title: 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.
abstract: 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.
authors.affiliation: Institute of Poliomyelitis and Viral Encephalitides, USSR Academy of Medical Sciences, Moscow Region.
authors.forename: A E
authors.initials: AE
authors.lastname: Gorbalenya
authors.forename: E V
authors.initials: EV
authors.lastname: Koonin
authors.forename: M M
authors.initials: MM
authors.lastname: Lai
mesh_terms: D000524:Alphavirus / Q000201:enzymology; D000595:Amino Acid Sequence; D005537:Aphthovirus / Q000201:enzymology; D003332:Coronaviridae / Q000201:enzymology; D003546:Cysteine Endopeptidases / Q000737:chemistry*; D008969:Molecular Sequence Data; D010206:Papain / Q000737:chemistry*; D010942:Plant Viruses / Q000201:enzymology; D021382:Protein Sorting Signals / Q000737:chemistry; D012328:RNA Viruses / Q000201:enzymology*; D012412:Rubella virus / Q000201:enzymology; D016415:Sequence Alignment
chemical_list: D021382:Protein Sorting Signals; D003546:Cysteine Endopeptidases; D010206:Papain