Solvent participation in Serratia marcescens endonuclease complexes

The monomer and dimer of the bacterium Serratia marcescens endonuclease (SMnase) are each catalytically active and the two subunits of the dimer function independently of each other. Specific interfacial waters may play a role in stability, complex formation, and functionality. We performed molecular dynamics simulations of both a subunit of SMnase and its model built complex with DNA and analyzed the relation of the hydration sites to the catalytic mechanism. It was found that the binding of DNA has little influence on the global hydration properties of the protein, including occupancy and water residence time distributions. DNA and protein recognition in our model mainly involves direct contacts by hydrogen bond and hydrophobic interactions. Water-mediated contacts exist, but are less common. Three interior water clusters were identified for SMnase. One cluster around the active site in the monomer-DNA complex shows relatively strong interactions between hydration sites as well as between the sites and the biomolecules. The simulated cluster properties agreed well with experimental data. The magnesium ion shows ligand exchange. Although Mg²⁺ keeps six ligands during the entire simulation, upon the binding of DNA, Asn119 loses its coordination with Mg ²⁺, while one nonbridging oxygen of the phosphate of a DNA residue and two oxygen atoms of the side chain of Glu127 become the ligands. Waters in a nearby cluster exchange and participate in the resolvation of groups in the presence of DNA. Water thus not only participates in the cleavage of DNA but also can stabilize the transition state and the leaving groups in our model.