Winged helix transcription factors contain two polypeptide loops, or “wings,” that make minor groove contacts with DNA from
either side of a three-helix bundle that binds the DNA major groove. While wing 1 is stabilized by a β-sheet, parameters that
stabilize wing 2 are unknown. Herein we identify two bulky aromatic residues in wing 2 that stabilize the loop structure and,
thereby, the entire
... [Show full abstract] protein's DNA binding and transcriptional stimulatory activity by interacting with other residues in the
three-helix bundle. Mutations of these wing 2 residues create proteins that are temperature-sensitive for transcriptional
activity. Aromatic and/or hydrophobic residues are highly conserved among the 150 known winged helix proteins, suggesting
conserved function. We suggest that the winged helix structure evolved by the acquisition of aromatic and/or hydrophobic residues
in distal polypeptide sequences that helped stabilize the association of a protein loop (wing 2) with the three-helix bundle,
thereby enhancing DNA binding.