4J3U

Crystal structure of barley limit dextrinase in complex with maltosyl-S-betacyclodextrin

Summary for 4J3U

• Entry DOI: 10.2210/pdb4j3u/pdb
• Related: 4J3S 4J3T 4J3V 4J3W 4J3X
• Descriptor: Limit dextrinase, Cyclic alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-[alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-1)]6-thio-alpha-D-glucopyranose, IODIDE ION, ... (6 entities in total)
• Functional Keywords: gh13 hydrolase, hydrolase
• Biological source: Hordeum vulgare (barley)
• Total number of polymer chains: 2
• Total formula weight: 206772.29

Authors

Sim, L.,Windahl, M.S.,Moeller, M.S.,Henriksen, A. (deposition date: 2013-02-06, release date: 2014-02-12, Last modification date: 2023-11-08)

Primary citation

Moeller, M.S.,Windahl, M.S.,Sim, L.,Bjstrup, M.,Abou Hachem, M.,Hindsgaul, O.,Palcic, M.,Svensson, B.,Henriksen, A.
Oligosaccharide and substrate binding in the starch debranching enzyme barley limit dextrinase
J.Mol.Biol., 427:1263-1277, 2015

PubMed 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.

PubMed: 25562209
DOI: 10.1016/j.jmb.2014.12.019

Experimental method

X-RAY DIFFRACTION (1.7 Å)