title: Structural basis of ligand binding by a c-di-GMP riboswitch.
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 A 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.
authors.affiliation: Department of Chemistry, Yale University, New Haven, Connecticut, USA.
authors.forename: Kathryn D
authors.initials: KD
authors.lastname: Smith
authors.forename: Sarah V
authors.initials: SV
authors.lastname: Lipchock
authors.forename: Tyler D
authors.initials: TD
authors.lastname: Ames
authors.forename: Jimin
authors.initials: J
authors.lastname: Wang
authors.forename: Ronald R
authors.initials: RR
authors.lastname: Breaker
authors.forename: Scott A
authors.initials: SA
authors.lastname: Strobel
mesh_terms: D020029:Base Pairing; D018360:Crystallography, X-Ray; D006152:Cyclic GMP / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D015226:Dinucleoside Phosphates / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D007364:Intercalating Agents; D007700:Kinetics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D053838:Scattering, Small Angle; D015290:Second Messenger Systems / Q000502:physiology*; D014734:Vibrio cholerae / Q000737:chemistry / Q000502:physiology*
chemical_list: D015226:Dinucleoside Phosphates; D007364:Intercalating Agents; D012329:RNA, Bacterial; C528998:cyclic diadenosine phosphate; C062025:bis(3',5')-cyclic diguanylic acid; D006152:Cyclic GMP