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 tertiary structure of the replicative unit of most RdRps is highly conserved (2) . It resembles that of a right-handed palm, with finger-like folds curved inward to form a tunnel that encircles the template that is being processed (3) . Most single-unit polymerases are 400-800 residues in length. Early polymerase studies found that $22 residues are highly conserved in all polymerases, and in most species they are in the same sequential order (4) . Some are clustered, with two to four highly conserved residues within a segment $10 residues in length. The sequence segment that includes each of the highly conserved residues or clusters has been described as a motif. The motifs are arranged in most species in the order: G-F1-F2-F3-A-B-C-D-E. The birnaviruses (IBDV and IPNV) differ from this scheme due to a *To whom correspondence should be addressed. Tel: [phone]; Fax: [phone]; Email: Correspondence may also be addressed to A. T. Zemla. Tel: [phone]; Fax: [phone]; Email: transversion involving the C Motif (C-A-B) (5) . The references for each of the motifs and species that have been studied are listed in Table 2 ; these references were selected because they included either alignments of one or more motifs with several species, or alignments for a particular motif not found elsewhere. Apart from these conserved motifs, the RdRp sequences are highly variable. An extensive study of picornaviruses by Koonin et al.(6) illustrates this variability. The basis of Koonin et al.'s study was an alignment of 64 species using the algorithm multiple sequence comparison by log expectation (MUSCLE) (7) and a manual adjustment. The alignment included four species that are also in our sample group, and these had a total of 32 conserved residues within sequences $550 residues in length.