R1398 is the GTP-𝛾-phosphate sensor that drives the ROC G-domain switching mechanism unique to Parkinson's disease-associated LRRK2

Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common genetic cause of Parkinson’s disease (PD). Strategies that directly inhibit the LRRK2 kinase active site have not demonstrated disease-modifying efficacy in recent clinical testing. A naturally occurring protective variant, R1398H, provides an alternative route for understanding how reduced disease risk may be achieved by tuning the regulatory GTPase domain rather than the kinase domain itself. Here, we combine structural, computational, biochemical, and cell-based analyses to define how R1398H alters the Ras of complex proteins (ROC) G domain of LRRK2. Purified ROC carrying R1398H is folded but resolves as a stable homodimer corresponding to the GDP-bound off state previously defined for wild-type ROC. A 2.0 Å crystal structure shows unambiguous density for H1398 and reveals close superposition with the GDP-bound wild-type ROC dimer. Molecular dynamics modeling predicts that R1398 engages the 𝛾-phosphate of GTP to stabilize switch-region interactions required for activation, whereas histidine at this position weakens 𝛾-phosphate sensing. Consistent with this model, R1398H reduces GTP hydrolysis, selectively weakens GTP-state stabilization while preserving GDP binding, and decreases Rab29-dependent trans-Golgi recruitment of full-length LRRK2. These findings identify R1398 as a 𝛾-phosphate sensor that couples nucleotide chemistry to ROC conformational switching and suggest a genetics-anchored strategy for stabilizing a protective off-state conformation of LRRK2.