Ancestral Sequence Reconstruction and Comprehensive Computational Simulations Unmask an Efficient PET Hydrolase with the Wobbled Catalytic Triad

Abstract

Beyond directed evolution, ancestral sequence reconstruction (ASR) has emerged as a powerful strategy for engineering proteins with superior functional properties. Herein, we harnessed ASR to uncover robust PET hydrolase variants, expanding the repertoire of PET-degrading enzymes and providing deeper insights into the underlying mechanisms of PET hydrolysis. As a result, ASR1-PETase, featuring a unique cysteine catalytic site, was discovered. Despite having only 19.3 % sequence identity with IsPETase, ASR1-PETase demonstrated improved PET degradation efficiency, with a finely-tuned substrate-binding cleft. Comprehensive experimental validation, including mutagenesis studies and comparisons with six state-of-the-art PET hydrolases, combined with microsecond-scale molecular dynamics (MD) simulations and QM-cluster calculations, revealed that ASR1-PETase's C161 catalytic residue assisted with the wobbled H242 can simultaneously cleave both ester bonds of BHET – a feature not commonly observed in other PET hydrolases. This mechanism may serve as the primary driving force for accelerating PET hydrolysis while minimizing the accumulation of the intermediate MHET, thereby enhancing the efficiency of TPA production.