InterPro: IPR018238 Glycoside hydrolase, family 14, conserved site

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.

Glycoside hydrolase family 14 GH14 comprises enzymes with only one known activity; beta-amylase (EC:3.2.1.2). A Glu residue has been proposed as a catalytic residue, but it is not known if it is the nucleophile or the proton donor.

Beta-amylase [5, 6] is an enzyme that hydrolyses 1,4-alpha-glucosidic linkages in starch-type polysaccharide substrates so as to remove successive maltose units from the non-reducing ends of the chains. Beta-amylase is present in certain bacteria as well as in plants.

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 [7]. 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 [7]. 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 [7]. 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 [7].

This entry represents two highly conserved sequence regions found in all known beta-amylases. The first of these regions (BETA_AMYLASE_1) is located in the N-terminal section of the enzymes and contains an aspartate which is known [8] to be involved in the catalytic mechanism. The second (BETA_AMYLASE_2), located in a more central location, is centred around a glutamate which is also involved [9] in the catalytic mechanism.