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 homomorphs of all species are similarly distributed over the length of the polymerase ( Figure 1 ). The ss-RdRps (PV, COXS, HRV, FMDV, NV, RHDV, SAPV, HCV, BVDV, KUNJ and DENV) are most similar to each other. The spacing between homomorphs is more variable in the ds-RdRps (PHI6, REOV, ROTAV, IBDV and IPNV), and in general larger than in the ss-RdRps. The homomorph of Motif C (hmC) is identified in the birnaviruses despite a sequence inversion that places it before Motif A (5) . Relatively large segments between homomorphs occur in PHI6 between F1 and F3, and in KUNJ, DENV and PHI6 between B and C. The spacing between motifs is notably reduced in HIV and TERT (RdDps). In birnaviruses (IBDV, IPNV), the homomorphs of C and A are only three residues apart, and the distance between the homomorphs of Motif F3 and C is greater than the typical F3-B distance. Most homomorphs are separated from each other by a segment that contains a turn (secondary structure), or there is a turn at the beginning or end of the homomorph.