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

In total, 18 well-studied viral species with solved RNA polymerase structures and four viral species with solved DNA polymerase structures were selected for analysis. We used the StralSV algorithm (http://proteinmodel.org/), described in detail previously (1) , to perform the analyses. StralSV compares the R2R (structural) correspondence of each sequence in a set of reference sequences to a specified query sequence, beginning at the start of the sequence and continuing to the end, by evaluating successive overlapping segments of a user-selected length. Each of the selected structures was used as a query to all structures available in the Protein Data Bank (PDB release 2011_01_25; number of chains 176 365) (8) . The results were filtered for structural segments of at least 55% LGA_S structure similarity (1) to at least one query segment of 90 amino acids in length (size cutoff for the structural context) from which R2R correspondences were extracted from local tightly superimposed spans: continuous segments of the minimum length of five amino acids. These parameters together contributed to the identification of common regions of structure similarity, which were used to distinguish regions of conservation (structure matches) from regions in which structure deviates (non-matches). The StralSV comparison of each initial query to all structures in PDB resulted in the identification of a final set of 37 PDB structures that were used as a reference polymerase structure set in this study. One representative of each species within the set of 37 PDB structures was used to create an all-against-all structure comparison using StralSV. The species and PDB identities of this reference set are summarized in Table 1 .