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: 2.8 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.216 

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:  

  • 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 ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-DIRECTED RNA POLYMERASE
A, B, C
664Pseudomonas phage phi6Mutation(s): 1 
Gene Names: P2
EC: 2.7.7.48
Find proteins for P11124 (Pseudomonas phage phi6)
Go to UniProtKB:  P11124
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*DT DT DT DC DCP)-3'D,E,F5Pseudomonas virus phi6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
C
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GTP
Query on GTP

Download SDF File 
Download CCD File 
A, B, C
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.216 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 109.026α = 90.00
b = 109.026β = 90.00
c = 158.835γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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