X-ray Crystal Structure Analysis of Soybean β-Amylase

The structure of soybean β-amylase has been determined by X-ray crystallography by using multiple isomorphous replacement technique. The low resolution analysis at 6 A revealed that the enzyme is composed of a large and a small domain. The difference Fourier synthesis for the enzyme-a-cyclodextrin complex and the enzyme-maltose complex showed that the substrate analogs bind to a deep cleft between the two domains. One maltose molecule is supposed to occupy the binding site of nonreducing ends of the substrate (subsite 1). The higher resolution analysis at 3 A of the enzyme-a-cyclodextrin complex clearly showsthat the large domain contains a (αβ)8 supersecondary structure. The chain following shows that the smaller domain is inserted in the loop region after β4. The structure of β-amylase is quite different from that of β-amylases except for the (αβ)8 barrel structure. The chain following also shows that the two SH groups, Cys95 and Cys343, are located in the edges of the active cleft. Cys95 is near the maltose specific binding site and Cys343 is near the α-cyclodextrin binding site. These two SH groups were demonstrated to be responsible for the inactivation of the enzyme by chemical modification.