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PMID: 18806797 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism.

Nature structural & molecular biology ·Vol. 15 ·No. 10 ·2008-10-00 ·Pages 1076-83

Lu C, Smith AM, Fuchs RT, Ding F, Rajashankar K, Henkin TM, Ke A

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 S(MK) box (SAM-III) translational riboswitch has been identified in the SAM synthetase gene in members of the Lactobacillales. Here we report the 2.2-A crystal structure of the Enterococcus faecalis S(MK) 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 S(MK) 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.

MeSH Terms
Base Sequence Binding Sites Crystallography, X-Ray Enterococcus faecalis/enzymology,genetics Genes, Reporter/genetics Methionine Adenosyltransferase/chemistry,genetics,metabolism Mutation/genetics Nucleic Acid Conformation Protein Binding Protein Biosynthesis S-Adenosylmethionine/chemistry,metabolism
Chemicals
S-Adenosylmethionine Methionine Adenosyltransferase
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Lu Changrui
Department of Molecular Biology and Genetics, Cornell University, 251 Biotechnology Building, Ithaca, New York 14853, USA.
Smith Angela M
Fuchs Ryan T
Ding Fang
Rajashankar Kanagalaghatta
Henkin Tina M
Ke Ailong
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Article Info
Journal
Nature structural & molecular biology
Abbr.
Nat Struct Mol Biol
ISSN
1545-9985
DOI
10.1038/nsmb.1494
Published
2008-10-00
Epub
2008-00-21
Pages
1076-83
Language
English
Region
United States
NLM ID
101186374
PMCID
PMC3467307
Subset
IM
Grants
NIGMS NIH HHS · R01 GM086766-01A2 · United States
NCRR NIH HHS · P41 RR015301 · United States
NIGMS NIH HHS · R01 GM086766-01A2S1 · United States
NCRR NIH HHS · RR-15301 · United States
NIGMS NIH HHS · GM63615 · United States
NIGMS NIH HHS · R01 GM086766 · United States
NCRR NIH HHS · P41 RR001646 · United States
NCRR NIH HHS · RR-01646 · United States
NIGMS NIH HHS · DMR0225180 · United States
NIGMS NIH HHS · R01 GM063615 · United States
Databases
PDB
3E5C, 3E5E, 3E5F
External Links
PubMed source DOI: 10.1038/nsmb.1494 PMC Full Text View journal details
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