title: Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA.
abstract: Cyclic diadenosine monophosphate (c-di-AMP) is a second messenger that is essential for growth and homeostasis in bacteria. A recently discovered c-di-AMP-responsive riboswitch controls the expression of genes in a variety of bacteria, including important pathogens. To elucidate the molecular basis for specific binding of c-di-AMP by a gene-regulatory mRNA domain, we have determined the co-crystal structure of this riboswitch. Unexpectedly, the structure reveals an internally pseudo-symmetric RNA in which two similar three-helix-junction elements associate head-to-tail, creating a trough that cradles two c-di-AMP molecules making quasi-equivalent contacts with the riboswitch. The riboswitch selectively binds c-di-AMP and discriminates exquisitely against other cyclic dinucleotides, such as c-di-GMP and cyclic-AMP-GMP, via interactions with both the backbone and bases of its cognate second messenger. Small-angle X-ray scattering experiments indicate that global folding of the riboswitch is induced by the two bound cyclic dinucleotides, which bridge the two symmetric three-helix domains. This structural reorganization likely couples c-di-AMP binding to gene expression.
authors.affiliation: Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA.
authors.forename: Christopher P
authors.initials: CP
authors.lastname: Jones
authors.affiliation: Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA adrian.ferre@nih.gov.
authors.forename: Adrian R
authors.initials: AR
authors.lastname: Ferré-D'Amaré
mesh_terms: D001412:Bacillus subtilis / Q000737:chemistry* / Q000235:genetics; D018360:Crystallography, X-Ray; D015226:Dinucleoside Phosphates / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry* / Q000235:genetics; D058928:Riboswitch
chemical_list: D015226:Dinucleoside Phosphates; D012329:RNA, Bacterial; D058928:Riboswitch; C528998:cyclic diadenosine phosphate
keywords: X‐ray crystallography; cyclic di‐AMP; riboregulation; riboswitch; small‐angle X‐ray scattering