X-ray structure of Novamyl, the five-domain "maltogenic" alpha-amylase from Bacillus stearothermophilus: Maltose and acarbose complexes at 1.7 angstrom resolution

The three-dimensional structure of the Bacillus stearothermophilus "maltoge nic" alpha-amylase, Novamyl, has been determined by X-ray crystallography a t a resolution of 1.7 Angstrom. Unlike conventional alpha-amylases from gly coside hydrolase family 13, Novamyl exhibits the five-domain structure more usually associated with cyclodextrin glycosyltransferase. Complexes of the enzyme with both maltose and the inhibitor acarbose have been characterize d. In the maltose complex, two molecules of maltose are found in the -1 to -2 and +2 to +3 subsites of the active site, with two more on the C and E d omains. The C-domain maltose occupies a position identical to one previousl y observed in the Bacillus circulans CGTase structure [Lawson, C, L., et al . (1994) J. Mol. Biol. 236, 590-600], suggesting that the C-domain plays a genuine biological role in saccharide binding. In the acarbose-maltose comp lex, the tetrasaccharide inhibitor acarbose is found as an extended hexasac charide species, bound in the -3 to +3 subsites, The transition state mimic king pseudosaccharide is bound in the -1 subsite of the enzyme in a H-2(3) half-chair conformation, as expected. The active site of Novamyl lies in an open gully, fully consistent with its ability to perform internal cleavage via an endo as opposed to an exo activity.