Article abstract
Nature Structural & Molecular Biology 15, 1076 - 1083 (2008)
Published online: 21 September 2008 | doi:10.1038/nsmb.1494
Crystal structures of the SAM-III/SMK riboswitch reveal the SAM-dependent translation inhibition mechanism
Changrui Lu1, Angela M Smith2, Ryan T Fuchs2, Fang Ding1, Kanagalaghatta Rajashankar3, Tina M Henkin2 & Ailong Ke1
Abstract
Three distinct classes of S-adenosyl-L-methionine (SAM)-responsive riboswitches have been identified that regulate bacterial gene expression at the levels of transcription attenuation or translation inhibition. The SMK box (SAM-III) translational riboswitch has been identified in the SAM synthetase gene in members of the Lactobacillales. Here we report the 2.2-Å crystal structure of the Enterococcus faecalis SMK box riboswitch. The Y-shaped riboswitch organizes its conserved nucleotides around a three-way junction for SAM recognition. The Shine-Dalgarno sequence, which is sequestered by base-pairing with the anti–Shine-Dalgarno sequence in response to SAM binding, also directly participates in SAM recognition. The riboswitch makes extensive interactions with the adenosine and sulfonium moieties of SAM but does not appear to recognize the tail of the methionine moiety. We captured a structural snapshot of the SMK box riboswitch sampling the near-cognate ligand S-adenosyl-L-homocysteine (SAH) in which SAH was found to adopt an alternative conformation and fails to make several key interactions.
- Department of Molecular Biology and Genetics, Cornell University, 251 Biotechnology Building, Ithaca, New York 14853, USA.
- Department of Microbiology and Center for RNA Biology, Ohio State University, 376 Biological Science Building, 484 West 12th Avenue, Columbus, Ohio 43210, USA.
- Northeastern Collaborative Access Team, Advanced Photon Source, Building 436, 9700 South Cass Avenue, Argonne, Illinois 60439, USA.
Correspondence to: Ailong Ke1 e-mail: ailong.ke@cornell.edu
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