Abstract
Artificial ribozymes catalyze a variety of chemical reactions. Their structures and reaction mechanisms are largely unknown. We have analyzed a ribozyme catalyzing Diels-Alder cycloaddition reactions by comprehensive mutation analysis and a variety of probing techniques. New tertiary interactions involving base pairs between nucleotides of the 5′ terminus and a large internal loop forming a pseudoknot fold were identified. The probing data indicate a preformed tertiary structure that shows no major changes on substrate or product binding. Based on these observations, a molecular architecture featuring a Y-shaped arrangement is proposed. The tertiary structure is formed in a rather unusual way; that is, the opposite sides of the asymmetric internal loop are clamped by the four 5′-terminal nucleotides, forming two adjacent two base-pair helices. It is proposed that the catalytic pocket is formed by a wedge within one of these helices.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 1217-1227 |
| Number of pages | 11 |
| Journal | Chemistry and Biology |
| Volume | 11 |
| Issue number | 9 |
| DOIs | |
| State | Published - Sep 2004 |
| Externally published | Yes |
Bibliographical note
Funding Information:This work was supported by the Deutsche Forschungsgemeinschaft (Ja 794/3 and SFB 623), the Bundesministerium für Bildung und Forschung (BioFuture 0311861), and the Fonds der Chemischen Industrie (all to A.J.). E.W. would like to acknowledge support from the Institut Universitaire de France. The authors appreciate helpful suggestions and critical discussion by Dr. M. Helm, R. Wombacher (both Heidelberg University, Germany), and Dr. J. Wrzesinski (Polish Academy of Sciences, Poznan, Poland).