Structural changes in the region directly adjacent to the DNA-binding helix highlight a possible mechanism to explain the observed changes in the sequence-specific binding of winged helix proteins

J Mol Biol. 1998 May 1;278(2):293-9. doi: 10.1006/jmbi.1998.1703.


The hepatocyte nuclear factor 3 (HNF-3)/fork head (fkh) family contains a large number of transcription factors and folds into a winged helix motif. Despite having almost invariable amino acid sequences in their principal DNA-binding helices, HNF-3/fkh proteins show a wide diversity of sequence-specific binding. Previous studies of chimeric HNF-3/fkh proteins demonstrated that the binding specificity is primarily influenced by a region directly adjacent to the binding helix. We report our findings of an NMR structural study performed on an HNF-3/fkh family member (Genesis, formerly HFH-2) and compare it to that of another family member (HNF-3gamma) complexed to DNA and determined by X-ray crystallography. It is found that in comparison to HNF-3gamma, Genesis contains an extra small helix directly prior to the N terminus of the primary DNA contact helix. Due to the insertion of this helix, a shorter and slightly re-positioned primary DNA contact helix is observed, which we believe leads to the DNA-binding specificity differences among family members.

Publication types

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

MeSH terms

  • Binding Sites
  • Crystallography, X-Ray
  • DNA / metabolism
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / metabolism
  • Forkhead Transcription Factors
  • Helix-Turn-Helix Motifs*
  • Hepatocyte Nuclear Factor 3-gamma
  • Models, Molecular
  • Nuclear Magnetic Resonance, Biomolecular
  • Nuclear Proteins / chemistry
  • Nuclear Proteins / metabolism
  • Protein Conformation
  • Repressor Proteins / chemistry*
  • Repressor Proteins / metabolism
  • Structure-Activity Relationship
  • Transcription Factors*


  • DNA-Binding Proteins
  • Forkhead Transcription Factors
  • Foxd3 protein, rat
  • Nuclear Proteins
  • Repressor Proteins
  • Transcription Factors
  • Hepatocyte Nuclear Factor 3-gamma
  • DNA