3VNV

Complex structure of viral RNA polymerase II

Summary for 3VNV

• Entry DOI: 10.2210/pdb3vnv/pdb
• Related: 3AGP 3AGQ 3VNU
• Descriptor: Elongation factor Ts, Elongation factor Tu, LINKER, Q beta replicase, RNA (5'-R(*CP*CP*CP*UP*AP*CP*C)-3'), RNA (5'-R(*GP*GP*GP*UP*AP*GP*GP*G)-3'), ... (6 entities in total)
• Functional Keywords: rna polymerase, translation, transferase-rna complex, transferase/rna
• Biological source: Escherichia coli O157:H7; More
• Total number of polymer chains: 3
• Total formula weight: 146742.97

Authors

Takeshita, D.,Tomita, K. (deposition date: 2012-01-18, release date: 2012-08-08, Last modification date: 2023-11-08)

Primary citation

Takeshita, D.,Yamashita, S.,Tomita, K.
Mechanism for template-independent terminal adenylation activity of Q beta replicase
Structure, 20:1661-1669, 2012

PubMed 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.

PubMed: 22884418
DOI: 10.1016/j.str.2012.07.004

Experimental method

X-RAY DIFFRACTION (2.604 Å)