Skip to main content
. 2017 May 22;114(23):6010–6015. doi: 10.1073/pnas.1704845114

Fig. 3.

Fig. 3.

Mobile arch and DNA substrate motions before catalysis. (A) DNA motion (red arrows indicate screw motion) transitioning from stage 1 (Left, rI) to 2 (Right, rIII). The double-stranded section of the DNA translocates, shifting the contact to H2TH from d6 to d7. In rIII, the dsDNA-ssDNA junction at the d1 base pair contacts the wedge domain. The unprocessed single strand (u1–u3) is disordered in rI (dashed line) and moves in rIII to place u1 between the α2- and α3-helices, organizing u2-u3 to form an ordered, sharp bend around the α2-α3 wedge. (B) Mobile arch transitions (red arrows, rotation A) from the open (Top; stage 1, rI) to closed (Bottom; stage 2, rIII) conformation. (C) Mobile arch transitions (red arrows, rotation B) from the closed (stage 2, rIII, light green) to clamped (stage 3, rIV, dark green) conformation, placing the scissile bond next to metals M1 and M2 in a catalytically competent geometry. R92 and K85 contribute to transition-state stabilization. E150 always orients K85 (only shown in clamped form for simplicity). The clamped conformation is “latched” by S84, T281, and the Y312 main chain carbonyl.