title: 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.
abstract: 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.
authors.affiliation: College of Medicine, University of Illinois at Chicago, 1819 West Polk Street, Chicago, IL 60612, USA.
authors.forename: I
authors.initials: I
authors.lastname: Marsden
authors.forename: C
authors.initials: C
authors.lastname: Jin
authors.forename: X
authors.initials: X
authors.lastname: Liao
mesh_terms: D001665:Binding Sites; D018360:Crystallography, X-Ray; D004247:DNA / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D051858:Forkhead Transcription Factors; D019077:Helix-Turn-Helix Motifs; D051543:Hepatocyte Nuclear Factor 3-gamma; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009687:Nuclear Proteins / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D012097:Repressor Proteins / Q000737:chemistry* / Q000378:metabolism; D013329:Structure-Activity Relationship; D014157:Transcription Factors
chemical_list: D004268:DNA-Binding Proteins; D051858:Forkhead Transcription Factors; C491100:Foxd3 protein, rat; D009687:Nuclear Proteins; D012097:Repressor Proteins; D014157:Transcription Factors; D051543:Hepatocyte Nuclear Factor 3-gamma; D004247:DNA