title: c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets.
abstract: 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.
authors.affiliation: Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.
authors.forename: Aiming
authors.initials: A
authors.lastname: Ren
authors.affiliation: Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.
authors.forename: Dinshaw J
authors.initials: DJ
authors.lastname: Patel
mesh_terms: D001412:Bacillus subtilis / Q000737:chemistry / Q000378:metabolism; D002151:Calorimetry; D018360:Crystallography, X-Ray; D015226:Dinucleoside Phosphates / Q000235:genetics* / Q000378:metabolism; D005798:Genes, Bacterial / Q000235:genetics*; D005812:Genes, Switch / Q000235:genetics; D008024:Ligands; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000235:genetics; D058928:Riboswitch / Q000235:genetics*; D015290:Second Messenger Systems / Q000235:genetics; D046968:Thermoanaerobacter / Q000235:genetics / Q000378:metabolism
chemical_list: D015226:Dinucleoside Phosphates; D008024:Ligands; D012329:RNA, Bacterial; D058928:Riboswitch; C528998:cyclic diadenosine phosphate
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