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

Motif B is near the center of a very large homomorph that contacts the exterior surface at nearly opposite positions. As stated by Bruenn (38) , Motif B forms the base of the template-entry channel and may function in guiding the template entry into the active site. Choi et al. (17) observed that the highly conserved asn (N414 in BVDV) is conserved in all picornavirus. Hansen et al. (47) found that in HRV, N297 is involved in positioning NTP for recognition. Ferrer-Orta et al. (2) determined that the equivalent FMDV-N307 and D245 (Motif A) together are involved in ribonucleoside triphosphate (rNTP) selection. Tao et al. (21) and Butcher et al. (20) proposed that Motif B interacts with the 2 0 -OH group on the incoming nucleotide. Korneeva and Cameron (48) determined that FMDV-N307 interacts with the C-terminal-OH in the uridylylation complex, but with the 2 0 -OH in the elongation complex. The role of Motif B in the mechanisms of active site closure has recently been described in detail by Gong and Peersen (9) . These experiments document the role of the highly conserved asn in the motif in multiple species and suggest that structural alignment may be useful for the identification of potential functionally equivalent residues in structures that have R2R correspondences.