SNAP output for PDB entry 3vnu [SNAP web server]

PDB-id

3vnu; SNAP-derived features in text and JSON formats; DNAproDB

Class

translation, transferase-RNA

Method

X-ray (3.2 Å)

Summary

Complex structure of viral RNA polymerase i

Reference

Takeshita D, Yamashita S, Tomita K (2012): "Mechanism for template-independent terminal adenylation activity of Q beta replicase." Structure, 20, 1661-1669. doi: 10.1016/j.str.2012.07.004.

Abstract

The genomic RNA of Qβ virus is replicated by Qβ replicase, a template-dependent RNA polymerase complex. Qβ 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 Qβ replicase has remained elusive. We determined the structure of a complex that includes Qβ 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 3'-penultimate 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 Qβ replicase is the RNA and protein ribonucleoprotein complex.