Rotational Mechanism Model of the Bacterial V1 Motor Based on Structural and Computational Analyses.

Abhishek Singharoy,Mitsunori Ikeguchi,Toru Ekimoto,Takeshi Murata,Kano Suzuki,Chris Chipot,Ichiro Yamato

doi:10.3389/fphys.2019.00046

Abstract

V1-ATPase exemplifies the ubiquitous rotary motor, in which a central shaft DF complex rotates inside a hexagonally arranged catalytic A3B3 complex, powered by the energy from ATP hydrolysis. We have recently reported a number of crystal structures of the Enterococcus hirae A3B3DF (V1) complex corresponding to its nucleotide-bound intermediate states, namely the forms waiting for ATP hydrolysis (denoted as catalytic dwell), ATP binding (ATP-binding dwell), and ADP release (ADP-release dwell) along the rotatory catalytic cycle of ATPase. Furthermore, we have performed microsecond-scale molecular dynamics simulations and free-energy calculations to investigate the conformational transitions between these intermediate states and to probe the long-time dynamics of the molecular motor. In this article, the molecular structure and dynamics of the V1-ATPase are reviewed to bring forth a unified model of the motor’s remarkable rotational mechanism.

Highlights

The F, A, and V-ATPases are unique biological rotary motors, which perform active ion transport by utilizing the energy from ATP hydrolysis (Forgac, 2007)
A-ATPase functions as the ATP synthase similar to F-ATP synthase; its structure and subunit composition resemble those of the V-ATPase (Grüber et al, 2014)
Based on the various structures of A3B3 and V1 obtained with or without the nucleotides, we propose a chronology of the main events occurring during one ATP hydrolysis and 120◦ rotation (Figure 3, model 1 and model 2) as follows: 1. ‘Catalytic dwell’ state: ATP bound to the ‘tight’ form is ready to be hydrolyzed, which produces the products, ADP and Pi

Summary

INTRODUCTION

The F-, A-, and V-ATPases are unique biological rotary motors, which perform active ion transport by utilizing the energy from ATP hydrolysis (Forgac, 2007). Since electron density of Pi is not observed, even in the presence of 200 μM Pi in the crystallization solution, Pi must have been released soon after ATP hydrolysis at ‘tight’ form, which changes the conformation of 2ATPV1 to that of 2ADPV1; 2ADPV1 is believed to be in the ‘ATP-binding dwell’ state, waiting for ATP to bind This early release of Pi, in good contrast to the late release in F-ATP synthase as reported (Rees et al, 2012), may be related to their functional differences; F-ATP synthase works as both ATP synthase and ATPase but V-ATPase works as ATP hydrolyzing enzyme. Since the 3ADPV1 structure was obtained at an unusually high concentration of ADP (2 mM) for an E. hirae cell, the ‘ADPrelease dwell’ state might be a minor intermediate state, which might exist in the catalytic cycle with high ADP and low ATP concentrations (Suzuki et al, 2016; Ueno et al, 2018)

A ROTATIONAL MECHANISM MODEL BASED ON THE CRYSTAL STRUCTURES

CONCLUSION AND PERSPECTIVES