(A) Structural basis for nucleotide binding-dependent conformational changes. All six subunits (A/D dark blue, B/E light blue, C/F green) are overlaid based on their large AAA domains, and their small AAA domains are represented by a single α-helix, residues 323–342. (B) Relative orientation of large and small AAA domains in different subunit types. Bound ADP and SO4− ions are shown as sticks. While the small AAA domain position varies widely between subunits, all six subunit–subunit interfaces are equivalent, forming six rigid-body units within the hexamer (see Figure 3—figure supplement 1). (C) ‘Closed’ (blue) and ‘open’ (green) ClpX monomers in the nucleotide-free ClpX hexamer (PDB ID 3HTE; [Glynn et al., 2009]). Later work showed that the ‘closed’ conformation is compatible with nucleotide binding (Stinson et al., 2013). (D) Top view of the asymmetric PCH-2 hexamer, with subunits colored as in (A) and (B), and pore loops (residues 217–226) colored magenta. (E) Pore-side view of PCH-2 D/E/F chains (A/B/C chains removed), showing the axial staggering of these subunits' pore loops. (F) Top view of the nucleotide-free ClpX hexamer (Glynn et al., 2009), with ‘closed’ and ‘open’ subunits colored as in PCH-2 and pore loops (residues 145–153) colored magenta. (G) Pore-side view of ClpX D/E/F chains (A/B/C removed), colored as in (F). (H) Sequence alignment of pore loop region in PCH-2 orthologs, and equivalent region of human p97 and NSF, and E. coli ClpX. Magenta box: PCH-2 pore loop; Yellow boxes: NSF ‘YVG’ and ClpX ‘GYVG’ motifs. (I) Schematic model for ATP-driven conformational changes in PCH-2, with pore-side view equivalent to panel F. As the left-most subunit binds ATP (blue; represented by the closed ‘ATP’-like state in chain D), hydrolyzes ATP to ADP (light blue; represented by PCH-2 chain E), then releases hydrolyzed ADP (green; represented by PCH-2 chain F), its pore loop (magenta) undergoes axial motions that drive substrate remodeling.