Oligosaccharide and Substrate Binding in the Starch Debranching Enzyme Barley Limit Dextrinase

Complete hydrolytic degradation of starch requires hydrolysis of both the alpha-1,4- and alpha-1,6-glucosidic bonds in amylopectin. Limit dextrinase (LD) is the only endogenous barley enzyme capable of hydrolyzing the alpha-1,6-glucosidic bond during seed germination, and impaired LD activity inevitably reduces the maltose and glucose yields from starch degradation. Crystal structures of barley LD and active-site mutants with natural substrates, products and substrate analogues were sought to better understand the facets of LD-substrate interactions that confine high activity of LD to branched maltooligosaccharides. For the first time, an intact alpha-1,6-glucosidically linked substrate spanning the active site of a LD or pullulanase has been trapped and characterized by crystallography. The crystal structure reveals both the branch and main-chain binding sites and is used to suggest a mechanism for nucleophilicity enhancement in the active site. The substrate, product and analogue complexes were further used to outline substrate binding subsites and substrate binding restraints and to suggest a mechanism for avoidance of dual alpha-1,6- and alpha-1,4-hydrolytic activity likely to be a biological necessity during starch synthesis. (C) 2015 Elsevier Ltd. All rights reserved.