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.

gollark: ++tel rdial
gollark: ++magic reload_ext telephone
gollark: Oh no.
gollark: ++magic reload_ext telephone
gollark: I may need to work out how to make this legible.

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.
  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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