Fig. 6.

Working models for viral RdRP elongation NAC and translocation. (A) The NAC model shown in a circle format. Previously reported native PV RdRP EC and three of its derivative structures obtained by CTP, 3′-deoxy-CTP (3dCTP), or ddCTP soaking serve as the reference states 1, 2, 4, and 5 (gray fonts; PDB ID codes are listed). All seven structures reported in the current study obtained by natural NTP soaking were assigned at corresponding positions in the cycle. A norovirus (NV) polymerase–RNA–CTP complex exhibiting a precatalysis closed-conformation active site represents reference state 3. (B) A schematic free energy diagram for translocation. The pretranslocation state could establish fast equilibrium with the S₆ intermediate state, and the subsequent transition to the posttranslocation state 1 of the next NAC is rate-limiting. Empty triangles indicate the interactions needed to maintain the irregular backbone conformation of the template −2 position and the +1/+2 bend of the template. These interactions include those between the motif G T114–S115 backbone and the +1/+2 junction of the template strand backbone and those between pinky finger K127 and R188 side chain and the template strand backbone phosphates stabilizing the irregular conformation of the ribose–phosphate linkage at the −2 position. These interactions must be broken (indicated by the unlocked symbol) during the final step toward the posttranslocation state. P, product; T, template; T1/T2, transition states.