PSI Structural Biology Knowledgebase

PSI Nature Structural Biology Knowledgebase
Header Icons
 

research advances

January 2010 research highlights

Seeing double

PSI-SGKB [doi:10.1038/nchembio.270]

Two groups have independently solved the X-ray crystal structures of a c-di-GMP riboswitch from Vibrio cholerae.

Seeing double

Bis (3′,5′)-cyclic dimeric guanosine monophosphate (c-di-GMP) is a cyclic nucleotide produced by bacteria and used as a second messenger in processes such as biofilm formation and virulence. Recent studies have revealed that a class of 'GEMM' riboswitches regulates expression of key bacterial genes in response to c-di-GMP binding. Now two groups have independently solved the X-ray crystal structures of a c-di-GMP riboswitch from Vibrio cholerae. The riboswitch architecture is based on a three-helical junction in which two helical stems are packed side-to-side and anchored by a GNRA-tetraloop receptor interaction and an extrahelical base pair. The asymmetric c-di-GMP binding site lies in the three-helix junction that creates a pocket in which one guanine pairs with a riboswitch cytosine and the other is contacted by a guanine base through its Hoogsteen edge. The electron density reported by Smith et al. suggests that the cyclic phosphate of c-di-GMP may contact one or more metal ions. This group also measured a K d of 10 pM for c-di-GMP binding and was able to convert the wild-type riboswitch into a c-di-AMP receptor by rational nucleotide replacements at the binding site. Using small-angle X-ray scattering, Kulshina et al. showed that the riboswitch undergoes a major conformational compaction upon ligand binding. Taken together, these two complementary studies provide our first structural insights into the ligand binding and conformational dynamics of a c-di-GMP–responsive riboswitch. ( Nat. Struct. Mol. Biol., published online 8 November 2009, doi:10.1038/nsmb.1701 and doi:10.1038/nsmb.1702) TLS

Written by Mirella Bucci, Catherine Goodman, Joanne Kotz & Terry L. Sheppard

 

Protein Structure Initiative Corner

Publications

Search through over 2000 peer-reviewed publications by the PSI Network

Latest News

News from the Protein Structure Initiative and Nature

Community Nominations

Nominate proteins for structure determination by the PSI