Structures of the TetR-like simocyclinone efflux pump repressor, SimR, and the mechanism of ligand-mediated derepression

J Mol Biol. 2011 Apr 22;408(1):40-56. doi: 10.1016/j.jmb.2011.02.035. Epub 2011 Feb 24.


Simocyclinone D8 (SD8), a potent DNA gyrase inhibitor made by Streptomyces antibioticus, is exported from the producing organism by the SimX efflux pump. The expression of simX is under the control of SimR, a member of the TetR family of transcriptional regulators. SimR represses simX transcription by binding to operators in the intergenic region between simR and simX. Previously, we have shown that the mature antibiotic SD8 or its biosynthetic intermediate, simocyclinone C4, can dissociate SimR from its operators, leading to derepression of simX and export of SD8 from the cell. This provides a mechanism that couples the biosynthesis of the antibiotic to its export. Here, we report the crystal structures of SimR alone and in complex with either SD8 or simocyclinone C4. The ligand-binding pocket is unusual compared to those of other characterized TetR-family transcriptional regulators: the structures show an extensive ligand-binding pocket spanning both monomers in the functional dimeric unit, with the aminocoumarin moiety of SD8 buried in the protein core, while the angucyclic polyketide moiety is partially exposed to bulk solvent. Through comparisons of the structures, we postulate a derepression mechanism for SimR that invokes rigid-body motions of the subunits relative to one another, coupled with a putative locking mechanism to restrict further conformational change.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Coumarins / chemistry
  • Coumarins / metabolism
  • Crystallography, X-Ray
  • Glycosides / chemistry
  • Glycosides / metabolism
  • Molecular Sequence Data
  • Protein Conformation
  • Repressor Proteins / chemistry*
  • Repressor Proteins / metabolism*
  • Sequence Homology, Amino Acid
  • Streptomyces antibioticus
  • Tetracycline Resistance*


  • Coumarins
  • Glycosides
  • Repressor Proteins
  • simocyclinone D8
  • tetracycline resistance-encoding transposon repressor protein

Associated data

  • PDB/2Y2Z
  • PDB/2Y30
  • PDB/2Y31