Many viruses utilize ringed packaging ATPases to translocate double-stranded DNA into procapsids during replication. A critical step in the mechanochemical cycle of such ATPases is ATP binding, which causes a subunit within the motor to grip DNA tightly. Here, we probe the underlying molecular mechanism by which ATP binding is coupled to DNA gripping and show that a glutamate-switch residue found in AAA+ enzymes is central to this coupling in viral packaging ATPases. Using free-energy landscapes computed through molecular dynamics simulations, we determined the stable conformational state of the ATPase active site in ATP- and ADP-bound states. Our results show that the catalytic glutamate residue transitions from an active to an inactive pose upon ATP hydrolysis and that a residue assigned as the glutamate switch is necessary for regulating this transition. Furthermore, we identified via mutual information analyses the intramolecular signaling pathway mediated by the glutamate switch that is responsible for coupling ATP binding to conformational transitions of DNA-gripping motifs. We corroborated these predictions with both structural and functional experimental measurements. Specifically, we showed that the crystal structure of the ADP-bound P74-26 packaging ATPase is consistent with the structural coupling predicted from simulations, and we further showed that disrupting the predicted signaling pathway indeed decouples ATPase activity from DNA translocation activity in the φ29 DNA packaging motor. Our work thus establishes a signaling pathway that couples chemical and mechanical events in viral DNA packaging motors.
|Original language||English (US)|
|Journal||Proceedings of the National Academy of Sciences of the United States of America|
|State||Published - Apr 27 2021|
Bibliographical noteFunding Information:
ACKNOWLEDGMENTS. We thank Dr. Sukrit Singh for valuable discussion about the nature of MI as calculated by CARDS. This work was supported by NIH grants GM118817 (to G.A.), GM127365 (to M.C.M.), and GM122979 (to P.J.J. and M.C.M.) and NSF grant MCB1817338 (to B.A.K.). Computational resources were provided by the NSF Extreme Science and Engineering Discovery Environment Program ACI-1053575.
© 2021 National Academy of Sciences. All rights reserved.
- Allosteric coupling
- DNA packaging
- Molecular motor