The structure of classical swine fever virus N(pro): a novel cysteine Autoprotease and zinc-binding protein involved in subversion of type I interferon induction

PLoS Pathog. 2013;9(10):e1003704. doi: 10.1371/journal.ppat.1003704. Epub 2013 Oct 17.


Pestiviruses express their genome as a single polypeptide that is subsequently cleaved into individual proteins by host- and virus-encoded proteases. The pestivirus N-terminal protease (N(pro)) is a cysteine autoprotease that cleaves between its own C-terminus and the N-terminus of the core protein. Due to its unique sequence and catalytic site, it forms its own cysteine protease family C53. After self-cleavage, N(pro) is no longer active as a protease. The released N(pro) suppresses the induction of the host's type-I interferon-α/β (IFN-α/β) response. N(pro) binds interferon regulatory factor-3 (IRF3), the key transcriptional activator of IFN-α/β genes, and promotes degradation of IRF3 by the proteasome, thus preventing induction of the IFN-α/β response to pestivirus infection. Here we report the crystal structures of pestivirus N(pro). N(pro) is structurally distinct from other known cysteine proteases and has a novel "clam shell" fold consisting of a protease domain and a zinc-binding domain. The unique fold of N(pro) allows auto-catalysis at its C-terminus and subsequently conceals the cleavage site in the active site of the protease. Although many viruses interfere with type I IFN induction by targeting the IRF3 pathway, little information is available regarding structure or mechanism of action of viral proteins that interact with IRF3. The distribution of amino acids on the surface of N(pro) involved in targeting IRF3 for proteasomal degradation provides insight into the nature of N(pro)'s interaction with IRF3. The structures thus establish the mechanism of auto-catalysis and subsequent auto-inhibition of trans-activity of N(pro), and its role in subversion of host immune response.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Catalysis
  • Catalytic Domain
  • Classical Swine Fever Virus / enzymology*
  • Classical Swine Fever Virus / genetics
  • Crystallography, X-Ray
  • Cysteine Proteases / chemistry*
  • Cysteine Proteases / genetics
  • Cysteine Proteases / metabolism
  • Interferon Type I*
  • Protein Folding*
  • Structure-Activity Relationship
  • Swine


  • Interferon Type I
  • Cysteine Proteases

Grant support

This work was supported by Agriculture and Food Research Initiative competitive grant no. 2008-35204-04625 from the USDA National Institute of Food and Agriculture (KHC) and the Swiss National Science Foundation (SNSF) grant #31003A-116608 (NR). KG is supported by James W. McLaughlin Fellowship Fund. HB is partially supported by the Louisiana Governor's Biotechnology Initiative. The beamline at CAMD is supported and operated by the Gulf Coast Protein Crystallography Consortium. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.