EcoRV is a type II restriction endonuclease that cleaves sequences GAT|ATC, and has a structure that is similar to that of HincII, however EcoRV does not shift the base planes of its bound DNA nearly so far into the minor groove as does HincII. As a result, the two enzymes distort their bound DNA in different ways. EcoRV is also believed to utilize indirect readout in recognition of its DNA (Martin, et. al (1999) Nat. Struct. Biol. 6, 269-77), however, the distortion and the specificity are different than those of HincII. The two structures can be aligned and analyzed for how they distort DNA differently. Below is a morph between the two structures. The dimerization domains are different for the two enzymes: over the top in HincII, and at the bottom in EcoRV (using segments not shown in the figure, and present only in EcoRV). The dimerization domain of HincII brings the tops of the two subunits closer together, which is accomplished by a 15 degree rotation of each subunit (green and cyan). This brings the R loops deeper into the major groove of the bound DNA, which in turn pushes the base planes into the minor groove. Thus the DNA distortion induced by HincII appears to be a result of the positioning of the R loops, which in turn is influenced by the position of the dimerization domain. EcoRV appears to use its B helices to distort the bound DNA by prying apart the minor groove. (see Horton & Perona (2000) "Crystallographic snapshots along a protein-induced DNA-bending pathway", Proc. Nat. Acad. Sci, USA 97, 5729-34). The domain positioning in EcoRV places the B helices deeper into the minor groove. New experiments to test this proposed relationship are currently under way.

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Department of Biochemistry and Molecular Biophysics
University of Arizona
nhorton@u.arizona.edu
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January 11, 2008

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