The solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif

Domain 5 (D5) is the central core of group II intron ribozymes. Many base and backbone substituents of this highly conserved hairpin participate in catalysis and are crucial for binding to other intron domains. We report the solution structures of the 34-nucleotide D5 hairpin from the group II intron ai5 gamma in the absence and presence of divalent metal ions. The bulge region of D5 adopts a novel fold, where G26 adopts a syn conformation and flips down into the major groove of helix 1, close to the major groove face of the catalytic AGC triad. The backbone near G26 is kinked, exposing the base plane of the adjacent A-U pair to the solvent and causing bases of the bulge to stack intercalatively. Metal ion titrations reveal strong Mg(2+) binding to a minor groove shelf in the D5 bulge. Another distinct metal ion-binding site is observed along the minor groove side of the catalytic triad, in a manner consistent with metal ion binding in the ribozyme active site. DOI: https://doi.org/10.1038/nsmb717 Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-1709 Accepted Version Originally published at: Sigel, Roland K O; Sashital, D G; Abramovitz, D L; Palmer, A G; Butcher, S E; Pyle, A M (2004). Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif. Nature Structural and Molecular Biology, 11(2):187-192. DOI: https://doi.org/10.1038/nsmb717 1 The solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif Roland K. O. Sigel, Dipali G. Sashital, Dana L. Abramovitz, Samuel E. Butcher, Arthur G. Palmer III, Anna Marie Pyle 1 Department of Chemistry, Winterthurerstrasse 190, University of Zürich, CH-8057 Zürich, Switzerland; Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA; Department of Biochemistry and Molecular Biophysics, 650 W 168 Street, Columbia University, New York, NY 10032, USA; Department of Molecular Biophysics and Biochemistry and the Howard Hughes Medical Institute, Yale University, 266 Whitney Avenue; New Haven, CT 06520, USA correspondence should be addressed to A.M.P. [email protected], ++1-203-432-5633; ++1-203-432-5316 (FAX) or S.E.B. [email protected], ++1-608-263-3890; ++1-608-262-3453 (FAX)