The structure of the staphylococcal nuclease (EC 3.1.4.7)-thymidine 3',5'-bisphosphate-Ca2+ (enzyme-inhibitor) complex has been extended to 1.5-A resolution by using much additional data and a phase refinement scheme based on an electron-density map modification procedure. By correlating this structure with the known properties of the enzyme, a mechanism of action is proposed that involves nucleophilic attack on phosphorus by a water molecule, which is bound to Glu43, in line with the 5'-CH20(H) leaving group. Staphylococcal or micrococcal nuclease (nucleate 3'-oligonucleotidohydrolase, EC 3.1.4.7) is a Ca2+-dependent, extracellular enzyme produced by certain strains of Staphylococcus aureus. As isolated, the enzyme has a single peptide chain of 149 amino acid residues with no intrachain crosslinkages and a molecular weight of about 16,800. The small size, availability in highly purified form, and interesting properties of this enzyme have led to its use as a model in several significant studies in protein chemistry and as a practical tool in nucleic acid research. We have recently prepared a comprehensive, four-part review of the nuclease (1-4), and other reviews dealing with this enzyme have also appeared (5, 6). We restrict ourselves here to a description of the structure of the active site of the enzyme based on our interpretation of the nuclease-thymidine 3',5'-bisphosphate (pdTp)-Ca2+ complex at 1.5-A resolution and to the proposal of a plausible mechanism of action based on this structure and certain known chemical and enzymological properties of the nuclease. We note that, to the best of our knowledge, this is one of a very few enzyme structures that has been determined at a resolution as high as 1.5 A. MATERIALS AND METHODSCrystals of the nuclease-pdTp-Ca2+ complex were grown as described (7,8). Data were collected with a Syntex P1 autodiffractometer by using an abbreviated w scan. Our earlier high-resolution structure (8) of the enzyme-inhibitor complex was based on some 4600 independent reflections phased by the use of two heavy-atom derivatives, but, between d-spacings of 4 A and 2 A, the data set included only that third of the reflections having the highest intensities. By using these phased reflections as a base, phases were extended and refined by an iterative, electron-density map modification procedure (9, 10) to a total of some 18,400 (of a possible 25,000) measured reflections within a d-spacing of 1.5 A. The resultant electrondensity map was fitted to a model by using an interactive computer graphics system developed in the laboratory of Edgar Meyer at this university (9). A full description of these methods, the detailed results of their application, and the nominal 1.5-A structure of the nuclease-pdTp-Ca2+ complex are as yet unpublished. RESULTS AND DISCUSSIONEnzymological properties of the nuclease Staphylococcal nuclease catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond yielding a free 5'-hydroxyl group and a 3'-phosphate monoester (1)(2)...