Structure of HAP1-18-DNA Implicates Direct Allosteric Effect of protein-DNA Interactions on Transcriptional Activation

Nat Struct Biol. 1999 Jan;6(1):22-7. doi: 10.1038/4893.


HAP1 is a yeast transcriptional activator that binds with equal affinity to the dissimilar upstream activation sequences UAS1 and UAS(CYC7), but activates transcription differentially when bound to each site. HAP1-18 harbors an amino acid change in the DNA binding domain. While binding UAS1 poorly, HAP1-18 binds UAS(CYC7) with wild-type properties and activates transcription at elevated levels relative to HAP1. We have determined the structure of HAP1-18-UAS(CYC7) and have compared it to HAP1-UAS(CYC7). Unexpectedly, the single amino acid substitution in HAP1-18 nucleates a significantly altered hydrogen bond interface between the protein and DNA resulting in DNA conformational changes and an ordering of one N-terminal arm of the protein dimer along the DNA minor groove. These observations, together with a large subset of transcriptionally defective mutations in the HAP1 DNA-binding domain that map to the HAP1-DNA interface, suggest that protein-DNA interactions may have direct allosteric effects on transcriptional activation.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Carbon-Oxygen Lyases / chemistry*
  • Carbon-Oxygen Lyases / metabolism
  • DNA, Fungal / chemistry*
  • DNA, Fungal / genetics
  • DNA, Fungal / metabolism
  • DNA-(Apurinic or Apyrimidinic Site) Lyase*
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Protein Binding
  • Saccharomyces cerevisiae
  • Transcriptional Activation*


  • DNA, Fungal
  • DNA-Binding Proteins
  • Carbon-Oxygen Lyases
  • DNA-(Apurinic or Apyrimidinic Site) Lyase

Associated data

  • PDB/2HAP