α-Amylase: an enzyme specificity found in various families of glycoside hydrolases

Abstract

α-Amylase (EC 3.2.1.1) represents the best known amylolytic enzyme. It catalyzes the hydrolysis of α-1,4-glucosidic bonds in starch and related α-glucans. In general, the α-amylase is an enzyme with a broad substrate preference and product specificity. In the sequence-based classification system of all carbohydrate-active enzymes, it is one of the most frequently occurring glycoside hydrolases (GH). α-Amylase is the main representative of family GH13, but it is probably also present in the families GH57 and GH119, and possibly even in GH126. Family GH13, known generally as the main α-amylase family, forms clan GH-H together with families GH70 and GH77 that, however, contain no α-amylase. Within the family GH13, the α-amylase specificity is currently present in several subfamilies, such as GH13_1, 5, 6, 7, 15, 24, 27, 28, 36, 37, and, possibly in a few more that are not yet defined. The α-amylases classified in family GH13 employ a reaction mechanism giving retention of configuration, share 4-7 conserved sequence regions (CSRs) and catalytic machinery, and adopt the (β/α)8-barrel catalytic domain. Although the family GH57 α-amylases also employ the retaining reaction mechanism, they possess their own five CSRs and catalytic machinery, and adopt a (β/α)7-barrel fold. These family GH57 attributes are likely to be characteristic of α-amylases from the family GH119, too. With regard to family GH126, confirmation of the unambiguous presence of the α-amylase specificity may need more biochemical investigation because of an obvious, but unexpected, homology with inverting β-glucan-active hydrolases.

New insight in cereal starch degradation: identification and structural characterization of four α-amylases in bread wheat

“…The tertiary structure of four representatives of each wheat α-amylase isoform were modelled and the results confirmed both the fold and domain arrangement typical for family GH13 members [5]: (i) the catalytic (β/α) 8 -barrel domain; (ii) domain B protruding out from the barrel between the strand β3 and helix α3; and (iii) domain C succeeding the barrel (Figure 3). Although they all most resemble the structures of both barley α-amylase isozymes [10,48], the structure of the low pI isozyme (Figure 3a) was used for comparison.…”

“…The α-amylase family has always shown a high level of complexity and multiplicity throughout the plant kingdom from the Prasinophyceae to the Poaceae [5]. Even in the case of unicellular green algae, like Ostreococcus tauri, the presence of three different isoforms of α-amylase despite reductions occurring within other important metabolic processes, such as cell cycle control, illustrated this high level of complexity [55,56].…”

“…Available amino acid sequences were taken from a few previous bioinformatics studies [5,[26][27][28][29][30] focusing mainly on the α-amylases from subfamilies GH13_6 (29 plant α-amylases accompanied by 2 bacterial representatives) and GH13_7 (10 archaeal and 2 bacterial sources). These 43 sequences, retrieved from the UniProt knowledge database ( [31]; http://www.uniprot.org/), were completed by the consensus protein sequence for each wheat isoform.…”

“…The tree is based on the alignment of the sequence segment spanning almost the entire catalytic (β/α) 8 -barrel domain including the domain B. Except for the α-amylases from wheat determined in the present study (each starts with "TaAmy"), all remaining α-amylases classified in the CAZy database within the α-amylase family GH13 were taken according to previous bioinformatics studies [5,[26][27][28][29][30]. They are characterized in the tree by the letter P, B or A for "Plants", "Bacteria" and "Archaea", respectively, the GH13 subfamily number 6 or 7 for subfamilies GH13_6 and GH13_7, respectively [33], the source of origin (the organism) and the accession number from the UniProt database.…”

“…This class of α-1,4-glucan hydrolytic enzymes has been thoroughly described from unicellular organisms to plants and humans (for a review, see [5]). In plants, the role and number of α-amylase isoforms vary significantly across monocots and dicots.…”