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

DENV as the structure of this segment has not been resolved. Motifs F1 and F2 are always continuous if F2 is present, and Motif F2 is present in most species. Motif F2 is represented by a single residue in PHI6, REOV and ROTAV (dsRNA), two residues in HIV (RdDp), 15 residues in BVDV and 10 residues in HCV (two of which, in HCV, are structurally aligned to the other RdRps). Motif F2 varied in length from 6 to 15 residues. In PHI6, there was a 61-residue segment between F1 and F3. HmF3 was present in all RdRp species. Figure 3B and C illustrates the tertiary position of hmF. Most of the structure is hairpin-like, with some residues of Motif F2 at the apex, which is located at the exterior surface of the protein. HmF1 and hmF3 are approximately parallel for several residues. HmF3 then independently extends to the surface of the protein approximately opposite the Motif F2 site. Figure 3D shows the N-and C-terminal residues and some residues of the C-segment of hmF3 at the surface of the protein. Figure 3E shows the position of Motif F2 relative to the template tunnel.