Structural Insights into the Allosteric Operation of the Lon AAA+ Protease

The Lon AAA+ protease (LonA) is an evolutionarily conserved protease that couples the ATPase cycle into motion to drive substrate translocation and degradation. A hallmark feature shared by AAA+ proteases is the stimulation of ATPase activity by substrates. Here we report the structure of LonA bound to three ADPs, revealing the first AAA+ protease assembly where the six protomers are arranged alternately in nucleotide-free and bound states. Nucleotide binding induces large coordinated movements of conserved pore loops from two pairs of three non-adjacent protomers and shuttling of the proteolytic groove between the ATPase site and a previously unknown Arg paddle. Structural and biochemical evidence supports the roles of the substrate-bound proteolytic groove in allosteric stimulation of ATPase activity and the conserved Arg paddle in driving substrate degradation. Altogether, this work provides a molecular framework for understanding how ATP-dependent chemomechanical movements drive allosteric processes for substrate degradation in a major protein-destruction machine. [Display omitted] •First structure of a hexameric AAA+ protease assembly bound to three ADPs•The six protomers are arranged alternately in nucleotide-free and bound states•Pore loops from two pairs of three non-adjacent protomers move cooperatively•Occupied substrate-binding groove forms the allosteric site for ATPase stimulation Lin et al. use the structure of an AAA+ protease assembly, in which the six protomers are captured in distinct nucleotide-free and ADP-bound conformations, to explain how the ATP hydrolysis cycle induces coordinated structural movements to drive substrate unfolding, translocation, degradation, and stimulation of the ATPase activity.