Structural basis for the dimerization and substrate recognition specificity of porcine epidemic diarrhea virus 3C-like protease

Virology. 2016 Jul:494:225-35. doi: 10.1016/j.virol.2016.04.018. Epub 2016 Apr 26.

Abstract

Porcine epidemic diarrhea virus (PEDV), a member of the genus Alphacoronavirus, has caused significant damage to the Asian and American pork industries. Coronavirus 3C-like protease (3CL(pro)), which is involved in the processing of viral polyproteins for viral replication, is an appealing antiviral drug target. Here, we present the crystal structures of PEDV 3CL(pro) and a molecular complex between an inactive PEDV 3CL(pro) variant C144A bound to a peptide substrate. Structural characterization, mutagenesis and biochemical analysis reveal the substrate-binding pockets and the residues that comprise the active site of PEDV 3CL(pro). The dimerization of PEDV 3CL(pro) is similar to that of other Alphacoronavirus 3CL(pro)s but has several differences from that of SARS-CoV 3CL(pro) from the genus Betacoronavirus. Furthermore, the non-conserved motifs in the pockets cause different cleavage of substrate between PEDV and SARS-CoV 3CL(pro)s, which may provide new insights into the recognition of substrates by 3CL(pro)s in various coronavirus genera.

Keywords: Corona virus; Crystal structure; Dimerization; PEDV 3CL(pro); Substrate specificity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Animals
  • Binding Sites
  • Catalysis
  • Catalytic Domain
  • Enzyme Activation
  • Models, Molecular*
  • Peptide Hydrolases / chemistry*
  • Peptide Hydrolases / metabolism
  • Porcine epidemic diarrhea virus / enzymology*
  • Protein Binding
  • Protein Conformation
  • Protein Interaction Domains and Motifs
  • Protein Multimerization*
  • Structure-Activity Relationship
  • Substrate Specificity
  • Swine
  • Viral Proteins / chemistry*
  • Viral Proteins / metabolism

Substances

  • Viral Proteins
  • Peptide Hydrolases