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Nat Struct Mol Biol. 2009 Dec;16(12):1218-23. doi: 10.1038/nsmb.1702. Epub 2009 Nov 8.

Structural basis of ligand binding by a c-di-GMP riboswitch.

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1
Department of Chemistry, Yale University, New Haven, Connecticut, USA.

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.

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PMID:
19898477
PMCID:
PMC2850612
DOI:
10.1038/nsmb.1702
[Indexed for MEDLINE]
Free PMC Article
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