8R1M

Structure of TxGH116 with covalently bound N-azido-octyl aziridine

Summary for 8R1M

• Entry DOI: 10.2210/pdb8r1m/pdb
• Descriptor: Glucosylceramidase, CALCIUM ION, CHLORIDE ION, ... (6 entities in total)
• Functional Keywords: beta-glucosidase, covalent complex, aziridine, hydrolase
• Biological source: Thermoanaerobacterium xylanolyticum LX-11
• Total number of polymer chains: 2
• Total formula weight: 184667.89

Authors

Offen, W.A.,Davies, G.J. (deposition date: 2023-11-02, release date: 2024-10-02, Last modification date: 2024-10-09)

Primary citation

Su, Q.,Louwerse, M.,Lammers, R.F.,Maurits, E.,Janssen, M.,Boot, R.G.,Borlandelli, V.,Offen, W.A.,Linzel, D.,Schroder, S.P.,Davies, G.J.,Overkleeft, H.S.,Artola, M.,Aerts, J.M.F.G.
Selective labelling of GBA2 in cells with fluorescent beta-d-arabinofuranosyl cyclitol aziridines.
Chem Sci, 15:15212-15220, 2024

PubMed Abstract: GBA2, the non-lysosomal β-glucosylceramidase, is an enzyme involved in glucosylceramide metabolism. Pharmacological inhibition of GBA2 by -alkyl iminosugars is well tolerated and benefits patients suffering from Sandhoff and Niemann-Pick type C diseases, and GBA2 inhibitors have been proposed as candidate-clinical drugs for the treatment of parkinsonism. With the ultimate goal to unravel the role of GBA2 in (patho)physiology, we sought to develop a GBA2-specific activity-based probe (ABP). A library of probes was tested for activity against GBA2 and the two other cellular retaining β-glucosidases, lysosomal GBA1 and cytosolic GBA3. We show that β-d-arabinofuranosyl cyclitol aziridine (β-d-Araf aziridine) reacts with the GBA2 active site nucleophile to form a covalent and irreversible bond. Fluorescent β-d-Araf aziridine probes potently and selectively label GBA2 both and , allowing for visualization of the localization of overexpressed GBA2 using fluorescence microscopy. Co-staining with an antibody selective for the lysosomal β-glucosylceramidase GBA1, shows distinct subcellular localization of the two enzymes. We proffer our ABP technology for further delineating the role and functioning of GBA2 in disease and propose the β-d-Araf aziridine scaffold as a good starting point for the development of GBA2-specific inhibitors for clinical development.

PubMed: 39246358
DOI: 10.1039/d3sc06146a

Experimental method

X-RAY DIFFRACTION (1.9 Å)