Fig. 4: The periplasmic domain of ExbD interacts with the peptidoglycan layer.
From: Ton motor conformational switch and peptidoglycan role in bacterial nutrient uptake
a 2D [1H-15N]-TROSY spectra of 15N ExbDSm, peri without (black) and with (orange) E. coli peptidoglycan. The interaction of ExbDSm, peri with peptidoglycan leads to the disappearance (broadening) of peaks. b Mapping this peak intensity loss in terms of a peak height ratio (pink to green, grey color means no value) onto the dimeric ExbDSm, peri structure shows that the interface within the dimer experiences the largest increase in exchange contribution to the R2 relaxation rate upon interaction with peptidoglycan. This suggests that possibly the dimer dissociates upon interaction. c This increase in R2 relaxation rate due to exchange can be measured by Car-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments and reveals that ExbDSm, peri selectively interacts with peptidoglycan from E. coli (orange), S. aureus (blue) – they all show decaying profiles – but not B. subtilis (green), which shows the same flat curve as the control experiment without peptidoglycan (black). Peak intensities are plotted as mean values with error bars showing the SD, which quantifies the relative measurement error arising from noise in the NMR spectra. d Schematic representation of the full mechanism. In the resting state in the absence of ligand (i.), closed ExbD (pink) is in exchange with a minor open conformation (ii.). This extended, open conformation can reach the peptidoglycan layer, in interaction with which its dimer interface is loosened (iii.). This allows TonB/HasB (blue) to enter in between the ExbD monomers (iv.) and to subsequently select the open state of ExbD by binding to it (v.). Also, the C-terminal domain of TonB/HasB interacts with a ligand (grey) bound TonB-dependent transporter (TBDT). Proton motive force induced rotation of ExbD within ExbB leads to a pulling through the IDR of TonB/HasB, opening the TBDT and enabling active transport of ligands (vi.). Eventually, the pulling force becomes too large and leads to the dissociation of TonB/HasB from the TBDT, and the return to the resting state of the system (vii.). Source data are provided as a Source Data file.
