The Structure of the Guanidine-II Riboswitch. Issue 6 (22nd June 2017)

• Record Type: Journal Article
• Authors: Huang, Lin; Wang, Jia; Lilley, David M.J.
• Is Part Of: Cell chemical biology. Volume 24:Issue 6(2017)
• Page Start: 695
• Page End: 702.e2
• Publication Date: 2017-06-22
• Subjects: gene regulation -- RNA structure -- X-ray crystallography -- riboregulation; Biochemistry -- Periodicals; 572.05
• DOI: 10.1016/j.chembiol.2017.05.014
• Languages: English
• ISSNs: 2451-9456

Abstract

Summary: The guanidine-II (mini- ykkC ) riboswitch is the smallest of the guanidine-responsive riboswitches, comprising two stem loops of similar sequence. We have solved high-resolution crystal structures of both stem loops for the riboswitch from Gloeobacter violaceus . The stem loops have a strong propensity to dimerize by intimate loop-loop interaction. The dimerization creates specific binding pockets for two guanidine molecules, explaining their cooperative binding. Within the binding pockets the ligands are hydrogen bonded to a guanine at O6 and N7, and to successive backbone phosphates. Additionally they are each stacked upon a guanine nucleobase. One side of the pocket has an opening to the solvent, slightly lowering the specificity of ligand binding, and structures with bound methylguanidine, aminoguanidine, and agmatine show how this is possible. Graphical Abstract: Highlights: Guanidine-II riboswitch stem loops dimerize in the presence of the ligand Loop-loop interaction generates specific binding sites for two guanidine molecules Guanidine is hydrogen bonded to a guanine nucleobase, and to the phosphate backbone Some modified guanidine compounds also bind to the pocket, which is open on one side Abstract : Huang et al. use structural biology to show that the stem loops of the guanidine-II dimerize by loop-loop interaction. Guanidine is hydrogen bonded to the Hoogsteen edge of a guanine that forms a base pair with a cytosine from the second stem loop. Guanidine stabilizes the structure to activate the gene.