| Article ID | Journal | Published Year | Pages | File Type |
|---|---|---|---|---|
| 2047956 | FEBS Letters | 2011 | 5 Pages |
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.
