4B02

The C-terminal Priming Domain is Strongly Associated with the Main Body of Bacteriophage phi6 RNA-Dependent RNA Polymerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

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This is version 1.0 of the entry. See complete history


Literature

The C-Terminal Priming Domain is Strongly Associated with the Main Body of Bacteriophage Phi6 RNA-Dependent RNA Polymerase.

Sarin, L.P.Wright, S.Chen, Q.Degerth, L.H.Stuart, D.I.Grimes, J.M.Bamford, D.H.Poranen, M.M.

(2012) Virology 432: 184

  • DOI: 10.1016/j.virol.2012.05.035
  • Primary Citation of Related Structures:  
    4B02

  • PubMed Abstract: 
  • Double-stranded RNA viruses encode a single protein species containing RNA-dependent RNA polymerase (RdRP) motifs. This protein is responsible for RNA transcription and replication. The architecture of viral RdRPs resembles that of a cupped right hand with fingers, palm and thumb domains ...

    Double-stranded RNA viruses encode a single protein species containing RNA-dependent RNA polymerase (RdRP) motifs. This protein is responsible for RNA transcription and replication. The architecture of viral RdRPs resembles that of a cupped right hand with fingers, palm and thumb domains. Those using de novo initiation have a flexible structural elaboration that constitutes the priming platform. Here we investigate the properties of the C-terminal priming domain of bacteriophage ϕ6 to get insights into the role of an extended loop connecting this domain to the main body of the polymerase. Proteolyzed ϕ6 RdRP that possesses a nick in the hinge region of this loop was better suited for de novo initiation. The clipped C-terminus remained associated with the main body of the polymerase via the anchor helix. The structurally flexible hinge region appeared to be involved in the control of priming platform movement. Moreover, we detected abortive initiation products for a bacteriophage RdRP.


    Organizational Affiliation

    Department of Biosciences, University of Helsinki, Biocenter 2, 00014 University of Helsinki, Finland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-DIRECTED RNA POLYMERASEA, B, C664Pseudomonas virus phi6Mutation(s): 0 
Gene Names: P2
EC: 2.7.7.48
UniProt
Find proteins for P11124 (Pseudomonas phage phi6)
Explore P11124 
Go to UniProtKB:  P11124
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
D [auth A], E [auth B], F [auth C]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.07α = 90
b = 105.07β = 90
c = 157.53γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-01
    Type: Initial release