Atomic structure of the Serratia marcescens ­endonuclease at 1.1 Å resolution and the enzyme reaction mechanism

The three-dimensional crystal structure of Serratia marcescens endonuclease has been refined at 1.1 Å resolution to an R factor of 12.9% and an R_free of 15.6% with the use of anisotropic temperature factors. The model contains 3694 non-H atoms, 715 water molecules, four sulfate ions and two Mg²⁺-binding sites at the active sites of the homodimeric protein. It is shown that the magnesium ion linked to the active-site Asn119 of each monomer is surrounded by five water molecules and shows an octahedral coordination geometry. The temperature factors for the bound Mg²⁺ ions in the A and B subunits are 7.08 and 4.60 Å², respectively, and the average temperature factors for the surrounding water molecules are 12.13 and 10.3 Å², respectively. In comparison with earlier structures, alternative side-chain conformations are defined for 51 residues of the dimer, including the essential active-site residue Arg57. A plausible mechanism of enzyme function is proposed based on the high-resolution S. marcescens nuclease structure, the functional characteristics of the natural and mutational forms of the enzyme and consideration of its structural analogy with homing endo­nuclease I-PpoI.