Structure of a Leu3-DNA complex: recognition of everted CGG half-sites by a Zn2Cys6 binuclear cluster protein

Structure. 2006 Apr;14(4):725-35. doi: 10.1016/j.str.2005.11.025.


Gal4 is the prototypical Zn2Cys6 binuclear cluster transcriptional regulator that binds as a homodimer to DNA containing inverted CGG half-sites. Leu3, a member of this protein family, binds to everted (opposite polarity to inverted) CGG half-sites, and an H50C mutation within the Leu3 Zn2Cys6 binuclear motif abolishes its transcriptional repression function without impairing DNA binding. We report the X-ray crystal structures of DNA complexes with Leu3 and Leu3(H50C) and solution DNA binding studies of selected Leu3 mutant proteins. These studies reveal the molecular details of everted CGG half-site recognition, and suggest a role for the H50C mutation in transcriptional repression. Comparison with the Gal4-DNA complex shows an unexpected conservation in the DNA recognition mode of inverted and everted CGG half-sites, and points to a critical function of a linker region between the Zn2Cys6 binuclear cluster and dimerization regions in DNA binding specificity. Broader implications of these findings are discussed.

Publication types

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

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Base Sequence
  • Binding Sites
  • Crystallography, X-Ray
  • Cysteine / chemistry
  • DNA / chemistry*
  • DNA, Fungal / metabolism
  • DNA-Binding Proteins / chemistry*
  • Dimerization
  • Fungal Proteins / chemistry
  • Histidine / chemistry
  • Models, Molecular
  • Molecular Sequence Data
  • Mutation
  • Nucleic Acid Conformation
  • Plasmids / metabolism
  • Protein Binding
  • Protein Conformation
  • Protein Structure, Tertiary
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Saccharomyces cerevisiae Proteins / metabolism
  • Trans-Activators / chemistry*
  • Transcription Factors / metabolism
  • Transcription, Genetic
  • Zinc / chemistry*


  • DNA, Fungal
  • DNA-Binding Proteins
  • Fungal Proteins
  • GAL4 protein, S cerevisiae
  • LEU3 protein, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • Trans-Activators
  • Transcription Factors
  • Histidine
  • DNA
  • Zinc
  • Cysteine

Associated data

  • PDB/2ER8
  • PDB/2ERE
  • PDB/2ERG