Three-Dimensional Structure of Soybean β-Amylase Determined at 3.0 Å Resolution: Preliminary Chain Tracing of the Complex with α-Cyclodextrin

Abstract

The three-dimensional structure of a complex of soybean β-amylase [EC 3.2.1.2] with an inhibitor, α-cyclodextrin, has been determined at 3.0 A resolution by X-ray diffraction analysis. Preliminary chain tracing showed that the enzyme folded into large and small domains. The large domain has a (βα)₃ super-secondary structure, while the smaller one is formed from two long loops extending from the β3 and β4 strands of the (βα)₃ structure. The interface of the two domains together with shorter loops from the (βα)³ structure form a deep cleft, in which α-cyclodextrin binds slightly away from the center. Two maltose molecules also bind in the cleft. One shares a binding site with α-cyclodextrin and the other is situated more deeply in the cleft.