3CW4

Large c-terminal domain of influenza a virus RNA-dependent polymerase PB2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of the influenza A virus RNA polymerase PB2 RNA-binding domain containing the pathogenicity-determinant lysine 627 residue

Kuzuhara, T.Kise, D.Yoshida, H.Horita, T.Murazaki, Y.Nishimura, A.Echigo, N.Utsunomiya, H.Tsuge, H.

(2009) J.Biol.Chem. 284: 6855-6860

  • DOI: 10.1074/jbc.C800224200

  • PubMed Abstract: 
  • Because the influenza A virus has an RNA genome, its RNA-dependent RNA polymerase, comprising the PA, PB1, and PB2 subunits, is essential for viral transcription and replication. The binding of RNA primers/promoters to the polymerases is an initiatio ...

    Because the influenza A virus has an RNA genome, its RNA-dependent RNA polymerase, comprising the PA, PB1, and PB2 subunits, is essential for viral transcription and replication. The binding of RNA primers/promoters to the polymerases is an initiation step in viral transcription. In our current study, we reveal the 2.7 A tertiary structure of the C-terminal RNA-binding domain of PB2 by x-ray crystallography. This domain incorporates lysine 627 of PB2, and this residue is associated with the high pathogenicity and host range restriction of influenza A virus. We found from our current analyses that this lysine is located in a unique "phi"-shaped structure consisting of a helix and an encircled loop within the PB2 domain. By electrostatic analysis, we identified a highly basic groove along with this phi loop and found that lysine 627 is located in the phi loop. A PB2 domain mutant in which glutamic acid is substituted at position 627 shows significantly lower RNA binding activity. This is the first report to show a relationship between RNA binding activity and the pathogenicity-determinant lysine 627. Using the Matras program for protein three-dimensional structural comparisons, we further found that the helix bundles in the PB2 domain are similar to that of activator 1, the 40-kDa subunit of DNA replication clamp loader (replication factor C), which is also an RNA-binding protein. This suggests a functional and structural relationship between the RNA-binding mechanisms underlying both influenza A viral transcription and cellular DNA replication. Our present results thus provide important new information for developing novel drugs that target the primer/promoter RNA binding of viral RNA polymerases.


    Organizational Affiliation

    Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, and Institute for Health Sciences, Tokushima Bunri University, Tokushima 770-8514, Japan. kuzuhara@ph.bunri-u.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase basic protein 2
A
225Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)Mutation(s): 0 
Gene Names: PB2
Find proteins for P03428 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Go to UniProtKB:  P03428
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.237 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 52.527α = 90.00
b = 52.527β = 90.00
c = 156.357γ = 120.00
Software Package:
Software NamePurpose
SOLVEphasing
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-01-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-11-09
    Type: Database references