Exploring the role of glutamine 50 in the homeodomain-DNA interface: Crystal structure of engrailed (Gln50 -> Ala) complex at 2.0 angstrom

We have determined the crystal structure of a complex containing the engrai led homeodomain Gln50 --> Ala variant (QA50) bound to the wild-type optimal DNA site (TAATTA) at 2.0 Angstrom resolution. Biochemical and genetic stud ies by other groups have suggested that residue 50 is an important determin ant of differential DNA-binding specificity among homeodomains (distinguish ing among various sites of the general form TAATNN). However, biochemical s tudies of the QA50 variant had revealed that it binds almost as tightly as the wild-type protein and with only modest changes in specificity. We have now determined the crystal structure of the QA50 variant to help understand the role of residue 50 in site-specific recognition. Our cocrystal structu re shows some interesting changes in the water structure at the site of the substitution and shows some changes in the conformations of neighboring si de chains. However, the structure, like the QA50 biochemical data, suggests that Gln50 plays a relatively modest role in determining the affinity and specificity of the engrailed homeodomain.