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. 2010 Apr 14;84(12):6188–6199. doi: 10.1128/JVI.02420-09

FIG. 4.

FIG. 4.

Structures and interactions in the FMDV 3D active site in different complexes. (A) 3D(M296I)-RNA template-primer, (B) 3D(wild type)-RNA (PDB code 1WNE), (C) 3D(M296I)-RNA-GTP, and (D) 3D(wild type)-RNA-RTP (PDB code 2E9R). The polymerase residues at the active site are shown as sticks in atom type color and explicitly labeled. The RNA template-primers are shown in yellow (only the first base pairs are represented). In panel C, the newly incorporated nucleotide and the PPi by-product are shown in green. When the RTP molecule (orange) is located at the active site of wild-type 3D (in panel D), the R pseudobase establishes a number of specific contacts with residues Ser298 and Gly299, within the loop β9-α11 of 3D. This β9-α11 loop changes its conformation to accommodate the nucleoside analog in the cavity. The side chains of residues Asp245 of motif A and Asn307 of motif B have also changed their rotamer conformations to facilitate the interactions with the ribose moiety of the mutagenic nucleotide. The substitution M296I seems to prevent the conformational changes in loop β9-α11, as well as the side-chain rearrangements in residues Asp245 and Asn307 required to interact with R.