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

PDB id:

4j3u

Name:

Hydrolase

Title:

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

Structure:

Limit dextrinase. Chain: a, b. Fragment: unp residues 22-905. Engineered: yes

Source:

Hordeum vulgare. Barley. Organism_taxid: 4513. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.70Å R-factor: 0.175 R-free: 0.218

Authors:

L.Sim,M.S.Windahl,M.S.Moeller,A.Henriksen

Key ref:

M.S.Møller et al. (2015). Oligosaccharide and substrate binding in the starch debranching enzyme barley limit dextrinase. J Mol Biol, 427, 1263-1277. PubMed id: 25562209 DOI: 10.1016/j.jmb.2014.12.019

Date:

06-Feb-13 Release date: 12-Feb-14

Protein chains

Q9FYY0  (Q9FYY0_HORVU) -  Limit dextrinase from Hordeum vulgare

Seq: 905 a.a.

Struc: 870 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.2.1.41 - pullulanase.
• Reaction: Hydrolysis of (1->6)-alpha-D-glucosidic linkages in pullulan and in amylopectin and glycogen, and the alpha- and beta-limit dextrins of amylopectin and glycogen.

DOI no: 10.1016/j.jmb.2014.12.019

J Mol Biol 427:1263-1277 (2015)

PubMed id: 25562209

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

M.S.Møller, M.S.Windahl, L.Sim, M.Bøjstrup, M.Abou Hachem, O.Hindsgaul, M.Palcic, B.Svensson, A.Henriksen.

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.