Viral cysteine proteases are homologous to the trypsin-like family of serine proteases: structural and functional implications.

Abstract

Proteases that are encoded by animal picornaviruses and plant como-and potyviruses form a related group of cysteine-active-center enzymes that are essential for virus maturation. We show that these proteins are homologous to the family of trypsin-like serine proteases. In our model, the active-site nucleophile of the trypsin catalytic triad, , is changed to a Cys residue in these viral proteases. The other two residues of the triad, His-57 and Asp-102, are otherwise absolutely conserved in all the viral protease sequences. Secondary structure analysis of aligned sequences suggests the location of the component strands of the twin fl-barrel trypsin fold in the viral proteases. Unexpectedly, the 2a and 3c subclasses of viral cysteine proteases are, respectively, homologous to the small and large structural subclasses oftrypsin-like serine proteases. This classification allows the molecular mapping of residues from viral sequences onto related tertiary structures; we precisely identify amino acids that are strong determinants of specificity for both small and large viral cysteine proteases.

Secoviridae: a proposed family of plant viruses within the order Picornavirales that combines the families Sequiviridae and Comoviridae, the unassigned genera Cheravirus and Sadwavirus, and the proposed genus Torradovirus

“…Each genome segment encodes a large polyprotein. This polyprotein is cleaved by cysteine proteinases (such as the picornavirus 3C proteinase) that are structurally related to chymotrypsin [1,9,13]. The genome organization is conserved among picornavirales.…”

Characterization of the S1 binding site of the glutamic acid‐specific protease from Streptomyces griseus

“…SGPE and the human rhinovirus 3C proteinase (3CPr0) both have a trypsin-like three-dimensional fold, although the latter is a thiol protease (Nienaber et al, 1993;Matthews et al, 1994). The specificity of 3CPr0 is assumed to be due to interactions between the carboxyamide group of the PI glutamine and the side-chains of the highly conserved Thr 141 and His 160 (one acting as a hydrogen bond donor and the other as an acceptor) (Bazan & Fletterick, 1988;Gorbalenya et al, 1989;Matthews et al, 1994 (Nienaber et al, 1993;Matthews et al, 1994). However, in SGPE, both residues act as hydrogen bond donors and it is conceivable that this can explain the different specificities of the two classes of enzymes.…”

The picornaviral 3C proteinases: Cysteine nucleophiles in serine proteinase folds

“…Sequence alignment had suggested that one of two residues, either aspartate 85 or glutamate 71 in poliovirus might function as the third member of a catalytic triad (Gorbalenya et al, 1986;Bazan & Fletterick, 1988) similar to the one established for chymotrypsin and trypsin (Blow et al, 1969; Sprang et al, 1987;Warshel et al, 1989). Site-directed mutagenesis studies were suggestive but inconclusive (Ivanoff et al, 1986;Cheah et al, 1990;Hammerle et al, 1991;Kean et al, 1991).…”

“…This prediction has been borne out by the structure determinations. Prior to the elucidation of the three-dimensional structure, sequence alignment and secondary structure predictions (Gorbalenya et al, 1986(Gorbalenya et al, , 1989Bazan & Fletterick, 1988, 1990) and site-directed mutagenesis studies (Ivanoff et al, 1986;Cheah et al, 1990;Hammerle et al, 1991;Kean et al, 1991; had strongly implicated cysteine 147 (poliovirus numbering) and histidine 40 as the nucleophile and general base, respectively, of the 3C proteinases. Again, the crystal structures confirm these assignments.…”