3IRW

Structure of a c-di-GMP riboswitch from V. cholerae

Summary for 3IRW

• Entry DOI: 10.2210/pdb3irw/pdb
• Descriptor: U1 small nuclear ribonucleoprotein A, c-di-GMP Riboswitch, 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one), ... (6 entities in total)
• Functional Keywords: riboswitch, c-di-gmp, rna, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: P09012
• Total number of polymer chains: 2
• Total formula weight: 44671.71

Authors

Smith, K.D. (deposition date: 2009-08-24, release date: 2009-11-10, Last modification date: 2024-02-21)

Primary citation

Smith, K.D.,Lipchock, S.V.,Ames, T.D.,Wang, J.,Breaker, R.R.,Strobel, S.A.
Structural basis of ligand binding by a c-di-GMP riboswitch.
Nat.Struct.Mol.Biol., 16:1218-1223, 2009

PubMed 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.

PubMed: 19898477
DOI: 10.1038/nsmb.1702

Experimental method

X-RAY DIFFRACTION (2.7 Å)