Oligosaccharide and substrate binding in the starch debranching enzyme barley limit dextrinase.

Marie S Møller, Michael S Windahl, Lyann Sim, Marie Bøjstrup, Maher Abou Hachem, Ole Hindsgaul, Monica Palcic, Birte Svensson, Anette Henriksen

Index: J. Mol. Biol. 427(6 Pt B) , 1263-77, (2015)

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Abstract

Complete hydrolytic degradation of starch requires hydrolysis of both the α-1,4- and α-1,6-glucosidic bonds in amylopectin. Limit dextrinase (LD) is the only endogenous barley enzyme capable of hydrolyzing the α-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 α-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 α-1,6- and α-1,4-hydrolytic activity likely to be a biological necessity during starch synthesis. Copyright © 2015 Elsevier Ltd. All rights reserved.