Cryo-TEM structure of β-glucocerebrosidase in complex with its transporter LIMP-2

Nearly all lysosomal enzymes reach the lysosome via the mannose-6-phosphate receptor pathway. One of the few known exceptions is the enzyme β-glucocerebrosidase (GCase) that requires the lysosomal integral membrane protein type-2 (LIMP-2) as a proprietary lysosomal transporter. Genetic variations in the GCase encoding gene GBA1 are the cause of Gaucher’s disease (GD) and the highest genetic risk factor for developing Parkinson’s disease (PD). Activators targeting GCase have emerged as a promising therapeutic approach for the treatment of both GD and PD, with pre-clinical and clinical trials ongoing. In this study, we resolved the complex of GCase and LIMP-2 to 3.6 Å using cryo-electron microscopy with the aid of an engineered LIMP-2 shuttle and two GCase-targeted pro-macrobodies. We identified helix 5 and helix 7 of LIMP-2 to interact with a binding pocket in GCase, forming a mostly hydrophobic interaction interface. Understanding the interplay of GCase and LIMP-2 on a structural level is crucial for identifying potential activation sites and conceptualizing novel therapeutic approaches targeting GCase. Here, we unveil the protein structure of a mannose-6-phosphate-independent lysosomal transporting complex and provide fundamental knowledge for translational clinical research to overcome GD and PD.