The SKN-1 amino-terminal arm is a DNA specificity segment

The Caenorhabditis elegans SKN-1 protein binds DNA through a basic region l ike those of bZIP proteins and through a flexible amino-terminal arm segmen t similar to those with which numerous helix-turn-helix proteins bind to ba ses in the minor groove. A recent X-ray crystallographic structure suggests that the SKN-1 aminoterminal arm provides only nonspecific DNA binding. In this study, however, we demonstrate that this segment mediates recognition of an AT-rich element that is part of the preferred SKN-1 binding site and thereby significantly increases the sequence specificity with which SKN-1 binds DNA. Mutagenesis experiments show that multiple amino acid residues w ithin the arm are involved in binding. These residues provide binding affin ity through distinct but partially redundant interactions and enhance speci ficity by discriminating against alternate sites. The AT-rich element minor groove is important for binding of the arm, which appears to affect DNA co nformation in this region. This conformational effect does not seem to invo lve DNA bending, however, because the arm does not appear to affect a modes t DNA bend that is induced by SKN-1. The data illustrate an example of how a small, flexible protein segment can make an important contribution to DNA binding specificity through multiple interactions and mechanisms.