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The structural basis for an essential subunit interaction in influenza virus RNA polymerase

Nature volume 454, pages 1127–1131 (2008)Cite this article

Abstract

Influenza A virus is a major human and animal pathogen with the potential to cause catastrophic loss of life. The virus reproduces rapidly, mutates frequently and occasionally crosses species barriers. The recent emergence in Asia of avian influenza related to highly pathogenic forms of the human virus has highlighted the urgent need for new effective treatments1. Here we demonstrate the importance to viral replication of a subunit interface in the viral RNA polymerase, thereby providing a new set of potential drug binding sites entirely independent of surface antigen type. No current medication targets this heterotrimeric polymerase complex. All three subunits, PB1, PB2 and PA, are required for both transcription and replication2,3,4. PB1 carries the polymerase active site, PB2 includes the capped-RNA recognition domain, and PA is involved in assembly of the functional complex5,6,7, but so far very little structural information has been reported for any of them8,9,10,11. We describe the crystal structure of a large fragment of one subunit (PA) of influenza A RNA polymerase bound to a fragment of another subunit (PB1). The carboxy-terminal domain of PA forms a novel fold, and forms a deep, highly hydrophobic groove into which the amino-terminal residues of PB1 can fit by forming a 310 helix.

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Figure 1: Crystal structure of the C-terminal domain of PA bound to the N-terminal peptide of PB1.
Figure 2: Hydrogen bonds between PA and PB1.
Figure 3: Hydrophobic contacts between PA and PB1.
Figure 4: Transcriptional activity of PA mutants.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors of the complex have been deposited in the Protein Data Bank under accession code 2ZNL.

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Acknowledgements

We thank the staff at the SPring-8 BL41XU and Photon Factory BL5A beamlines for assistance with data collection, and M. Yao and Y. Zhou for help with data processing. This work was supported in part by the ISS applied research partnership program (S.-Y.P.).

Author Contributions E.O., J.R.H.T., K.N. and S.-Y.P. conceived and designed the project. E.O. carried out complex purification and crystallization, and pull-down assays. E.O., H.Y., F.K., N.S. and S.-Y.P. conducted experimental work including cloning, expression, purification, binding assays, data collection and structure analysis. A.K. and K.N. tested the transcriptional activity of mutants. E.O., J.R.H.T. and S.-Y.P. wrote the manuscript, and all authors discussed the results and conclusions.

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Authors and Affiliations

  1. Protein Design Laboratory, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama 230-0045, Japan ,

    Eiji Obayashi, Hisashi Yoshida, Fumihiro Kawai, Jeremy R. H. Tame & Sam-Yong Park

  2. Department of Physiology, Division of Biophysics, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan,

    Naoya Shibayama

  3. Department of Infection Biology, Graduate School of Comprehensive Human Sciences and Institute of Basic Medical Sciences, University of Tsukuba, Tsukuba 305-8575, Japan

    Atsushi Kawaguchi & Kyosuke Nagata

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  1. Eiji Obayashi
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Correspondence to Sam-Yong Park.

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Obayashi, E., Yoshida, H., Kawai, F. et al. The structural basis for an essential subunit interaction in influenza virus RNA polymerase. Nature 454, 1127–1131 (2008). https://doi.org/10.1038/nature07225

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