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

The structurally aligned sequences that comprise the hmD are shown in Figure 8A . The homomorph is 21 residues long and consists of a 10-residue extension from the N-terminal edge of the motif plus the motif itself. The structure of the N-terminal segment is more highly conserved (i.e. has more R2R matches) than the motif. Various query sequences were tested with the expectation that they would capture additional alignments. The middle section of Figure 8A illustrates that this produced some improvement. For example, using an HCV query, there are R2R matches to TERT, TAQ and T7 DNAP. The C-terminal edge of the motif has some R2R correspondence, suggesting that the structure of the motif is moderately conserved. Using T7 DNAP as a query (lowest segment of the figure) , only a small portion of the C-terminal edge of Motif D and a few species have similar structures. There is no alignment of PHI6 within the N-terminal segment of the homomorph, because in this region PHI6 consists of a 24-residue loop between the end of Motif C and the start of Motif D.