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- Title
Structural basis of ligand binding by a c-di-GMP riboswitch.
- Authors
Smith, Kathryn D.; Lipchock, Sarah V.; Ames, Tyler D.; Jimin Wang; Breaker, Ronald R.; Strobel, Scott A.
- Abstract
The second messenger signaling molecule bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP) regulates many processes in bacteria, including motility, pathogenesis and biofilm formation. c-di-GMP–binding riboswitches are important downstream targets in this signaling pathway. Here we report the crystal structure, at 2.7 Å resolution, of a c-di-GMP riboswitch aptamer from Vibrio cholerae bound to c-di-GMP, showing that the ligand binds within a three-helix junction that involves base-pairing and extensive base-stacking. The symmetric c-di-GMP is recognized asymmetrically with respect to both the bases and the backbone. A mutant aptamer was engineered that preferentially binds the candidate signaling molecule c-di-AMP over c-di-GMP. Kinetic and structural data suggest that genetic regulation by the c-di-GMP riboswitch is kinetically controlled and that gene expression is modulated through the stabilization of a previously unidentified P1 helix, illustrating a direct mechanism for c-di-GMP signaling.
- Subjects
LIGAND binding (Biochemistry); CYCLIC guanylic acid; MOTILITY of bacteria; GENE expression; GENETIC regulation; MOLECULAR genetics
- Publication
Nature Structural & Molecular Biology, 2009, Vol 16, Issue 12, p1218
- ISSN
1545-9993
- Publication type
Article
- DOI
10.1038/nsmb.1702