Figure 5. Only a subset of pore-1 loops in ClpX appear to mediate substrate grip.
(A) Model of an extended poly-alanine substrate in the axial pore of ClpX and its interactions with different pore-1 loops based on cryo-EM structures of ClpXP (X.Fei, T.A. Bell, B.M. Stinson, S. Jenni, T.A. Baker, S.C. Harrison, and R.T. Sauer, in preparation). Similar loop-substrate interactions are observed in the yeast AAA+ protease Yme1 (Puchades et al., 2017). On the right, a heatmap of Vmax values from Figure 2C is shown. The substrate tail residues are numbered relative to where a folded domain would be expected to sit at the apical surface of the AAA+ ring during unfolding. Tail residues 2–6, which promote strong grip in ClpX, are positioned to interact with the three pore-1 loops at the top of the axial pore. (B) Two models for asymmetric contribution of pore-1 loops to substrate grip.