Steric mechanism of auto-inhibitory regulation of specific and non-specific DNA binding by the ETS transcriptional repressor ETV6

J Mol Biol. 2014 Apr 3;426(7):1390-406. doi: 10.1016/j.jmb.2013.11.031. Epub 2013 Dec 12.

Abstract

DNA binding by the ETS transcriptional repressor ETV6 (or TEL) is auto-inhibited ~50-fold due to an α-helix that sterically blocks its ETS domain binding interface. Using NMR spectroscopy, we demonstrate that this marginally stable helix is unfolded, and not displaced to a non-inhibitory position, when ETV6 is bound to DNA containing a consensus (5')GGAA(3') recognition site. Although significantly lower in affinity, binding to non-specific DNA is auto-inhibited ~5-fold and is also accompanied by helix unfolding. Based on NMR chemical shift perturbations, both specific and non-specific DNA are bound via the same canonical ETS domain interface. However, spectral perturbations are smaller for the non-specific complex, suggesting weaker and less well-defined interactions than in the specific complex. In parallel, the crystal structure of ETV6 bound to a specific DNA duplex was determined. The structure of this complex reveals that a non-conserved histidine residue in the ETS domain recognition helix helps establish the specificity of ETV6 for DNA-binding sites containing (5')GGAA(3')versus(5')GGAT(3'). These studies provide a unified steric mechanism for attenuating ETV6 binding to both specific and non-specific DNA and expand the repertoire of characterized auto-inhibitory strategies utilized to regulate ETS factors.

Keywords: ETS family; helix unfolding; inhibitory module; protein–DNA interface; winged helix–turn–helix.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • DNA / chemistry
  • DNA / metabolism*
  • ETS Translocation Variant 6 Protein
  • Magnetic Resonance Spectroscopy / methods*
  • Mice
  • Protein Binding
  • Protein Structure, Secondary
  • Proto-Oncogene Proteins c-ets / chemistry*
  • Proto-Oncogene Proteins c-ets / metabolism*
  • Repressor Proteins / chemistry*
  • Repressor Proteins / metabolism*

Substances

  • Proto-Oncogene Proteins c-ets
  • Repressor Proteins
  • DNA