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Crystal structure of an avian influenza polymerase PAN reveals an endonuclease active site

Abstract

The heterotrimeric influenza virus polymerase, containing the PA, PB1 and PB2 proteins, catalyses viral RNA replication and transcription in the nucleus of infected cells. PB1 holds the polymerase active site1 and reportedly harbours endonuclease activity2, whereas PB2 is responsible for cap binding2,3,4. The PA amino terminus is understood to be the major functional part of the PA protein and has been implicated in several roles, including endonuclease5 and protease activities6 as well as viral RNA/complementary RNA promoter binding7. Here we report the 2.2 ångström (Å) crystal structure of the N-terminal 197 residues of PA, termed PAN, from an avian influenza H5N1 virus. The PAN structure has an α/β architecture and reveals a bound magnesium ion coordinated by a motif similar to the (P)DXN(D/E)XK motif characteristic of many endonucleases. Structural comparisons and mutagenesis analysis of the motif identified in PAN provide further evidence that PAN holds an endonuclease active site. Furthermore, functional analysis with in vivo ribonucleoprotein reconstitution and direct in vitro endonuclease assays strongly suggest that PAN holds the endonuclease active site and has critical roles in endonuclease activity of the influenza virus polymerase, rather than PB1. The high conservation of this endonuclease active site among influenza strains indicates that PAN is an important target for the design of new anti-influenza therapeutics.

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Figure 1: The PA N structure.
Figure 2: Structural comparisons suggest PA N holds an endonuclease active site.
Figure 3: Effects of mutations in the PA and PB1 subunits on RNA polymerase function.

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Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the reported crystal structure have been deposited with the Protein Data Bank under the accession number 3EBJ.

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Acknowledgements

We thank H. Chen and K. Yu for providing the A/goose/Guangdong/1/96 influenza PA gene, R. Zhang and A. Joachimiak for assistance with data collection, and G. G. Brownlee for providing materials and for valuable advice. This work was supported by the National Natural Science Foundation of China (grant numbers 30599432, 30221003 and 30721003), the Ministry of Science and Technology International Cooperation Project (2006DFB32420), the Ministry of Science and Technology 863 Project (2006AA02A314 and 2006AA02A322), the Ministry of Science and Technology 973 Project (2006CB504300 and 2007CB914300) and the Medical Research Council (G0700848).

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Correspondence to Zihe Rao or Yingfang Liu.

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Yuan, P., Bartlam, M., Lou, Z. et al. Crystal structure of an avian influenza polymerase PAN reveals an endonuclease active site. Nature 458, 909–913 (2009). https://doi.org/10.1038/nature07720

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