Fig. 2: Mechanism of the selective interaction of ZK53 and HsClpP.

a Overall structure of ZK53/HsClpP complex, shown from the side (left) view and top view (middle), and the active sites in the monomer of HsClpP (right). HsClpP protein is shown in surface, ZK53 is shown in green sticks, and the residues of active sites are shown in red sticks. Structural drawings for ZK53/HsClpP complex were performed in PyMOL. b 2fo-fc density map contoured to 1.2σ (blue mesh) for ZK53 in situ binding in the hydrophobic site. The amino acids in chain G are presented as yellow sticks and those in chain A are shown as cyan sticks. c Stereo-view of the interactions of ZK53 binding to HsClpP. The key amino acids involved in interactions with ZK53 are shown by sticks. The hydrogen bonds are indicated in dark dotted lines. d Part of the sequence (top) and structure (bottom) alignments of HsClpP and SaClpP showing the essential residues for selective binding with activators. These amino acids are highlighted with an orange background in the sequence alignment. The side chains of the two amino acids are shown in stick. e Heatmap showing the EC₅₀ values of activators-promoted α-casein hydrolysis by ClpP variants in the PAGE-based assay. f Heatmap representation of ΔTm values showing the activators’ effect on the thermal stabilization of ClpP variants. g Antibiotic effects of ClpP activators and tetracycline on gut microbes. Tetracycline was assayed as a positive control. The IC₅₀ is displayed in a heatmap.