Fig. 4: Identification of a potential lipid II binding site in MraY.
a, Periplasmic view of the cryo-EM structure of the EcMraY(T23P) dimer within the YES complex shown in surface representation, with the unmodelled electron density shown (green). b, As in a, but membrane view of the electron density within the dimer interface of the EcMraY dimer with the foreground MraY removed. c, Top view of the MraY dimer in a mixed CG membrane. Two lipid II molecules (highlighted as green and pink spheres) freely enter the MraY cavity during unbiased MD simulations. In 8/9 repeats, 2 or 3 lipid I or II molecules bind the cavity. In the last repeat, one lipid II and one C55P molecule bind. d, Lipid II contacts with MraY residues that interact with lipid II for over 60% of atomistic MD simulations, where the dashed line indicates the 60% cutoff. Dots represent the values obtained for the independent replicates; bars and error bars indicate mean ± s.e. from 5 repeats. Darker green bars represent residues altered in hyperactive variants. e, Lipid II contacts with MraY residues by part of lipid II that is interacting (tail and phosphate, MurNAc, GlcNAc or pentapeptide). Residues shown are the same as those in d. Darker bars represent residues altered in hyperactive variants. f, Average density of lipid II molecules (green) from atomistic MD simulations of MraY (grey) bound to lipid II. Shown as inside view of dimer interface, where only one monomer of MraY is shown and residues altered in hyperactive variants are coloured in purple.
