Relationship of sequence and structure to specificity in the alpha-amylasefamily of enzymes

The hydrolases and transferases that constitute the a-amylase family are mu ltidomain proteins, but each has a catalytic domain in the form. of a (beta /alpha )8-barrel, with the active site being at the C-terminal end of the b arrel beta -strands. Although the enzymes are believed to share the same ca talytic acids and a common mechanism of action, they have been assigned to three separate families - 13, 70 and 77 - in the classification scheme for glycoside hydrolases and transferases that is based on amino acid sequence similarities. Each enzyme has one glutamic acid and two aspartic acid resid ues necessary for activity, while most enzymes of the family also contain t wo histidine residues critical for transition state stabilisation. These fi ve residues occur in four short sequences conserved throughout the family, and within such sequences some key amino acid residues are related to enzym e specificity. A table is given showing motifs distinctive for each specifi city as extracted from 316 sequences, which should aid in identifying the e nzyme from primary structure information. Where appropriate, existing probl ems with identification of some enzymes of the family are pointed out. For enzymes of known three-dimensional structure, action is discussed in terms of molecular architecture. The sequence-specificity and structure-specifici ty relationships described may provide useful pointers for rational protein engineering. (C) 2001 Elsevier Science B.V. All rights reserved.