4QLN

structure of ydao riboswitch binding with c-di-dAMP

Summary for 4QLN

• Entry DOI: 10.2210/pdb4qln/pdb
• Related: 4QLM
• Descriptor: RNA (117-MER), (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: ydao riboswitch, c-di-amp, rna
• Biological source: Thermoanaerobacter tengcongensis
• Total number of polymer chains: 1
• Total formula weight: 41879.67

Authors

Ren, A.M.,Patel, D.J. (deposition date: 2014-06-12, release date: 2014-08-13, Last modification date: 2024-02-28)

Primary citation

Ren, A.,Patel, D.J.
c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets.
Nat.Chem.Biol., 10:780-786, 2014

PubMed 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.

PubMed: 25086509
DOI: 10.1038/nchembio.1606

Experimental method

X-RAY DIFFRACTION (2.65 Å)