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 homomorph of Motif A (hmA) are summarized in Figure 4A . and IPNV (ds-RdRps) have fewer aligned residues. REOV (ds-RdRp) and HIV and TERT (RdDps) do not have R2R correspondence with the ss-RdRps. The DdRps (T7 RNAP and N4) and DdDps (TAQ and T7DNAP) share a homomorphic structure within the N-terminal segment, but it is substantially different from the RdRp structure and therefore is not included in the homomorph or Figure 4A . Within the motif, HIV corresponds only to NV and SAPV (only found using an HIV query), indicating a significant structural difference from other species; HIV also lacks R2R correspondence beyond the motif and therefore is not included in the homomorph. At the C-terminal segment of the homomorph, most species in the sample set, except HIV, have a homologous structure. At some sequence positions within hmA, a particular residue composition is conserved throughout a viral family (e.g. picornavirus), and a different residue composition is conserved in another viral family at the same position. This within-family sequence conservation (!75%) occurs at the following sequence positions (shown in Figure 4A , PV numbering): 214, 234, 237-240, 245 and 249.