COMMD3 coordinates mannose-6-phosphate receptor trafficking to sustain lysosomal protease maturation.

Lysosomal function depends on the cation-independent and cation-dependent mannose-6-phosphate receptors (CI-MPR and CD-MPR), which deliver newly synthesized acid hydrolases from the trans-Golgi network (TGN) to the endolysosomal system. However, how the trafficking of these receptors is coordinately regulated remains incompletely understood. Here we identify COMMD3 as a regulator of both MPRs that promotes their exit from early endosomes and sustains lysosomal hydrolase maturation. Loss of COMMD3 causes accumulation of CI-MPR and CD-MPR in early endosomal compartments and profoundly impairs the maturation and activity of Cathepsin L (CTSL). Combined deletion of both MPRs phenocopies COMMD3 deficiency, functionally linking COMMD3-dependent MPR trafficking to CTSL maturation. Unexpectedly, this trafficking activity is mediated primarily by the N-terminal domain of COMMD3 rather than its canonical C-terminal COMM domain involved in Commander complex assembly. Disruption of COMMD3 or both MPRs also selectively restricts CTSL-dependent entry of SARS-CoV-2 and Ebola virus. Together, our findings uncover a COMMD3-MPR trafficking axis that couples endosomal sorting to lysosomal protease maturation and supports endosome-dependent viral entry.