3CW4

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

Summary for 3CW4

• Entry DOI: 10.2210/pdb3cw4/pdb
• Descriptor: Polymerase basic protein 2 (2 entities in total)
• Functional Keywords: rna polymerase, mitochondrion, mrna capping, mrna processing, nucleus, virion, transferase
• Biological source: Influenza A virus
• Cellular location: Virion: P03428
• Total number of polymer chains: 1
• Total formula weight: 25295.22

Authors

Kuzuhara, T.,Kise, D.,Yoshida, H.,Horita, T.,Murasaki, Y.,Utsunomiya, H.,Fujiki, H.,Tsuge, H. (deposition date: 2008-04-21, release date: 2009-01-13, Last modification date: 2024-03-20)

Primary citation

Kuzuhara, T.,Kise, D.,Yoshida, H.,Horita, T.,Murazaki, Y.,Nishimura, A.,Echigo, N.,Utsunomiya, H.,Tsuge, H.
Structural basis of the influenza A virus RNA polymerase PB2 RNA-binding domain containing the pathogenicity-determinant lysine 627 residue
J.Biol.Chem., 284:6855-6860, 2009

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 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.

PubMed: 19144639
DOI: 10.1074/jbc.C800224200

Experimental method

X-RAY DIFFRACTION (2.7 Å)