2JL9

Structural explanation for the role of Mn in the activity of phi6 RNA- dependent RNA polymerase

Summary for 2JL9

• Entry DOI: 10.2210/pdb2jl9/pdb
• Related: 1HHS 1HHT 1HI0 1HI1 1HI8 1UVI 1UVJ 1UVK 1UVL 1UVM 1UVN 1WAC
• Descriptor: RNA-DIRECTED RNA POLYMERASE (1 entity in total)
• Functional Keywords: nucleotide-binding, nucleotidyltransferase, rna-dependent rna polymerase, transferase, metal-binding, oligonucleotide, rna-directed rna polymerase, rna replication, polymerase-complex, virion, manganese, magnesium, polymerase
• Biological source: PSEUDOMONAS PHAGE PHI6
• Cellular location: Virion: P11124
• Total number of polymer chains: 3
• Total formula weight: 225100.24

Authors

Poranen, M.M.,Salgado, P.S.,Koivunen, M.R.L.,Wright, S.,Bamford, D.H.,Stuart, D.I.,Grimes, J.M. (deposition date: 2008-09-05, release date: 2008-11-04, Last modification date: 2024-05-08)

Primary citation

Poranen, M.M.,Salgado, P.S.,Koivunen, M.R.L.,Wright, S.,Bamford, D.H.,Stuart, D.I.,Grimes, J.M.
Structural Explanation for the Role of Mn2+ in the Activity of {Phi}6 RNA-Dependent RNA Polymerase.
Nucleic Acids Res., 36:6633-, 2008

PubMed Abstract: The biological role of manganese (Mn(2+)) has been a long-standing puzzle, since at low concentrations it activates several polymerases whilst at higher concentrations it inhibits. Viral RNA polymerases possess a common architecture, reminiscent of a closed right hand. The RNA-dependent RNA polymerase (RdRp) of bacteriophage 6 is one of the best understood examples of this important class of polymerases. We have probed the role of Mn(2+) by biochemical, biophysical and structural analyses of the wild-type enzyme and of a mutant form with an altered Mn(2+)-binding site (E491 to Q). The E491Q mutant has much reduced affinity for Mn(2+), reduced RNA binding and a compromised elongation rate. Loss of Mn(2+) binding structurally stabilizes the enzyme. These data and a re-examination of the structures of other viral RNA polymerases clarify the role of manganese in the activation of polymerization: Mn(2+) coordination of a catalytic aspartate is necessary to allow the active site to properly engage with the triphosphates of the incoming NTPs. The structural flexibility caused by Mn(2+) is also important for the enzyme dynamics, explaining the requirement for manganese throughout RNA polymerization.

PubMed: 18940872
DOI: 10.1093/NAR/GKN632

Experimental method

X-RAY DIFFRACTION (3.2 Å)