Mapping Ligand-Induced Conformational Changes during the Enzymatic Cycle of Human Geranylgeranyl Diphosphate Synthase

Geranylgeranyl diphosphate synthase (GGDPS) catalyzes the condensation reaction between two isoprenoid substrates: farnesyl diphosphate (FDP) and isopentenyl pyrophosphate (IPP), to form geranylgeranyl diphosphate (GGDP). Due to the flexible nature of the GGDPS active site and its capacity to bind multiple ligands during the reaction coordinate, understanding the structural changes that enable it to accommodate different ligands and catalyze the reaction is essential. While structures exist of substrate and product-bound GGDPS, a lack of high-resolution apo or Mg2+-only structures prevents complete understanding of the enzyme active site. Here, we report apo and Mg2+-only structures of human GGDPS, investigating the key differences between them and published GGDPS structures relating to the enzymatic cycle. A crystal structure resolved to 1.82 Å, the highest-resolution structure of human GGDPS to date, contains five product-bound subunits and one Mg2+-only subunit. The first cryo-EM structure of apo GGDPS is also reported, which exhibited an open hexamer conformation. Comparing the Mg2+-only and apo structures shows that the active site is posed and ready to bind Mg2+ without significant conformational changes. Comparing Mg2+-only to structures with either of the substrates or product bound, we observe changes in residues that actively obstruct or encourage the binding of certain ligands. We also propose an enzymatic mechanism for the structural states of GGDPS and highlight the possibility of Asp188 as the general base in the condensation reaction. These findings enhance our understanding of GGDPS ligand binding, which will improve the knowledge base for rational, structure-based design of future GGDPS inhibitors.