5LVX

Crystal structure of glucocerebrosidase with an inhibitory quinazoline modulator

Summary for 5LVX

• Entry DOI: 10.2210/pdb5lvx/pdb
• Descriptor: Glucosylceramidase, alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (9 entities in total)
• Functional Keywords: gcase, hydrolase, glycoprotein, glycosidase, glucosylceramidase, prot, proteros biostructures gmbh
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 4
• Total formula weight: 230629.43

Authors

Zheng, J.,Chen, L.,Skinner, O.S.,Lansbury, P.,Skerlj, R.,Mrosek, M.,Heunisch, U.,Krapp, S.,Weigand, S.,Charrow, J.,Schwake, M.,Kelleher, N.L.,Silverman, R.B.,Krainc, D. (deposition date: 2016-09-14, release date: 2017-10-25, Last modification date: 2024-10-23)

Primary citation

Zheng, J.,Chen, L.,Skinner, O.S.,Ysselstein, D.,Remis, J.,Lansbury, P.,Skerlj, R.,Mrosek, M.,Heunisch, U.,Krapp, S.,Charrow, J.,Schwake, M.,Kelleher, N.L.,Silverman, R.B.,Krainc, D.
beta-Glucocerebrosidase Modulators Promote Dimerization of beta-Glucocerebrosidase and Reveal an Allosteric Binding Site.
J. Am. Chem. Soc., 140:5914-5924, 2018

PubMed Abstract: β-Glucocerebrosidase (GCase) mutations cause Gaucher's disease and are a high risk factor in Parkinson's disease. The implementation of a small molecule modulator is a strategy to restore proper folding and lysosome delivery of degradation-prone mutant GCase. Here, we present a potent quinazoline modulator, JZ-4109, which stabilizes wild-type and N370S mutant GCase and increases GCase abundance in patient-derived fibroblast cells. We then developed a covalent modification strategy using a lysine targeted inactivator (JZ-5029) for in vitro mechanistic studies. By using native top-down mass spectrometry, we located two potentially covalently modified lysines. We obtained the first crystal structure, at 2.2 Å resolution, of a GCase with a noniminosugar modulator covalently bound, and were able to identify the exact lysine residue modified (Lys346) and reveal an allosteric binding site. GCase dimerization was induced by our modulator binding, which was observed by native mass spectrometry, its crystal structure, and size exclusion chromatography with a multiangle light scattering detector. Finally, the dimer form was confirmed by negative staining transmission electron microscopy studies. Our newly discovered allosteric site and observed GCase dimerization provide a new mechanistic insight into GCase and its noniminosugar modulators and facilitate the rational design of novel GCase modulators for Gaucher's disease and Parkinson's disease.

PubMed: 29676907
DOI: 10.1021/jacs.7b13003

Experimental method

X-RAY DIFFRACTION (2.2 Å)