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M. Zahran, T. Berezniak, P. Imhof, and J. C Smith (2011)

Role of Magnesium Ions in DNA Recognition by the EcoRV Restriction Endonuclease

FEBS Letters, 585(17):2739-2743.

The restriction endonuclease EcoRV binds two magnesium ions. One of these ions, Mg2+A, binds to the phosphate group where the cleavage occurs and is required for catalysis, but the role of the other ion, Mg2+B is debated. Here, multiple independent molecular dynamics simulations suggest that Mg2+B is crucial for achieving a tightly bound protein–DNA complex and stabilizing a conformation that allows cleavage. In the absence of Mg2+B in all simulations the protein–DNA hydrogen bond network is significantly disrupted and the sharp kink at the central base pair step of the DNA, which is observed in the two-metal complex, is not present. Also, the active site residues rearrange in such a way that the formation of a nucleophile, required for DNA hydrolysis, is unlikely.

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