The solution structure of the homeodomain of the rat insulin-gene enhancerprotein Isl-1. Comparison with other homeodomains

Homeodomains are one of the key families of eukaryotic DNA-binding motifs a nd provide an important model system for DNA recognition. We have determine d a high-quality nuclear magnetic resonance (NMR) structure of the DNA-bind ing homeodomain of the insulin gene enhancer protein Isl-1 (Isl-1-HD). It f orms the first solution structure of homeodomain from the LIM family. It co ntains a well-defined inner core (residues 12-55) consisting of the classic al three-helix structure observed in other homeodomains. The N terminus is unstructured up to residue 8, while the C terminus gradually becomes unstru ctured from residue 55 onwards. Some flexibility is evident in the loop par ts of the inner core. Isl-1-HD has, despite its low sequence identity (23-3 4%), a structure that is strikingly similar to that of the other homeodomai ns with known three-dimensional structures. Detailed analysis of Isl-1-HD a nd the other homeodomains rationalizes the differences in their temperature stability and explains the low stability of the Isl-1-HD in the free state (tm 22-30 degrees C). Upon DNA binding, a significant stabilization occurs (t(m) > 55 degrees C). The low stability of Isl-1-HD (and other mammalian homeodomains) suggests that in vivo Isl-1-HD recognizes its cognate DNA fro m its unfolded state. (C) 1999 Academic Press.