PDBsum entry 4j3u

Hydrolase

PDB id: 4j3u

Contents

Protein chains

870 a.a.

Ligands

SGD-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC ×2

IOD ×32

Metals

_CL ×2

_CA ×4

Waters ×1612

References listed in PDB file

Key reference

• Title: Oligosaccharide and substrate binding in the starch debranching enzyme barley limit dextrinase.
• Authors: M.S.Møller, M.S.Windahl, L.Sim, M.Bøjstrup, M.Abou hachem, O.Hindsgaul, M.Palcic, B.Svensson, A.Henriksen.
• Ref.: J Mol Biol, 2015, 427, 1263-1277. [DOI no: 10.1016/j.jmb.2014.12.019]
• PubMed id: 25562209

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.