Structure Comparison of Two Conserved HNF-3/fkh Proteins HFH-1 and Genesis Indicates the Existence of Folding Differences in Their Complexes with a DNA Binding Sequence,

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Abstract
The hepatocyte nuclear factor 3 (HNF-3)/fork head (fkh) family contains a large number of transcription factors that recognize divergent DNA sequences via a winged helix binding motif. HNF-3/fkh proteins show a broad profile of DNA sequence-specificity in which one DNA sequence can be recognized by more than one HNF-3/fkh protein and each individual HNF-3/fkh protein has several DNA binding sequences. In this study, heteronuclear NMR methods were used to study the structures of the DNA binding domain of a conserved winged helix protein HFH-1 and its DNA complexes. The structural comparison of winged helix proteins HFH-1 and Genesis and their DNA complexes indicates that even two highly conserved HNF-3 family members can adopt different local structures when they contact an identical DNA binding sequence, while one of these two HNF-3 proteins seems to adopt only slightly different structures on different DNA binding sites.

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