SNAP output for PDB entry 3irw [SNAP web server]

PDB-id

3irw; SNAP-derived features in text and JSON formats; DNAproDB

Class

RNA binding protein-RNA

Method

X-ray (2.7 Å)

Summary

Structure of a c-di-gmp riboswitch from v. cholerae

Reference

Smith KD, Lipchock SV, Ames TD, Wang J, Breaker RR, Strobel SA (2009): "Structural basis of ligand binding by a c-di-GMP riboswitch." Nat.Struct.Mol.Biol., 16, 1218-1223. doi: 10.1038/nsmb.1702.

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.