3E5F
Crystal Structures of the SMK box (SAM-III) Riboswitch with Se-SAM
Summary for 3E5F
| Entry DOI | 10.2210/pdb3e5f/pdb |
| Related | 3e5C 3e5e |
| Descriptor | SMK box (SAM-III) Riboswitch for RNA, STRONTIUM ION, [(3S)-3-amino-4-hydroxy-4-oxo-butyl]-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-methyl-selanium, ... (4 entities in total) |
| Functional Keywords | smk sam riboswitch shine-delgarno translation regulation, rna |
| Total number of polymer chains | 1 |
| Total formula weight | 19162.96 |
| Authors | |
| Primary citation | Lu, C.,Smith, A.M.,Fuchs, R.T.,Ding, F.,Rajashankar, K.,Henkin, T.M.,Ke, A. Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism. Nat.Struct.Mol.Biol., 15:1076-1083, 2008 Cited by PubMed 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. PubMed: 18806797DOI: 10.1038/nsmb.1494 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.7 Å) |
Structure validation
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