Structure-specific Binding of the Two Tandem HMG Boxes of HMG1 to Four-way Junction DNA is Mediated by the A Domain

Michelle Webb and Jean O. Thomas*

J.Mol.Biol. 294, 373-387 (1999)


Abstract:

       HMG-1 contain two homologous HMG-box domains (A and B) of about 80 amino acid residues whose structures have been determined. In this paper, they have used two approaches to investigate the interaction of the AB didomain with the four-way junction. AB didomain binding favors the open form of the junction, as shown by reaction with potassium permanganate. Site-directed cleavage of the DNA by a 1,10-phenanthroline-copper moiety attached to cysteine residues in the A or B domain shows that the two linked HMG boxes are not functionally equivalent in four-way junction binding. The A domain of the didomain binds to the central of the junction. The B domain makes contacts along one of the arms, presumably stabilizing the binding of the didomain through additional non-sequence-specific interactions. The isolated B domain can, however, bind to the central of the junction. The preferential binding of the A domain of the AB didomain to the central correlates with our previous binding of a higher preference of the isolated A domain than of the B domain for this structurally distinct DNA ligand. It is probably at least partly due to the higher positive surface potential on surface of the A domain and orientation of helix .

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