Crystal structure of the human Pax6 paired domain-DNA complex reveals specific roles for the linker region and carboxy-terminal subdomain in DNA binding

Pax6, a transcription factor containing the bipartite paired DNA-binding do main, has critical roles in development of the eye, nose, pancreas, and cen tral nervous system. The 2.5 Angstrom structure of the human Pax6 paired do main with its optimal 26-bp site reveals extensive DNA contacts from the am ino-terminal subdomain, the linker region, and the carboxy-terminal subdoma in. The Pax6 structure not only confirms the docking arrangement of the ami no-terminal subdomain as seen in cocrystals of the Drosophila Prd Pax prote in, but also reveals some interesting differences in this region and helps explain the sequence specificity of paired domain-DNA recognition. In addit ion, this structure gives the first detailed information about how the pair ed linker region and carboxy-terminal subdomain contact DNA. The extended l inker makes minor groove contacts over an 8-bp region, and the carboxy-term inal helix-turn-helix unit makes base contacts in the major groove. The str ucture and docking arrangement of the carboxy-terminal subdomain of Pax6 is remarkably similar to that of the amino-terminal subdomain, and there is a n approximate twofold symmetry axis relating the polypeptide backbones of t hese two helix-turn-helix units. Our structure of the Pax6 paired domain-DN A complex provides a framework for understanding paired domain-DNA interact ions, for analyzing mutations that map in the linker and carboxy-terminal r egions of the paired domain, and for modeling protein-protein interactions of the Pax family proteins.