A novel GH13 subfamily of α-amylases with a pair of tryptophans in the helix α3 of the catalytic TIM-barrel, the LPDlx signature in the conserved sequence region V and a conserved aromatic motif at the C-terminus

Abstract

AbstractThe α-amylase enzyme specificity has been classified in the Carbohydrate-Active enZyme (CAZy) database into the families GH13, GH57, GH119 and eventually also GH126. α-Amylase is a glycoside hydrolase (GH) that catalyses in an endo-fashion the hydrolysis of the α-1,4-glucosidic linkages in starch and related α-glucans employing the retaining reaction mechanism. The family GH13 is the main α-amylase family with more than 28,000 members and 30 different specificities. The entire family GH13 has already been divided into 40 subfamilies; the α-amylase enzyme specificity being found in the subfamilies GH13 1, 5, 6, 7, 15, 19, 24, 27, 28, 32, 36 and 37. The present in silico study delivers a proposal to create a novel GH13 subfamily with the specificity of α-amylase. The proposal is based on a detailed bioinformatics analysis consisting of sequence, structural and evolutionary comparison of experimentally characterized α-amylases from, e.g., Bacillus aquimaris, Anoxybacillus sp. SK3-4 and DT3-1 and Geobacillus thermoleovorans, and hypothetical proteins, accompanied by α-amylases from well-established GH13 subfamilies and by closely related amylolytic enzymes (mainly from the subfamily GH13 31). Three sequence-structural features can be ascribed to the members of the newly proposed GH13 subfamily: (i) the pair of adjacent tryptophan residues positioned between the CSR-V and CSR-II in the helix α3 of the catalytic TIM-barrel; (ii) the sequence LPDlx in their CSR-V; and (iii) a ~30-residue long C-terminal region with a motif of five conserved aromatic residues. From the evolutionary point of view, the novel GH13 α-amylase subfamily is most closely related to fungal and yeast α-amylases classified in the subfamily GH13_1.