The structural basis of RanGAP1 regulation and catalysis in nuclear transport

RanGAP1 promotes GTP hydrolysis of nuclear pore complex (NPC) transport complexes at the cytoplasmic face. A disordered linker connects its catalytic GAP domain to the C-terminal sumoylation domain, anchoring into NPC’s cytoplasmic filaments. This arrangement raises the question of how these distinct functions are coordinated within a crowded cellular environment. Using atomistic molecular dynamics simulations, we show that RanGAP1 adopts an autoinhibited conformation, where the C-terminal domain masks the catalytic GAP domain. Sumoylation allosterically relieves this autoinhibition, enabling GTP-bound Ran access to the GAP domain. In the cytosol, Ran-GTP/RanBP1 can bind a less populated open conformation of RanGAP1, providing a backup mechanism for GTP hydrolysis in Ran. Importantly, we observe that Arg191 of human RanGAP1 inserts into the GTP-binding pocket of Ran and directly interacts with the γ-phosphate, consistent with a canonical arginine finger. This observation contrasts with earlier models derived from yeast RanGAP and suggests that human RanGAP1 may follow a catalytic mechanism similar to classical small GTPase regulators like NF1. Together, these findings provide a framework of RanGAP1, linking autoinhibition, sumoylation, spatial organization at the NPC, and the catalytic mechanism. They also highlight how conformational regulation and post-translational modification coordinate efficient GTP hydrolysis in Ran during nuclear transport.