Comparison of crystal structures of crystallographic studies of barley alpha-amylase 1 and 2: implications for isozyme differences in stability and activity

The germinating barley seed contains two major alpha-amylase isozyme families AMY1 and AMY2 involved in starch degradation to provide energy used by the plant embryo for growth. The three-dimensional structure of AMY2 has been solved previously, both in the native state and in complex with acarbose, a pseudo-tetrasaccharide acting as a powerful inhibitor for several glycosidases. Furthermore, the endogenous bifunctional barley alpha-amylase/subtilisin inhibitor (BASI) present in the mature seeds inhibits both proteases from the subtilisin family and AMY2, but not AMY1. The crystal structure of the AMY2-BASI complex has earlier been solved at 1.9 Angstrom resolution. In addition to this difference, the isozymes AMY1 and AMY2 show several distinctly different properties, despite their high sequence identity. AMY1 and AMY2 thus differ in isoelectric point, in affinity for calcium ions, and in stability at acidic pH and elevated temperature. With regard to the enzymatic properties, large variation is found in the activity towards starch granules and in the affinity for soluble substrates. The crystal structure of AMY1 has recently been established at 1.5 Angstrom resolution, which allows a direct comparison of the two isozymes on the basis of the 3D structures. Detailed analysis shows that the structural organization of the isozymes is virtually identical, and that local changes are very small. AMY1 and AMY2 thus constitute a remarkable case of enzymes displaying very similar structures, but important differences in physico-chemical and enzymatic properties. Here, the recently solved crystal structure of AMY1 is compared to that of AMY2, with focus on isozyme differences at areas of interest, i.e. the active site, the starch- granule-binding surface site, the area where BASI is recognized by AMY2, and the three calcium binding sites.