The molecular coupling between substrate recognition and ATP turnover in a AAA+ hexameric helicase loader

Abstract

In many bacteria and in eukaryotes, replication fork establishment requires the controlled loading of hexameric, ring-shaped helicases around DNA by AAA+ ATPases. How loading factors use ATP to control helicase deposition is poorly understood. Here, we dissect how specific ATPase elements of E. coli DnaC, an archetypal loader for the bacterial DnaB helicase, play distinct roles in helicase loading and the activation of DNA unwinding. We identify a new element, the arginine-coupler, which regulates the switch-like behavior of DnaC to prevent futile ATPase cycling and maintains loader responsiveness to replication restart systems. Our data help explain how the ATPase cycle of a AAA+-family helicase loader is channeled into productive action on its target; comparative studies indicate elements analogous to the Arg-coupler are present in related, switch-like AAA+ proteins that control replicative helicase loading in eukaryotes, as well as polymerase clamp loading and certain classes of DNA transposases.

Allosteric communication in DNA polymerase clamp loaders relies on a critical hydrogen-bonded junction

“…These helices, along with the loops leading into them, form a contiguous surface in the center of the AAA+ assembly, wrapping around the DNA, making contact with ATP, and docking on the sliding clamp ( Figure 7 ). We refer to this unit as the ‘ central coupler ’ ( Figure 1C ), a term suggested by a recent analysis of DnaC, a DNA helicase loader, in which an arginine residue within this unit is referred to as a ‘coupler’ ( Puri et al, 2020 ).…”