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

The three-dimensional crystal structure of Serratia marcescens endonuclease has been refined at 1.1 Angstrom 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 sh own 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 s ubunits are 7.08 and 4.60 Angstrom(2), respectively, and the average temper ature factors for the surrounding water molecules are 12.13 and 10.3 Angstr om(2), respectively. In comparison with earlier structures, alternative sid e-chain conformations are defined for 51 residues of the dimer, including t he essential active-site residue Arg57. A plausible mechanism of enzyme fun ction is proposed based on the high-resolution S. marcescens nuclease struc ture, the functional characteristics of the natural and mutational forms of the enzyme and consideration of its structural analogy with homing endonuc lease I-PpoI.