Fig. 2: Structural analysis of the VirD/ACP5b interaction, and basis for specificity.
From: Decrypting the programming of β-methylation in virginiamycin M biosynthesis
a VirD crystal structure (PDB ID: 8AHZ). The three monomers of VirD are shown in cartoon representation and the three polypeptide chains are coloured in white, teal, and light blue. Helix α10, which is partially defined in the electron density maps, is indicated in marine blue. b holo-ACP5b–VirD crystal structure (PDB ID: 8AHQ), colour-coded as in (a) and with ACP5b shown in lime green. Within the context of the complex, helix α10 is fully structured. The side chains of S6871 and the Ppant arm, only the proximal end of which is visible in the electron density, are shown in stick representation (oxygen atoms are indicated in red, nitrogen atoms in blue, carbon atoms in yellow, and the sulphur atom in gold). c Zoom into the VirD active site. The side and main chains of N6865, L6869, L6894 and D6870 are shown in ball-and-stick representation. The hydrogen bond network between the residues and water molecules (red spheres) is represented as dashed lines. The positively-charged arginines of VirD (R125 and R192) participate in salt bridges with the phosphate moiety and D6870 of the ACP5b. The omit map of the Ppant arm and S6871 is contoured at 3σ in white. The distance of 13.9 Å between S6871 and the VirD catalytic E128 is shown as a red dashed line. The oxyanion hole established by the N-terminal portion of helix α3 comprises the NH moieties of D6870, I6872 and L6873. The orientation of the side chain of S6871 is maintained by the oxyanion hole as well as the side chain orientation of D6870. Abbreviation: Ppant phosphopantetheine.
