New structures of human formylglycine-generating enzyme reveal features important for catalysis, disease and structure-based drug design.

The formylglycine-generating enzyme (FGE) post-translationally modifies the active site of all human sulfatases. Mutations in the SUMF1 gene encoding FGE may lead to catalytically inactive FGE or destabilize the protein. The resulting lack of sulfatase modification causes the rare disease multiple sulfatase deficiency (MSD). Previously, FGE required elastase treatment for crystallization and the structures lacked copper, although FGE is a copper-dependent enzyme. Here, we show that highly active human FGE purified from insect cells natively contains one copper ion and we report six new crystal structures revealing previously unobserved features. Several structures contain the catalytic copper ion coordinated almost linearly by the two catalytic cysteines. A structure of the MSD-causing E130D variant shows distortions in coordination of a structural Ca2+ explaining its lower stability. As part of exploratory ligand-soaking experiments, a structure of FGE soaked with N-acetyl cysteine methyl ester shows the binding of a small molecule to a site other than the active site highlighting a potential binding site to be explored in the development of pharmacological chaperones for FGE. Crystallization of FGE without elastase treatment resulted in a structure in which the previously missing loop is well defined in the electron density and partly covers the active site, indicating that it needs to adopt a different conformation for substrate binding. This assumption is supported by a second structure in which the loop faces away from the active site and leaves the substrate binding groove open and by the occasional occurrence of crystals in which the loop becomes disordered.