4W90

Crystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO

Summary for 4W90

• Entry DOI: 10.2210/pdb4w90/pdb
• Descriptor: U1 small nuclear ribonucleoprotein A, riboswitch a pseudo-dimeric RNA, (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, ... (4 entities in total)
• Functional Keywords: riboswitch, cyclic-di-amp, protein-rna complex, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Homo Sapiens; More
• Cellular location: Nucleus: P09012
• Total number of polymer chains: 2
• Total formula weight: 50431.03

Authors

Jones, C.P.,Ferre-D'Amare, A.R. (deposition date: 2014-08-26, release date: 2014-10-15, Last modification date: 2024-11-06)

Primary citation

Jones, C.P.,Ferre-D'Amare, A.R.
Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA.
Embo J., 33:2692-2703, 2014

PubMed 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.

PubMed: 25271255
DOI: 10.15252/embj.201489209

Experimental method

X-RAY DIFFRACTION (3.118 Å)