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. 2015 Oct 1:35–71. doi: 10.1016/B978-0-12-800837-9.00002-2

Figure 2.6.

Figure 2.6

Polymerization by viral polymerases. (a) The structure of nucleic acid polymerases resembles that of a right hand. This was first evidenced with the structure of the Klenow fragment of the E. coli DNA polymerase I by T.A. Steitz and colleagues in 1985. On the left the Klenow fragment is represented with colored fingers, palm and thumb domains, next to an open right hand. The structure on the right is that of PV RdRp, next to a closed right hand. Courtesy of N. Verdaguer and L. Vives-Adrián (the hand is that of L. Vives-Adrián). (b) The structure of ternary complex between FMDV 3D, an RNA molecule and UTP as the substrate (PDB id. 2E9Z). The left panel is a front view of the complex, depicting the polymerase chain as a yellow ribbon, the RNA in dark blue (template) and cyan (primer). The incoming UTP and the pyrophosphate product are shown in atom type, and two Mg2 + ions as magenta balls. The right panel is the same complex in a top-down orientation. (Figure courtesy of C. Ferrer-Orta and N. Verdaguer). (c) Scheme of minimum number of steps involved in nucleotide incorporation. The first step consists of the binding of polymerase 0E to the template-primer Rn (elongated up to nucleotide n) to form a complex 0ERn. Formation of the activated complex ERn is governed by the rate constant kassembly (ka). The activated ERn complex binds a nucleotide NTP with an apparent binding affinity given by Kd,app to form the ERnNTP complex. Catalysis to incorporate covalently the NTP to the growing primer chain to yield ERn + 1 and pyrophosphate (PPi) is governed by the rate constant kpol. Other constants depicted in the scheme are the inactivation rate constant (kinact) of 0E, and dissociation of E from RNA (koff, ERn and koff, ERn + 1).

Based on (Arias et al., 2008), and previous studies with PV polymerase 3D by C. E. Cameron and his colleagues.