2JLG

STRUCTURAL EXPLANATION FOR THE ROLE OF MN IN THE ACTIVITY OF PHI6 RNA-DEPENDENT RNA POLYMERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Explanation for the Role of Mn2+ in the Activity of {Phi}6 RNA-Dependent RNA Polymerase.

Poranen, M.M.Salgado, P.S.Koivunen, M.R.L.Wright, S.Bamford, D.H.Stuart, D.I.Grimes, J.M.

(2008) Nucleic Acids Res 36: 6633

  • DOI: 10.1093/nar/gkn632
  • Primary Citation of Related Structures:  
    2JLG, 2JLF, 2JL9

  • 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 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.


    Organizational Affiliation

    Institute of Biotechnology and Department of Biological and Environmental Sciences, Viikki Biocenter, P.O. Box 56 (Viikinkaari 5) 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): 1 
Gene Names: P2
EC: 2.7.7.48
Find proteins for P11124 (Pseudomonas phage phi6)
Explore P11124 
Go to UniProtKB:  P11124
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*DT DT DT DC DCP)-3'D, E, F5Pseudomonas virus phi6
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GTP
    Query on GTP

    Download Ideal Coordinates CCD File 
    G [auth A], H [auth B], I [auth C], J [auth C]GUANOSINE-5'-TRIPHOSPHATE
    C10 H16 N5 O14 P3
    XKMLYUALXHKNFT-UUOKFMHZSA-N
     Ligand Interaction
    MN
    Query on MN

    Download Ideal Coordinates CCD File 
    K [auth C]MANGANESE (II) ION
    Mn
    WAEMQWOKJMHJLA-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.80 Å
    • R-Value Free: 0.295 
    • R-Value Work: 0.216 
    • R-Value Observed: 0.220 
    • Space Group: P 32
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 109.026α = 90
    b = 109.026β = 90
    c = 158.835γ = 120
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    DENZOdata reduction
    SCALEPACKdata scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2008-11-04
      Type: Initial release
    • Version 1.1: 2011-05-07
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance