Fig. 5: Specific interactions along the optimal path accommodate the transitioning primer end to ensure facile pol-to-exo switching.
From: Polymerization and editing modes of a high-fidelity DNA polymerase are linked by a well-defined path
a Key residues (critical nodes) for pol-to-exo mode switching determined from dynamic network, conservation, and persistent contacts analyses and mapped onto the Pol III structure. Critical nodes are shown as spheres, labeled and colored in red. Polymerase and exonuclease active site residues are shown as spheres and colored in black. b–d Palm and thumb domain residues of the α subunit forming contacts important for polymerization (b, c) and for transitioning the primer end (d). Residue sidechains are shown in stick representation and labeled and colored by atom type (C is green, N is blue, and S is yellow). Salt-bridge and polar interactions to the DNA are shown as dashed red lines. Hydrophobic interactions are shown as a dashed black line. e Stabilization of the incoming mismatched nucleotide by the hydrophobic cluster of the ε subunit. Residues from the ε subunit hydrophobic patch are shown as sticks, labeled and colored in green.
