Structural motif of the DNA binding domain of gamma delta-resolvase characterized by affinity cleaving

The DNA binding domain of gamma delta-resolvase, residues 141-183, is thought to bind DNA by a helix-turn-helix motif based on sequence similarities with other known DNA binding proteins. Incorporation of the DNA cleaving moiety, EDTA Fe, at the NH2 and COOH termini of gamma delta(141-183) allows the positions of these residues relative to the DNA bases at three resolvase binding sites, each consisting of inverted copies of an imperfectly conserved 9-base pair sequence, to be mapped by high resolution gel electrophoresis. The cleavage data for EDTA-gamma delta(141-183) reveals that the NH2 terminus of the DNA binding domain of gamma delta-resolvase is bound proximal to the minor groove of DNA near the center of the resolvase binding sites. Cleavage by EDTA Fe attached to a lysine side chain (Asn183----Lys183) at the COOH terminus of gamma delta(141-183) reveals that the putative recognition helix is in the adjacent major groove on the same face of the helix, oriented toward the center of the inverted repeats.