c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets.
Publication Type:Journal Article
Source:Nat Chem Biol, Volume 10, Issue 9, p.780-6 (2014)
Keywords:Bacillus subtilis, Calorimetry, Crystallography, X-Ray, Dinucleoside Phosphates, Genes, Bacterial, Genes, Switch, Ligands, Models, Molecular, Nucleic Acid Conformation, Riboswitch, RNA, Bacterial, Second Messenger Systems, Thermoanaerobacter
<p>The ydaO riboswitch, involved in sporulation, osmotic stress responses and cell wall metabolism, targets the second messenger cyclic-di-AMP with subnanomolar affinity. We have solved the structure of c-di-AMP bound to the Thermoanaerobacter tengcongensis ydaO riboswitch, thereby identifying a five-helical scaffold containing a zippered-up bubble, a pseudoknot and long-range tertiary base pairs. Highlights include the identification of two c-di-AMP binding pockets on the same face of the riboswitch, related by pseudo-two-fold symmetry, with potential for cross-talk between sites mediated by adjacently positioned base-stacking alignments connecting pockets. The adenine rings of bound c-di-AMP molecules are wedged between bases and stabilized by stacking, base-sugar and sugar-sugar intermolecular hydrogen bonding interactions. The structural studies are complemented by isothermal titration calorimetry-based binding studies of mutants mediating key tertiary intermolecular contacts. The T. tengcongensis ydaO riboswitch, like its Bacillus subtilis counterpart, most likely functions through a transcription termination mechanism, with the c-di-AMP bound state representing an 'off' switch.</p>