Molecular Basis of RNA-Driven ATP Hydrolysis in DExH-Box Helicases

The spliceosome machinery catalyzes precursor messenger
(pre-m)RNA
splicing. In each cycle, the spliceosome experiences massive compositional
and conformational remodeling fueled by the concerted action of specific
RNA-dependent ATPases/helicases. Intriguingly, these enzymes are allosterically
activated to perform ATP hydrolysis and trigger helicase activity
only upon pre-mRNA binding. Yet, the molecular mechanism underlying
the RNA-driven regulation of their ATPase function remains elusive.
Here, we focus on the Prp2 ATPase/helicase which contributes to reshaping
the spliceosome into its catalytic competent state. By performing
classical and quantum-classical molecular dynamics simulations, we
unprecedentedly unlock the molecular terms governing the Prp2 ATPase/helicase
function. Namely, we dissect the molecular mechanism of ATP hydrolysis,
and we disclose that RNA binding allosterically triggers the formation
of a set of interactions linking the RNA binding tunnel to the catalytic
site. This activates the Prp2’s ATPase function by optimally
placing the nucleophilic water and the general base of the enzymatic
process to perform ATP hydrolysis. The key structural motifs, mechanically
coupling RNA gripping and the ATPase/helicase functions, are conserved
across all DExH-box helicases. This mechanism could thus be broadly
applicable to all DExH-box helicase family.