SKN-1 DOMAIN FOLDING AND BASIC REGION MONOMER STABILIZATION UPON DNA-BINDING

The SKN-1 transcription factor specifies early embryonic cell fates in Caenorhabditis elegans. SKN-1 binds DNA at high affinity as a monomer , by means of a basic region like those of basic-leucine zipper (bZIP) proteins, which bind DNA only as dimers. We have investigated how the SKN-1 DNA-binding domain (the Skn domain) promotes stable binding of a basic region monomer to DNA. A flexible arm at the Skn domain amino terminus binds in the minor groove, but a support segment adjacent to the carboxy-terminal basic region can independently stabilize basic re gion-DNA binding. Off DNA, the basic region and arm are unfolded and, surprisingly, the support segment forms a molten globule of four alpha -helices. On binding DNA, the Skn domain adopts a tertiary structure i n which the basic region helix extends directly from a support segment alpha-helix, which is required for binding. The remainder of the supp ort segment anchors this uninterrupted helix on DNA, but leaves the ba sic region exposed in the major groove. This is similar to how the bZI P basic region extends from the leucine zipper, indicating that positi oning and cooperative stability provided by helix extension are conser ved mechanisms that promote binding of basic regions to DNA.