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Published July 17, 1990 | public
Journal Article

Importance of minor-groove contacts for recognition of DNA by the binding domain of Hin recombinase


Incorporation of the DNA-cleaving moiety EDTA•Fe at discrete amino acid residues along a DNA-binding protein allows the positions of these residues relative to DNA bases, and hence the organization of the folded protein, to be mapped by high-resolution gel electrophoresis. A 52-residue protein, based on the sequence-specific DNA-binding domain of Hin recombinase (139-190), with EDTA at the NH_2 terminus cleaves DNA at Hin recombination sites. The cleavage data for EDTA-Hin(139-190) reveal that the NH_2 terminus of Hin(139-190) is bound in the minor groove of DNA near the symmetry axis of Hin-binding sites [Sluka, J. P., Horvath, S. J., Bruist, M. F., Simon, M. I., & Dervan, P. B. (1987) Science 238, 1129]. Six proteins, varying in length from 49 to 60 residues and corresponding to the DNA-binding domain of Hin recombinase, were synthesized by solid-phase methods: Hin(142-190), Hin(141-190), Hin(140-190), Hin(139-190), Hin(135-190), and Hin(131-190) were prepared with and without EDTA at the NH_2 termini in order to test the relative importance of the residues Gly^(139)-Arg^(140)-Pro^(141)-Arg^(142), located near the minor groove, for sequence-specific recognition at five imperfectly conserved 12-base-pair binding sites. Footprinting and affinity cleaving reveal that deletion of Gly^(139) results in a protein with affinity and specificity similar to those of Hin(139-190) but that deletion of Gly^(139)-Arg^(140) affords a protein with altered affinities and sequence specificities for the five binding sites. It appears that Arg^(140) in the DNA-binding domain of Hin is important for recognition of the 5'-AAA-3' sequence in the minor groove of DNA. Our results indicate modular DNA and protein interactions with two adjacent DNA sites (major and minor grooves, respectively) bound on the same face of the helix by two separate parts of the protein.

Additional Information

© 1990 American Chemical Society. Received January 5, 1990; Revised Manuscript Received March 6, 1990. Supported by grants from the DARPA University Research Initiative Program, the National Foundation for Cancer Research, and the National Science Foundation and by a National Research Service Award from NIGMS to J.P.S.

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