Fig. 3: Overall structure and binding mode of PsiR with PsiO and allulose.

a The overall structure of PsiR and the binding mode with PsiO. The crystal structure of PsiR-allulose complex (PDB ID: 9KPR) was solved, and the PsiR-PsiO complex crystal structure was obtained with the aid of AlphaFold3. b The interaction between helix-turn-helix (HTH) of PsiR and the major groove nucleotides of PsiO. c The root-mean-square fluctuation (RMSF) data of PsiR-PsiO complex under 1-μs-long range MD simulation. In panel (c), the green, blue and yellow shaded regions denote the HTH, N-terminal and C-terminal subdomains of PsiR, respectively, and the purple shaded region in the lower plot marks the 20-bp core PsiO operator within the DNA. d The electrostatic interaction and van der Waals interactions between HTH and PsiO. e The binding conformation between PsiR and allulose in EBD. f Distributions of per-residue interaction energies between allulose and surrounding residues along a 1 µs MD trajectory. For each residue, total residue–allulose interaction energies (ΔE) were calculated every 10 ps, 100,000 frames in total. Violin plots show the kernel density of the per-frame interaction energies; inner boxes indicate the interquartile range (25–75th percentiles) with the center line representing the median, and whiskers denote the most extreme data points within 1.5 × IQR. g The fluorescence values and regulatory range (fold) of different PsiR mutants after alanine scanning under 0/10 mM allulose. h The ligand-TF binding mode in other LacI-family TFs. The D-R-D/R binding triad is shown. Data are presented as mean values +/−SD (n = 3 independent experiments). Source data for (c, d, f, g) are provided as a Source Data file.