Dynamics of Ligand Binding to a Rigid Glycosidase*

Fredj Ben Bdira; Christopher A Waudby; Alexander N Volkov; Sybrin P Schröder; Eiso Ab; Jeroen D C Codée; Hermen S Overkleeft; Johannes M F G Aerts; Hugo van Ingen; Marcellus Ubbink

doi:10.1002/anie.202003236

Dynamics of Ligand Binding to a Rigid Glycosidase*

Angew Chem Int Ed Engl. 2020 Nov 9;59(46):20508-20514. doi: 10.1002/anie.202003236. Epub 2020 Sep 3.

Authors

Affiliations

¹ Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
² Institute of Structural and Molecular Biology, University College London and Birkbeck College, London, WC1E 6BT, UK.
³ VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium.
⁴ Jean Jeener NMR Centre, VUB, Pleinlaan 2, 1050, Brussels, Belgium.
⁵ Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
⁶ ZoBio BV, BioPartner 2 building, J.H. Oortweg 19, 2333 CH, Leiden, The Netherlands.
⁷ Department of Medical Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
⁸ Present address: NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.

Abstract

The single-domain GH11 glycosidase from Bacillus circulans (BCX) is involved in the degradation of hemicellulose, which is one of the most abundant renewable biomaterials in nature. We demonstrate that BCX in solution undergoes minimal structural changes during turnover. NMR spectroscopy results show that the rigid protein matrix provides a frame for fast substrate binding in multiple conformations, accompanied by slow conversion, which is attributed to an enzyme-induced substrate distortion. A model is proposed in which the rigid enzyme takes advantage of substrate flexibility to induce a conformation that facilitates the acyl formation step of the hydrolysis reaction.

Keywords: NMR spectroscopy; dynamics; glycosidases; ligand binding; rigid fold.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Glycoside Hydrolases / metabolism*
Hydrolysis
Kinetics
Ligands
Models, Molecular
Protein Binding

Substances

Ligands
Glycoside Hydrolases