Role of magnesium ions in DNA recognition by the EcoRV restriction endonuclease

The restriction endonuclease EcoRV binds two magnesium ions. One of these ions, MgA2+, binds to the phosphate group where the cleavage occurs and is required for catalysis, but the role of the other ion, MgB2+ is debated. Here, multiple independent molecular dynamics simulations suggest that MgB2+ is crucial for achieving a tightly bound protein–DNA complex and stabilizing a conformation that allows cleavage. In the absence of MgB2+ 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.

► We perform multiple independent molecular dynamics simulations of EcoRV–DNA complexes bound to one or two Mg2+.
► Disruption of the hydrogen-bond network of the protein–DNA complex in the absence of MgB2+.
► MgB2+ is crucial to maintain the sharp kink at the central base pair step of the DNA.
► Without MgB2+, the formation of a nucleophile, required for DNA hydrolysis, is unlikely.