3Q3Z

Structure of a c-di-GMP-II riboswitch from C. acetobutylicum bound to c-di-GMP

Summary for 3Q3Z

• Entry DOI: 10.2210/pdb3q3z/pdb
• Descriptor: c-di-GMP-II 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), MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: riboswitch, c-di-gmp, rna
• Biological source: Clostridium acetobutylicum
• Total number of polymer chains: 2
• Total formula weight: 51768.17

Authors

Smith, K.D.,Shanahan, C.A.,Moore, E.L.,Simon, A.C.,Strobel, S.A. (deposition date: 2010-12-22, release date: 2011-05-11, Last modification date: 2024-02-21)

Primary citation

Smith, K.D.,Shanahan, C.A.,Moore, E.L.,Simon, A.C.,Strobel, S.A.
Structural basis of differential ligand recognition by two classes of bis-(3'-5')-cyclic dimeric guanosine monophosphate-binding riboswitches.
Proc.Natl.Acad.Sci.USA, 108:7757-7762, 2011

PubMed Abstract: The bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) signaling pathway regulates biofilm formation, virulence, and other processes in many bacterial species and is critical for their survival. Two classes of c-di-GMP-binding riboswitches have been discovered that bind this second messenger with high affinity and regulate diverse downstream genes, underscoring the importance of RNA receptors in this pathway. We have solved the structure of a c-di-GMP-II riboswitch, which reveals that the ligand is bound as part of a triplex formed with a pseudoknot. The structure also shows that the guanine bases of c-di-GMP are recognized through noncanonical pairings and that the phosphodiester backbone is not contacted by the RNA. Recognition is quite different from that observed in the c-di-GMP-I riboswitch, demonstrating that at least two independent solutions for RNA second messenger binding have evolved. We exploited these differences to design a c-di-GMP analog that selectively binds the c-di-GMP-II aptamer over the c-di-GMP-I RNA. There are several bacterial species that contain both types of riboswitches, and this approach holds promise as an important tool for targeting one riboswitch, and thus one gene, over another in a selective fashion.

PubMed: 21518891
DOI: 10.1073/pnas.1018857108

Experimental method

X-RAY DIFFRACTION (2.51 Å)