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 hmE are summarized in Figure 9A . HmE is large and in most of the ss-RdRps (PV, COXS, HRV, FMDV, NV, RHDV, SAPV, HCV, BVDV, WN and DENV) it is highly conserved. The motif is near the N-terminal edge and a loop region is located near the middle of the homomorph. The sequences vary in length due to the loop region. The length of hmE in the caliciviruses (30-34 residues) is shorter than those in the picornaviruses (36-37 residues); HCV and BVDV loops are 37 and 35 residues, respectively, and the loops of WN and DENV are the longest at 38 and 39 residues, respectively. There is strain-specific amino acid variability in this segment of HRV. HmE is well represented by all RdRps. No R2R correspondence was found with HIV or TERT. These species, however, are structurally matched to each other ( Figure 9A , middle section). There is considerable sequence similarity between PV and DENV within this homomorph; this is illustrated in the bottom section of Figure 9A by the shaded conserved residues. DdRps and DdRps are not included in the analysis of this region because the region is missing from the structures in our sample group.