Structure and functional role of protein-bonded magnesium-water cluster ofthe endonuclease from Serratia marcescens

The three-dimensional crystal structure of nonspecific Serratia marcescens endonuclease has been refined at 1.1-Angstrom resolution to R of 12.9% and R-free of 15.6% in the presence of the magnesium ion within the active site of the enzyme. The model contains 3694 non-H atoms and 715 water molecules and includes one Mg2+ binding site for each subunit of the homodimeric pro tein globule. The magnesium ion linked to the Asn-119 residue is also assoc iated with five water molecules to complete an octahedral coordination comp lex. The temperature factors for the bound Mg2+ ions in the A and B subunit s are 7.08 and 4.60 Angstrom (2), respectively. The average temperature fac tors for the surrounding water molecules are 11.14 and 10.3 Angstrom (2), r espectively. It is shown that the magnesium ion of the nuclease participate s in the catalytic hydrolysis of the phosphodiester bonds of nucleic acids via an inner-sphere mechanism, and a plausible mechanism of the enzyme func tion is proposed based on the high-resolution protein structure, the cataly tic properties of the enzyme, and its structural analogy with related nucle ases.