Fig. 5. ZntR effects on Zur-DNA interactions.

a Dependence of the apparent unbinding rate constant k₋₁ of ${\text{Zur}}_{\text{C}88\text{S}}^{\text{mE}}$ on its own concentration and at different [${\text{ZntR}}_{\text{apo}}^{\text{G}}$] in the cell (orange: n = 514 cells; green: n = 642 cells; blue: n = 532 cells). Lines: fits with Eq. (1). b Same as (a), but for k₋₁ of ${\text{Zur}}_{\text{Zn}}^{\text{mE}}$ and at different [${\text{ZntR}}_{\text{Zn}}^{\text{G}}$] in the cell (black: n = 611 cells; orange: n = 287 cells; green: n = 494 cells; blue: n = 623 cells). Lines: fits with Eq. (1) including 1st and 3rd terms only. c The facilitated unbinding rate constant k_f of ${\text{Zur}}_{\text{C}88\text{S}}^{\text{mE}}$ vs. cellular [${\text{ZntR}}_{\text{apo}}^{\text{G}}$] (magenta triangle) and of ${\text{Zur}}_{\text{Zn}}^{\text{mE}}$ vs. the cellular [${\text{ZntR}}_{\text{Zn}}^{\text{G}}$] (yellow square) (n = 1978 cells). Lines: linear (magenta) and horizontal line (yellow) fits. d Same as (c) but for the binding rate constant k₁. Lines: horizontal line fits (n = 2039 cells). e The impeded unbinding rate constant k_r (solid triangle) and the effective oligomer dissociation constant K_m (open triangle) of ${\text{Zur}}_{\text{C}88\text{S}}^{\text{mE}}$ vs. cellular [${\text{ZntR}}_{\text{apo}}^{\text{G}}$] (n = 2039 cells). Lines: linear fits. Error bars in (a–e) are SEM. f Mechanistic model for ZntR_apo-dependent Zur unbinding kinetics. Starting with oligomerized Zur (dark and light blue) at a tight-binding site on DNA, the unbinding of an incumbent Zur protein (dark blue) can be facilitated by a freely diffusing Zur (dark green) through the formation of a ternary complex i (step 1), leading to assisted dissociation (step 2) or direct substitution (step 3); this facilitated unbinding of Zur can be enhanced by ZntR_apo through the formation of a heteromeric quaternary complex (step 5). The oligomer-induced impedance of Zur unbinding (step 4) can be weakened by ZntR_apo through the formation of a heteromeric ternary complex ii (step 6), leading to faster Zur unbinding as well. White dashed lines on the ‘n dimers’ denote salt bridge interactions between Zur dimers. Source data are provided as a Source Data file and also available in Supplementary Table 7.