Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites

The crystal structure of a calcium-free alpha-amylase (AmyK38) from Bacillus sp. strain KSM-K38, which resists chelating reagents and chemical oxidants, has been determined by the molecular replacement method and refined to a crystallographic R-factor of 19.9% (R-free of 23.2%) at 2.13-A resolution. The main chain folding of AmyK38 is almost homologous to that of Bacillus licheniformis alpha-amylase. However, neither a highly conserved calcium ion, which is located at the interface between domains A and B, nor any other calcium ions appear to exist in the AmyK38 molecule, although three sodium ions were found, one of which is located at the position corresponding to that of a highly conserved calcium ion of other alpha-amylases. The existence of these sodium ions was crystallographically confirmed by the structures of three metal-exchanged and mutated enzymes. This is the first case in which the structure of the calcium-free alpha-amylase has been determined by crystallography, and it was suggested that these sodium ions, instead of calcium ions, are used to retain the structure and function of AmyK38.