RNA Tertiary Interactions in a Riboswitch Stabilize the Structure of a Kink Turn
| Autor: | David M.J. Lilley, Kersten T. Schroeder, Peter Daldrop |
|---|---|
| Rok vydání: | 2011 |
| Předmět: |
Riboswitch
Models Molecular RNA Stability RNA Folding Calorimetry Crystallography X-Ray Article Terminal loop 03 medical and health sciences Structural Biology Preribosomal RNA Magnesium Nucleic acid structure Nucleotide Motifs Molecular Biology 030304 developmental biology 0303 health sciences Base Sequence Chemistry Nucleic acid tertiary structure 030302 biochemistry & molecular biology RNA Hydrogen Bonding Crystallography Thermodynamics lipids (amino acids peptides and proteins) Alpha helix |
| Zdroj: | Structure(London, England:1993) |
| ISSN: | 0969-2126 |
| DOI: | 10.1016/j.str.2011.07.003 |
| Popis: | Summary The kink turn is a widespread RNA motif that introduces an acute kink into the axis of duplex RNA, typically comprising a bulge followed by a G⋅A and A⋅G pairs. The kinked conformation is stabilized by metal ions, or the binding of proteins including L7Ae. We now demonstrate a third mechanism for the stabilization of k-turn structure, involving tertiary interactions within a larger RNA structure. The SAM-I riboswitch contains an essential standard k-turn sequence that kinks a helix so that its terminal loop can make a long-range interaction. We find that some sequence variations in the k-turn within the riboswitch do not prevent SAM binding, despite preventing the folding of the k-turn in isolation. Furthermore, two crystal structures show that the sequence-variant k-turns are conventionally folded within the riboswitch. This study shows that the folded structure of the k-turn can be stabilized by tertiary interactions within a larger RNA structure. Graphical Abstract Highlights ► The folded conformation of a kink turn is stabilized by long-range tertiary interactions in RNA ► The SAM-I riboswitch contains a k-turn, that folds in the presence of Mg2+ ions in isolation ► Nucleotide substitution in the G•A pairs of the k-turn prevent folding in isolation, but some can be stabilized in the context of the riboswitch, allowing binding of SAM ligand ► The crystal structure of a SAM-I riboswitch with a variant k-turn provides the first example of a k-turn with an A•A pair at the 2b•2n position |
| Databáze: | OpenAIRE |
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