InterPro: IPR000125 Glycoside hydrolase, family 14A, bacterial

O-Glycosyl hydrolases EC:3.2.1. are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [1, 2, 3]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site [4]. Because the fold of proteins is better conserved than their sequences, some of the families can be grouped in clans.

Family 14 (EC:3.2.1.2, GH14) encompasses the beta-amylases. Beta-amylases, which are found in plants and bacteria, hydrolyse 1,4-alpha-glycosidic linkages in starch-type polysaccharide substrates, removing successive maltose units from the non-reducing ends of the chains [5]. In potato plants, the enzyme has been found to work optimally at 40 degrees C, becoming unstable above this temperature [5]. On the basis of sequence comparisons, plant and bacterial beta-amylases can be readily distinguished from each other.

The 3D structure of a complex of soybean beta-amylase with an inhibitor (alpha-cyclodextrin) has been determined to 3.0A resolution by X-ray diffraction [6]. The enzyme folds into large and small domains: the large domain has a (beta alpha)8 super-secondary structural core, while the smaller is formed from two long loops extending from the beta-3 and beta-4 strands of the (beta alpha)8 fold [6]. The interface of the two domains, together with shorter loops from the (beta alpha)8 core, form a deep cleft, in which the inhibitor binds [6]. Two maltose molecules also bind in the cleft, one sharing a binding site with alpha-cyclodextrin, and the other sitting more deeply in the cleft [6]. Sequence alignments allow us to relate features of the bacterial beta-amylases to the soybean structure.