Structures of the Middle East respiratory syndrome coronavirus 3C-like protease reveal insights into substrate specificity

Acta Crystallogr D Biol Crystallogr. 2015 May;71(Pt 5):1102-11. doi: 10.1107/S1399004715003521. Epub 2015 Apr 24.


Middle East respiratory syndrome coronavirus (MERS-CoV) is a highly pathogenic virus that causes severe respiratory illness accompanied by multi-organ dysfunction, resulting in a case fatality rate of approximately 40%. As found in other coronaviruses, the majority of the positive-stranded RNA MERS-CoV genome is translated into two polyproteins, one created by a ribosomal frameshift, that are cleaved at three sites by a papain-like protease and at 11 sites by a 3C-like protease (3 CL(pro)). Since 3 CL(pro) is essential for viral replication, it is a leading candidate for therapeutic intervention. To accelerate the development of 3 CL(pro) inhibitors, three crystal structures of a catalytically inactive variant (C148A) of the MERS-CoV 3 CL(pro) enzyme were determined. The aim was to co-crystallize the inactive enzyme with a peptide substrate. Fortuitously, however, in two of the structures the C-terminus of one protomer is bound in the active site of a neighboring molecule, providing a snapshot of an enzyme-product complex. In the third structure, two of the three protomers in the asymmetric unit form a homodimer similar to that of SARS-CoV 3 CL(pro); however, the third protomer adopts a radically different conformation that is likely to correspond to a crystallographic monomer, indicative of substantial structural plasticity in the enzyme. The results presented here provide a foundation for the structure-based design of small-molecule inhibitors of the MERS-CoV 3 CL(pro) enzyme.

Keywords: 3CLpro; MERS-CoV; coronavirus; main protease.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Antiviral Agents / pharmacology*
  • Catalytic Domain
  • Crystallography, X-Ray
  • Cysteine Endopeptidases / chemistry*
  • Cysteine Endopeptidases / metabolism*
  • Enzyme Inhibitors / pharmacology*
  • Humans
  • Middle East Respiratory Syndrome Coronavirus / enzymology*
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Conformation
  • Sequence Homology, Amino Acid
  • Substrate Specificity


  • Antiviral Agents
  • Enzyme Inhibitors
  • 3C-like proteinase, Coronavirus
  • Cysteine Endopeptidases

Associated data

  • PDB/4WMD
  • PDB/4WME
  • PDB/4WMF