Crystal Structure of Barley Limit Dextrinase-Limit Dextrinase Inhibitor (LD-LDI) Complex Reveals Insights into Mechanism and Diversity of Cereal Type Inhibitors

Møller, Marie Sofie; Vester-Christensen, Malene Bech; Jensen, Jørgen Dejgaard; Hachem, Maher Abou; Henriksen, A.; Svensson, Birte

doi:10.1074/jbc.m115.642777

Cited by 19 publications

(44 citation statements)

References 58 publications

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“…Moreover, structural information on other debranching enzymes, i.e. Hordeum vulgare limit dextrinase (HvLD;Møller, Vester-Christensen et al, 2015;Møller, Windahl et al, 2015), Bacillus stearothermophilus neopullulanase (Hondoh et al, 2003), Chlamydomonas reinhardtii isoamylase I (Sim et al, 2014) and Pseudomonas amyloderamosa isoamylase (Katsuya et al, 1998) have been deposited in the Protein Data Bank (PDB; http://www.rcsb.org/). Cyclodextrins (CDs) are cyclic oligosaccharides consisting of -1,4-glycosidic linked -d-glucose units and are known to occur as three types: -CD (six glucose units), -CD (seven glucose units) and -CD (eight glucose units) (Szejtli, 1998).…”

Section: Introductionmentioning

confidence: 99%

Elucidation of the mechanism of interaction between Klebsiella pneumoniae pullulanase and cyclodextrin

Saka

Iwamoto

Malle

et al. 2018

Acta Crystallogr D Struct Biol

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Crystal structures of Klebsiella pneumoniae pullulanase (KPP) in complex with α‐cyclodextrin (α‐CD), β‐cyclodextrin (β‐CD) and γ‐cyclodextrin (γ‐CD) were refined at around 1.98–2.59 Å resolution from data collected at SPring‐8. In the structures of the complexes obtained with 1 mM α‐CD or γ‐CD, one molecule of CD was found at carbohydrate‐binding module 41 only (CBM41). In the structures of the complexes obtained with 1 mM β‐CD or with 10 mM α‐CD or γ‐CD, two molecules of CD were found at CBM41 and in the active‐site cleft, where the hydrophobic residue of Phe746 occupies the inside cavity of the CD rings. In contrast to α‐CD and γ‐CD, one β‐CD molecule was found at the active site only in the presence of 0.1 mM β‐CD. These results were coincident with the solution experiments, which showed that β‐CD inhibits this enzyme more than a thousand times more potently than α‐CD and γ‐CD. The strong inhibition of β‐CD is caused by the optimized interaction between β‐CD and the side chain of Phe746. The increased Ki values of the F746A mutant for β‐CD supported the importance of Phe746 in the strong interaction of pullulanase with β‐CD.

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Section: Introductionmentioning

confidence: 99%

Elucidation of the mechanism of interaction between Klebsiella pneumoniae pullulanase and cyclodextrin

Saka

Iwamoto

Malle

et al. 2018

Acta Crystallogr D Struct Biol

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“…The X-ray structure of barley LD (PDB ID: 4CVW) (Møller et al, 2015a) was obtained from the RCSB Protein Data Bank. The LD inhibitor was removed from this structure.…”

Section: Systems Preparationmentioning

confidence: 99%

“…Several crystal structures of HvLD have been reported (Vester-Christensen et al, 2010;Møller et al, 2012a, Møller et al, 2015a. The HvLD structure contains four domains (Vester-Christensen et al, 2010) (shown in Figure 1): the N-terminal domain, a carbohydrate binding module 48 (CBM48), a catalytic (β/α) 8 domain containing the two catalytic residues (Asp473, nucleophile; Glu510, general acid/base) and the transition-state stabilizer (Asp642), and a C-terminal domain.…”

Section: Introductionmentioning

confidence: 99%

Understanding Thermostability Factors of Barley Limit Dextrinase by Molecular Dynamics Simulations

Dong²,

et al. 2020

Front. Mol. Biosci.

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Limit dextrinase (LD) is the only endogenous starch-debranching enzyme in barley (Hordeum vulgare, Hv), which is the key factor affecting the production of a high degree of fermentation. Free LD will lose its activity in the mashing process at high temperature in beer production. However, there remains a lack of understanding on the factor affecting the themostability of HvLD at the atomic level. In this work, the molecular dynamics simulations were carried out for HvLD to explore the key factors affecting the thermal stability of LD. The higher value of root mean square deviation (RMSD), radius of gyration (R g), and surface accessibility (SASA) suggests the instability of HvLD at high temperatures. Intra-protein hydrogen bonds and hydrogen bonds between protein and water decrease at high temperature. Long-lived hydrogen bonds, salt bridges, and hydrophobic contacts are lost at high temperature. The salt bridge interaction analysis suggests that these salt bridges are important for the thermostability of HvLD, including E568-R875, D317-R378, D803-R884, D457-R214, D468-R395, D456-R452, D399-R471, and D541-R542. Root mean square fluctuation (RMSF) analysis identified the thermal-sensitive regions of HvLD, which will facilitate enzyme engineering of HvLD for enhanced themostability.

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“…Thus some plants use inhibitors in defence against pests as seen by the structure of a cereal-type inhibitor RBI (Ragi bifunctional a-amylase/trypsin inhibitor) in complex with an insect a-amylase from yellow mealworm (Tenebrio molitor) (PDB: 1TMQ) [63]. The barley LD is regulated by an endogenous limit dextrinase inhibitor (LDI) with picomolar affinity and the LD:LDI structure was solved recently (PDB: 4CVW; Figure 3c) [64]. LDI is also a cereal-type inhibitor, but with a role in controlling LD activity rather than in pest defence [64].…”

Section: Inhibitors Of Starch Modifying Enzymesmentioning

confidence: 99%

“…The barley LD is regulated by an endogenous limit dextrinase inhibitor (LDI) with picomolar affinity and the LD:LDI structure was solved recently (PDB: 4CVW; Figure 3c) [64]. LDI is also a cereal-type inhibitor, but with a role in controlling LD activity rather than in pest defence [64]. Remarkably, although LDI belongs to the cereal-type inihibitor family it uses a fundamentally different orientation in binding ( Figure 3d) and has a unique motif that stabilizes the enzyme complex through an intermolecular hydrophobic cluster ( Figure 3c).…”

Section: Inhibitors Of Starch Modifying Enzymesmentioning

confidence: 99%

Structural biology of starch-degrading enzymes and their regulation

Møller

Svensson

2016

Current Opinion in Structural Biology

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Starch is a major energy source for all domains of life. Recent advances in structures of starch-degrading enzymes encompass the substrate complex of starch debranching enzyme, the function of surface binding sites in plant isoamylase, details on individual steps in the mechanism of plant disproportionating enzyme and a self-stabilised conformation of amylose accommodated in the active site of plant a-glucosidase.Important inhibitor complexes include a flavonol glycoside, montbretin A, binding at the active site of human pancreatic a-amylase and barley limit dextrinase inhibitor binding to the debranching enzyme, limit dextrinase using a new binding mode for cereal protein inhibitors.

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Crystal Structure of Barley Limit Dextrinase-Limit Dextrinase Inhibitor (LD-LDI) Complex Reveals Insights into Mechanism and Diversity of Cereal Type Inhibitors

Cited by 19 publications

References 58 publications

Elucidation of the mechanism of interaction between Klebsiella pneumoniae pullulanase and cyclodextrin

Elucidation of the mechanism of interaction between Klebsiella pneumoniae pullulanase and cyclodextrin

Understanding Thermostability Factors of Barley Limit Dextrinase by Molecular Dynamics Simulations

Structural biology of starch-degrading enzymes and their regulation

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