α-Amylases from Archaea: Sequences, Structures and Evolution

Abstract

α-Amylase (EC 3.2.1.1) catalyzes the hydrolysis of α-1,4-glucosidic linkages in starch and related α-glucans. Within the sequence-based classification of carbohydrate-active enzymes, the CAZy database, the specificity of α-amylase has been classified in glycoside hydrolase (GH) families GH13, GH57 and GH119. The polyspecific family GH13 with about 24,000 members is considered as the main α-amylase family forming the clan GH-H with families GH70 and GH77 (both without the α-amylase specificity). The family GH57, which is also a polyspecific one with, however, only about 1100 members, is known as the second α-amylase family related to the monospecific family GH119 (currently only 10 members). The α-amylases from the family GH13 employ a retaining reaction mechanism, share 7 conserved sequence regions (CSRs) and adopt a TIM-barrel domain with the GH13 catalytic machinery. Although the α-amylases from the family GH57 also use the retaining reaction mechanism, they exhibit their own 5 CSRs and have the catalytic machinery different from that present in the family GH13 within an incomplete TIM-barrel fold. In Archaea, α-amylases from families GH13 and GH57 have been found. The archaeal GH13 α-amylases form their subfamily GH13_7 that is remarkably closely related to the subfamily GH13_6 containing plant counterparts. There may also be another halophilic group of archaeal α-amylases in the family GH13 but currently without subfamily assignment. The archaeal GH57 α-amylases are most closely related to their α-amylase-like homologues, which are putative proteins with incomplete catalytic machinery originating mostly from Bacteria.