Mechanism for Template-Independent Terminal Adenylation Activity of Qβ Replicase

The genomic RNA of Q beta virus is replicated by Q beta replicase, a template-dependent RNA polymerase complex. Q beta replicase has an intrinsic template-independent RNA 3'-adenylation activity, which is required for efficient viral RNA amplification in the host cells. However, the mechanism of the template-independent 3'-adenylation of RNAs by Q beta replicase has remained elusive. We determined the structure of a complex that includes Q beta replicase, a template RNA, a growing RNA complementary to the template RNA, and ATP. The structure represents the terminal stage of RNA polymerization and reveals that the shape and size of the nucleotide-binding pocket becomes available for ATP accommodation after the nucleotide-binding template-dependent C-addition. The stacking interaction between the ATP and the neighboring Watson-Crick base pair, between the 5'-G in the template and the 3'-C in the growing RNA, contributes to the nucleotide specificity. Thus, the template for the template-independent 3'-adenylation by Q beta replicase is the RNA and protein ribonucleoprotein complex.