FIGURE 8.

Mechanism of RNA synthesis initiation, elongation, and termination. A, compact shape of primase in the initiation complex model. B, close-up view of the initiation mini duplex in the model. Position of the magnesium ion between the elongating and initiating GTPs was modeled to coordinate Asp-111, α-phosphate of elongating GTP, and O3′ of initiating GTP as in the active site of polymerases (58). C, models of the initiation and elongation complexes. The crystal structures of p58_C-D/R, human primase (PDB code 4RR2), and p49-p58_N–UTP complex (PDB code 4BPW) were used to build these models. Panel numbers correspond to the length of the growing RNA primer plus incoming NTP in the modeled complexes. Panel 2 corresponds to the initiation complex resulting in dinucleotide formation and also shows the position of p58_C in apo-primase. The clash area is depicted by dotted circles (colored green or red to indicate avoidable or unavoidable steric hindrance, respectively), whereas the arrows show the direction at which p58_C is pushing p58_N. Close-up view of the complex in panel 9, explaining how steric hindrance is avoided, is provided in Fig. 10B. The image on the right shows the typical pattern of primase-catalyzed reaction products.