c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets

Nat Chem Biol. 2014 Sep;10(9):780-6. doi: 10.1038/nchembio.1606. Epub 2014 Aug 3.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Bacillus subtilis / chemistry
  • Bacillus subtilis / metabolism
  • Calorimetry
  • Crystallography, X-Ray
  • Dinucleoside Phosphates / genetics*
  • Dinucleoside Phosphates / metabolism
  • Genes, Bacterial / genetics*
  • Genes, Switch / genetics
  • Ligands
  • Models, Molecular
  • Nucleic Acid Conformation
  • RNA, Bacterial / genetics
  • Riboswitch / genetics*
  • Second Messenger Systems / genetics
  • Thermoanaerobacter / genetics
  • Thermoanaerobacter / metabolism


  • Dinucleoside Phosphates
  • Ligands
  • RNA, Bacterial
  • Riboswitch
  • cyclic diadenosine phosphate