The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer

Structure. 2011 Oct 12;19(10):1413-23. doi: 10.1016/j.str.2011.06.019. Epub 2011 Sep 8.


Transport and biosynthesis of folate and its derivatives are frequently controlled by the tetrahydrofolate (THF) riboswitch in Firmicutes. We have solved the crystal structure of the THF riboswitch aptamer in complex with folinic acid, a THF analog. Uniquely, this structure reveals two molecules of folinic acid binding to a single structured domain. These two sites interact with ligand in a similar fashion, primarily through recognition of the reduced pterin moiety. 7-deazaguanine, a soluble analog of guanine, binds the riboswitch with nearly the same affinity as its natural effector. However, 7-deazaguanine effects transcriptional termination to a substantially lesser degree than folinic acid, suggesting that the cellular guanine pool does not act upon the THF riboswitch. Under physiological conditions the ligands display strong cooperative binding, with one of the two sites playing a greater role in eliciting the regulatory response, which suggests that the second site may play another functional role.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Aptamers, Nucleotide / metabolism*
  • Bacillus subtilis / genetics
  • Bacillus subtilis / metabolism
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Base Sequence
  • Binding Sites
  • Calorimetry / methods
  • Folic Acid / metabolism
  • Gene Expression Regulation, Bacterial
  • Guanine / analogs & derivatives
  • Guanine / metabolism
  • Leucovorin / metabolism
  • Ligands
  • Magnesium / metabolism
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Point Mutation
  • Protein Binding
  • Protein Structure, Secondary
  • RNA / metabolism
  • Riboswitch*
  • S-Adenosylmethionine / metabolism
  • Streptococcus mutans / genetics*
  • Streptococcus mutans / metabolism
  • Terminator Regions, Genetic
  • Tetrahydrofolates / metabolism*
  • Thermodynamics
  • Transcription, Genetic


  • Aptamers, Nucleotide
  • Bacterial Proteins
  • Ligands
  • Riboswitch
  • Tetrahydrofolates
  • 5,6,7,8-tetrahydrofolic acid
  • Guanine
  • RNA
  • S-Adenosylmethionine
  • Folic Acid
  • 7-deazaguanine
  • Magnesium
  • Leucovorin

Associated data

  • PDB/3SD1
  • PDB/3SD3