Putative papain-related thiol proteases of positive-strand RNA viruses. Identification of rubi- and aphthovirus proteases and delineation of a novel conserved domain associated with proteases of rubi-, alpha- and coronaviruses

FEBS Lett. 1991 Aug 19;288(1-2):201-5. doi: 10.1016/0014-5793(91)81034-6.


A computer-assisted comparative analysis of the amino acid sequences of (putative) thiol proteases encoded by the genomes of several diverse groups of positive-stranded RNA viruses and distantly related to the family of cellular papain-like proteases is presented. A high level of similarity was detected between the leader protease of foot-and-mouth-disease virus and the protease of murine hepatitis coronavirus which cleaves the N-terminal p28 protein from the polyprotein. Statistically significant alignment of a portion of the rubella virus polyprotein with cellular papain-like proteases was obtained, leading to tentative identification of the papain-like protease as the enzyme mediating processing of the non-structural proteins of this virus. Specific grouping between the sequences of the proteases of alpha-viruses, and poty- and bymoviruses was revealed. It was noted that papain-like proteases of positive-stranded RNA viruses are much more variable both in their sequences and in genomic locations than chymotrypsin-related proteases found in the same virus class. A novel conserved domain of unknown function has also been identified which flanks the papain-like proteases of alpha-, rubi- and coronaviruses.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alphavirus / enzymology
  • Amino Acid Sequence
  • Aphthovirus / enzymology
  • Coronaviridae / enzymology
  • Cysteine Endopeptidases / chemistry*
  • Molecular Sequence Data
  • Papain / chemistry*
  • Plant Viruses / enzymology
  • Protein Sorting Signals / chemistry
  • RNA Viruses / enzymology*
  • Rubella virus / enzymology
  • Sequence Alignment


  • Protein Sorting Signals
  • Cysteine Endopeptidases
  • Papain