SMK box riboswitch

The SMKbox riboswitch (also known as SAM-III) is a RNA element that regulates gene expression in bacteria.[2][3] The SMK box riboswitch is found in the 5' UTR of the MetK gene in lactic acid bacteria. The structure of this element changes upon binding to S-adenosyl methionine (SAM) to a conformation that blocks the shine-dalgarno sequence and blocks translation of the gene.

SMK box translational riboswitch
A representation of the SMK box translational riboswitch secondary structure including a colour scheme that indicates the degree of sequence conservation.
Identifiers
SymbolSMK_box_riboswitch
Alt. SymbolsSAM-III, SMK
RfamRF01767
Other data
RNA typeRiboswitch
Domain(s)Firmicutes
PDB structuresPDBe 3e5f 3e5e 3e5c
A 3D representation of the SMKbox riboswitch structure.[1]

There are other known SAM-binding riboswitches such as SAM-I and SAM-II, but these appear to share no similarity in sequence or structure to SAM-III.

Structure

The crystal structure of the riboswitch from E. faecalis was solved by X-ray crystallography. The structure showed that the most conserved nucleotides involved in SAM binding were organised around a junction between three helices.[1] In some species there are large insertions of up to 210 nucleotides within this structure.

See also

References
  1. Lu C, Smith AM, Fuchs RT, Ding F, Rajashankar K, Henkin TM, Ke A (2008). "Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism". Nat Struct Mol Biol. 15 (10): 1076–1083. doi:10.1038/nsmb.1494. PMC 3467307. PMID 18806797.
  2. Fuchs RT, Grundy FJ, Henkin TM (2006). "The S(MK) box is a new SAM-binding RNA for translational regulation of SAM synthetase". Nat. Struct. Mol. Biol. 13 (3): 226–233. doi:10.1038/nsmb1059. PMID 16491091. S2CID 8481958.
  3. Fuchs RT, Grundy FJ, Henkin TM (2007). "S-adenosylmethionine directly inhibits binding of 30S ribosomal subunits to the SMK box translational riboswitch RNA". Proc. Natl. Acad. Sci. U.S.A. 104 (12): 4876–4880. doi:10.1073/pnas.0609956104. PMC 1829232. PMID 17360376.
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