title: Structural basis for guanidine sensing by theykkCfamily of riboswitches.
abstract: Regulation of gene expression bycis-encoded riboswitches is a prevalent theme in bacteria. Of the hundreds of riboswitch families identified, the majority of them remain as orphans, without a clear ligand assignment. TheykkCorphan family was recently characterized as guanidine-sensing riboswitches. Herein we present a 2.3 Å crystal structure of the guanidine-boundykkCriboswitch fromDickeya dadantiiThe riboswitch folds into a boot-shaped structure, with a coaxially stacked P1/P2 stem forming the boot, and a 3'-P3 stem-loop forming the heel. Sophisticated base-pairing and cross-helix tertiary contacts give rise to the ligand-binding pocket between the boot and the heel. The guanidine is recognized in its positively charged guanidinium form, in its sp2hybridization state, through a network of coplanar hydrogen bonds and by a cation-π stacking contact on top of a conserved guanosine residue. Disruption of these contacts resulted in severe guanidinium-binding defects. These results provide the structural basis for specific guanidine sensing byykkCriboswitches and pave the way for a deeper understanding of guanidine detoxification-a previously unappreciated aspect of bacterial physiology.
authors.affiliation: Department of Molecular Biology and Genetics, Ithaca, New York 14853, USA.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Battaglia
authors.affiliation: Department of Molecular Biology and Genetics, Ithaca, New York 14853, USA.
authors.forename: Ian R
authors.initials: IR
authors.lastname: Price
authors.affiliation: Department of Molecular Biology and Genetics, Ithaca, New York 14853, USA.
authors.forename: Ailong
authors.initials: A
authors.lastname: Ke
mesh_terms: D020029:Base Pairing; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004755:Enterobacteriaceae / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D019791:Guanidine / Q000737:chemistry* / Q000378:metabolism; D006860:Hydrogen Bonding; D008024:Ligands; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D058928:Riboswitch / Q000235:genetics*; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D008024:Ligands; D012329:RNA, Bacterial; D058928:Riboswitch; D019791:Guanidine
keywords: Dickeya dadantii; RNA structure; gene regulation; guanidine; orphan riboswitch