Characterizing ATP processing by the AAA+ protein p97 at the atomic level

Characterizing ATP processing by the AAA+ protein p97 at the atomic level

March 2024 | Mikhail Shein, Manuel Hitzenberger, Tat Cheung Cheng, Smruti R. Rout, Kira D. Leitl, Yusuke Sato, Martin Zacharias, Eri Sakata & Anne K. Schütz
This study characterizes the ATP processing by the AAA+ protein p97 at the atomic level using cryo-EM, NMR spectroscopy, and molecular dynamics simulations. p97 is a hexameric enzyme that regulates various cellular pathways by unfolding protein substrates in an ATP-dependent manner. The enzyme undergoes significant conformational changes during its catalytic cycle, and the study reveals the molecular motions at the active site immediately before and after ATP hydrolysis. The research identifies a metastable reaction intermediate, the ADP·P_i state, which is poised between hydrolysis and product release. The active site is finely tuned to trap and eventually discharge the cleaved phosphate. Signaling pathways originating at the active site coordinate the action of the hexamer subunits and couple hydrolysis with allosteric conformational changes. The study provides a detailed understanding of the spatial and temporal orchestration of ATP handling by p97, a prototype AAA+ protein. The results show that the ADP·P_i state is stabilized by the Mg²+ ion and the Walker A and sensor residues. The study also identifies the contributions of active-site residues to ATP turnover and maps pathways that coordinate activity between adjacent subunits. The findings highlight the structural transitions and dynamical changes that accompany ATP processing by multimeric enzymes. The study also reveals the role of the sensor loop in inter-subunit communication and the impact of mutations on the ATP-hydrolysis cycle. The research provides insights into the mechanism of ATP hydrolysis and the release of phosphate, as well as the structural basis for the function of p97. The study demonstrates the importance of the arginine finger and the sensor loop in the regulation of p97 activity. The findings contribute to the understanding of the molecular mechanisms underlying the function of AAA+ proteins and their role in cellular processes.This study characterizes the ATP processing by the AAA+ protein p97 at the atomic level using cryo-EM, NMR spectroscopy, and molecular dynamics simulations. p97 is a hexameric enzyme that regulates various cellular pathways by unfolding protein substrates in an ATP-dependent manner. The enzyme undergoes significant conformational changes during its catalytic cycle, and the study reveals the molecular motions at the active site immediately before and after ATP hydrolysis. The research identifies a metastable reaction intermediate, the ADP·P_i state, which is poised between hydrolysis and product release. The active site is finely tuned to trap and eventually discharge the cleaved phosphate. Signaling pathways originating at the active site coordinate the action of the hexamer subunits and couple hydrolysis with allosteric conformational changes. The study provides a detailed understanding of the spatial and temporal orchestration of ATP handling by p97, a prototype AAA+ protein. The results show that the ADP·P_i state is stabilized by the Mg²+ ion and the Walker A and sensor residues. The study also identifies the contributions of active-site residues to ATP turnover and maps pathways that coordinate activity between adjacent subunits. The findings highlight the structural transitions and dynamical changes that accompany ATP processing by multimeric enzymes. The study also reveals the role of the sensor loop in inter-subunit communication and the impact of mutations on the ATP-hydrolysis cycle. The research provides insights into the mechanism of ATP hydrolysis and the release of phosphate, as well as the structural basis for the function of p97. The study demonstrates the importance of the arginine finger and the sensor loop in the regulation of p97 activity. The findings contribute to the understanding of the molecular mechanisms underlying the function of AAA+ proteins and their role in cellular processes.
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