphotransesterification reactions that result in self-splicing. To understand how the group I intron active site facilitates catalysis, we have solved the structure of an active ribozyme derived from the orf142-I2 intron from phage Twort bound to a four-nucleotide product RNA at a resolution of 3.6 Å. In addition to the three conserved domains characteristic of all group I introns, the Twort ribozyme has peripheral insertions characteristic of phage introns. These elements form a ring that completely envelops the active site, where a snug pocket for guanosine is formed by a series of stacked base triples. The structure of the active site reveals three potential binding sites for catalytic metals, and invokes a role for the 2′ hydroxyl of the guanosine substrate in organization of the active site for catalysis.

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Figure 1: Structure of the Twort orf142-I2 ribozyme.
Figure 2: A kink in the exon.
Figure 3: The P7.1–P7.2 subdomain.
Figure 4: The guanosine-binding site.
Figure 5: Comparison of the Twort ribozyme (green) and Azoarcus intron (pink) active sites.
Figure 6: Metals in the active site.

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Acknowledgements

We are grateful to P. Bevilacqua, J. Bolin, C. Correll, J. Piccirilli, E. Westhof and members of the Golden laboratory for critical discussions, and to J. Hougland, D. Herschlag and J. Piccirilli for communication of results prior to publication. We thank the staff of BioCars, NE-CAT and SBC for assistance with data collection. This work was supported by NASA (NAG8-1833), the Pew Scholars Program in Biomedical Sciences and the Purdue University Cancer Center. This is journal paper number 2004-17476 from the Purdue University Agricultural Experiment Station.

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  1. Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, 47907, Indiana, USA

    Barbara L Golden, Hajeong Kim & Elaine Chase

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  1. Barbara L Golden
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Correspondence to Barbara L Golden.

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Supplementary information

Supplementary Fig. 1

The Twort self-splicing reaction. (PDF 986 kb)

Supplementary Fig. 2

The Twort ribozyme reaction. (PDF 423 kb)

Supplementary Fig. 3

Ribozyme activity in manganese. (PDF 49 kb)

Supplementary Fig. 4

A manganese-binding site. (PDF 76 kb)

Supplementary Fig. 5 (PDF 84 kb)

Supplementary Table 1

Michaelis-Menten parameters for the Twort intron. (PDF 41 kb)

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Golden, B., Kim, H. & Chase, E. Crystal structure of a phage Twort group I ribozyme–product complex. Nat Struct Mol Biol 12, 82–89 (2005). https://doi.org/10.1038/nsmb868

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