Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases

Lang, Dorothy M.; Zemla, A. T.; Zhou, C. L. Ecale

Motif C is part of the classic 'RRM-fold' that forms the core of the palm domain of all these polymerases (together with that part of Motif A that forms a b-sheet with Motif C. Experimental studies have demonstrated that several residues within Motif C are sensitive to the position and composition of mutants. The highly conserved residues, GDD, occur near the center of the motif. The primary function of these residues is to coordinate the metal ions associated with the incoming rNTP (45, 43) . In PV, mutation of D to E in either or both positions (D328 or D329) is lethal (50) . In HCV, mutation of G317A is also lethal (51) . However, in birnaviruses the highly conserved residues are ADN, rather than GDD, and mutation to GDD increases RNA synthesis activity (5) . Certain mutations immediately upstream from the GDD motif are lethal in PV: Y326[CHIMS] (50) . This is similar to the effect of the L241-i-S242 at the downstream edge of Motif A in PV. Near the N-terminal end of Motif C in HCV (HCV T312), the mutation D311A characterizes chronic hepatitis (52) . Mutation at the edge of a highly conserved structure seems to have a substantial effect on the viral life cycle. The R2R comparisons summarized in these structure maps identify the types of sequence variability that can occur while maintaining the same spatial structure ( Figure 6A ) and demonstrates and identifies the variations in composition that can be tolerated even within a key functional motif. The R2R correspondence of other RdRps with birnaviruses in Motif C ( Figure 7A ), despite the sequence inversion in birnaviruses (CAB) supports the premise that conservation of structure is a significant, if not dominant, factor in evolution.