title: Cysteine proteases of positive strand RNA viruses and chymotrypsin-like serine proteases. A distinct protein superfamily with a common structural fold.
abstract: Evidence is presented, based on sequence comparison and secondary structure prediction, of structural and evolutionary relationship between chymotrypsin-like serine proteases, cysteine proteases of positive strand RNA viruses (3C proteases of picornaviruses and related enzymes of como-, nepo- and potyviruses) and putative serine protease of a sobemovirus. These observations lead to re-identification of principal catalytic residues of viral proteases. Instead of the pair of Cys and His, both located in the C-terminal part of 3C proteases, a triad of conserved His, Asp(Glu) and Cys(Ser) has been identified, the first two residues resident in the N-terminal, and Cys in the C-terminal beta-barrel domain. These residues are suggested to form a charge-transfer system similar to that formed by the catalytic triad of chymotrypsin-like proteases. Based on the structural analogy with chymotrypsin-like proteases, the His residue previously implicated in catalysis, together with two partially conserved Gly residues, is predicted to constitute part of the substrate-binding pocket of 3C proteases. A partially conserved ThrLys/Arg dipeptide located in the loop preceding the catalytic Cys is suggested to confer the primary cleavage specificity of 3C toward Glx/Gly(Ser) sites. These observations provide the first example of relatedness between proteases belonging, by definition, to different classes.
authors.affiliation: Institute of Poliomyelitis and Viral Encephalitides, USSR Academy of Medical Sciences, Moscow.
authors.forename: A E
authors.initials: AE
authors.lastname: Gorbalenya
authors.forename: A P
authors.initials: AP
authors.lastname: Donchenko
authors.forename: V M
authors.initials: VM
authors.lastname: Blinov
authors.forename: E V
authors.initials: EV
authors.lastname: Koonin
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D005075:Biological Evolution; D003546:Cysteine Endopeptidases; D008969:Molecular Sequence Data; D011487:Protein Conformation; D012328:RNA Viruses / Q000201:enzymology*; D012697:Serine Endopeptidases
chemical_list: D012697:Serine Endopeptidases; D003546:Cysteine Endopeptidases