ENGRAILED HOMEODOMAIN-DNA COMPLEX AT 2.2 ANGSTROM RESOLUTION - A DETAILED VIEW OF THE INTERFACE AND COMPARISON WITH OTHER ENGRAILED STRUCTURES

We report the 2.2 Angstrom resolution structure of the Drosophila engr ailed homeodomain bound to its optimal DNA site. The original 2.8 Angs trom resolution structure of this complex provided the first detailed three-dimensional view of how homeodomains recognize DNA, and has serv ed as the basis for biochemical studies, structural studies and molecu lar modeling.. Our refined structure confirms the principal conclusion s of the original structure, but provides important new details about the recognition interface. Biochemical and NMR studies of other homeod omains had led to the notion that Gln50 was an especially important de terminant of specificity. However, our refined structure shows that th is side-chain makes no direct hydrogen bonds to the DNA. The structure does reveal an extensive network of ordered water molecules which med iate contacts to several bases and phosphates (including contacts from Gln50), and our model provides a basis for detailed comparison with t he structure of an engrailed Q50K altered-specificity variant. Compari ng our structure with the crystal structure of the free protein confir ms that the N and C termini of the homeodomain become ordered upon DNA -binding. However, we also find that several key DNA contact residues in the recognition helix have the same conformation in the free and bo und protein, and that several water molecules also are ''preorganized' ' to contact the DNA. Our structure helps provide a more complete basi s for the detailed analysis of homeodomain-DNA interactions. (C) 1998 Academic Press.