Substrate size dependence of lysozyme-catalyzed reaction.

In the study of the mechanism of lysozyme-catalyzed reactions, it has been assumed that the rate constants in the catalytic process, the catalytic activity of catalytic group Glu 35, are independent of the degree of polymerization (size) of the substrate. The characteristics of substrate binding subsite F have recently been reexamined and the substrate binding mode at this subsite has been demonstrated to be more complex than expected from a model based on an X-ray analysis of the lysozyme-substrate complex. In the present study, the time courses of the lysozyme-catalyzed reactions with the substrates chitotetraose [(GlcNAc)4], chitopentaose [(GlcNAc)5], and chitohexaose [(GlcNAc)6], of 2-acetamido-2-deoxy-D-glucopyranose (GlcNAc), were obtained experimentally with high-performance liquid chromatography. From the experimental time courses, the values of the rate constants, k+1 (the cleavage of glycosidic linkage) and k-1/k+2 (relative efficiency of transglycosylation), were obtained by a data-fitting method with computer simulation of the lysozyme-catalyzed reaction (A. Masaki et al. (1981) J. Biochem. 90, 1167-1175). As a result, it was found that the k+1 value is dependent on the substrate size and the value of the binding free energy of subsite F is considerably smaller than previously estimated. The substrate size dependence of the k+1 value is considered to relate closely to the fine structure of the binding and catalytic sites.