4A8W

Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6 from De Novo Initiation to Elongation

Summary for 4A8W

• Entry DOI: 10.2210/pdb4a8w/pdb
• Related: 1HHS 1HHT 1HI0 1HI1 1HI8 1UVI 1UVJ 1UVK 1UVL 1UVM 1UVN 1WAC 2JL9 2JLF 2JLG 4A8F 4A8K 4A8M 4A8O 4A8Q 4A8S 4A8Y
• Descriptor: RNA-DIRECTED RNA POLYMERASE, 5'-D(*TP*TP*CP*GP*CP*GP*TP*AP*AP*GP*CP*GP)-3', MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: transferase-dna complex, transferase, transferase/dna
• Biological source: PSEUDOMONAS PHAGE PHI6; More
• Cellular location: Virion: P11124
• Total number of polymer chains: 6
• Total formula weight: 237729.89

Authors

Wright, S.,Poranen, M.M.,Bamford, D.H.,Stuart, D.I.,Grimes, J.M. (deposition date: 2011-11-21, release date: 2012-07-04, Last modification date: 2023-12-20)

Primary citation

Wright, S.,Poranen, M.M.,Bamford, D.H.,Stuart, D.I.,Grimes, J.M.
Noncatalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial Double-Stranded RNA Virus Phi6 from De Novo Initiation to Elongation.
J.Virol., 86:2837-, 2012

PubMed Abstract: RNA-dependent RNA polymerases (RdRps) are key to the replication of RNA viruses. A common divalent cation binding site, distinct from the positions of catalytic ions, has been identified in many viral RdRps. We have applied biochemical, biophysical, and structural approaches to show how the RdRp from bacteriophage ϕ6 uses the bound noncatalytic Mn(2+) to facilitate the displacement of the C-terminal domain during the transition from initiation to elongation. We find that this displacement releases the noncatalytic Mn(2+), which must be replaced for elongation to occur. By inserting a dysfunctional Mg(2+) at this site, we captured two nucleoside triphosphates within the active site in the absence of Watson-Crick base pairing with template and mapped movements of divalent cations during preinitiation. These structures refine the pathway from preinitiation through initiation to elongation for the RNA-dependent RNA polymerization reaction, explain the role of the noncatalytic divalent cation in 6 RdRp, and pinpoint the previously unresolved Mn(2+)-dependent step in replication.

PubMed: 22205747
DOI: 10.1128/JVI.05168-11

Experimental method

X-RAY DIFFRACTION (3.04 Å)