DNA recognition by the brinker repressor--an extreme case of coupling between binding and folding

J Mol Biol. 2006 Aug 25;361(4):659-72. doi: 10.1016/j.jmb.2006.06.045. Epub 2006 Jul 7.

Abstract

The Brinker (Brk) nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signaling pathway. Its N-terminal part has weak homology to the Antennapedia homeodomain and binds to GC-rich DNA sequences. We have investigated the conformation and dynamics of the N-terminal 101 amino acid residues of Brk in the absence and in the presence of cognate DNA by solution NMR spectroscopy. In the absence of DNA, Brk is unfolded and highly flexible throughout the entire backbone. Addition of cognate DNA induces the formation of a well-folded structure for residues R46 to R95. This structure consists of four helices forming a helix-turn-helix motif that differs from homeodomains, but has similarities to the Tc3 transposase, the Pax-6 Paired domain, and the human centromere-binding protein. The GC-rich DNA recognition can be explained by specific major groove hydrogen bonds from the N-terminal end of helix alpha3. The transition from a highly flexible, completely unfolded conformation in the absence of DNA to a well-formed structure in the complex presents a very extreme case of the "coupling of binding and folding" phenomenon.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Antennapedia Homeodomain Protein / chemistry
  • Antennapedia Homeodomain Protein / metabolism
  • DNA / metabolism*
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism
  • Drosophila Proteins / chemistry*
  • Drosophila Proteins / metabolism*
  • Drosophila melanogaster / chemistry*
  • Drosophila melanogaster / genetics
  • Drosophila melanogaster / metabolism
  • GC Rich Sequence
  • Helix-Turn-Helix Motifs
  • Models, Molecular
  • Molecular Sequence Data
  • Nuclear Magnetic Resonance, Biomolecular
  • Protein Conformation
  • Protein Folding
  • Protein Structure, Tertiary
  • Repressor Proteins / chemistry*
  • Repressor Proteins / metabolism*
  • Sequence Alignment
  • Transcription Factors / chemistry*
  • Transcription Factors / metabolism*

Substances

  • Antennapedia Homeodomain Protein
  • DNA-Binding Proteins
  • Drosophila Proteins
  • Repressor Proteins
  • Transcription Factors
  • brk protein, Drosophila
  • DNA

Associated data

  • PDB/2GLO