Structural basis for catalysis and substrate specificity of a 3C-like cysteine protease from a mosquito mesonivirus

Abstract

A R T I C L E I N F OKeywords: Mesonivirus Coronavirus 3C-like protease Crystal structure Active site of chymotrypsin-like proteases Invertebrate RNA virus A B S T R A C T Cavally virus (CavV) is a mosquito-borne plus-strand RNA virus in the family Mesoniviridae (order Nidovirales).We present X-ray structures for the CavV 3C-like protease (3CL pro ), as a free enzyme and in complex with a peptide aldehyde inhibitor mimicking the P4-to-P1 residues of a natural substrate. The 3CL pro structure (refined to 1.94 Å) shows that the protein forms dimers. The monomers are comprised of N-terminal domains I and II, which adopt a chymotrypsin-like fold, and a C-terminal α-helical domain III. The catalytic Cys-His dyad is assisted by a complex network of interactions involving a water molecule that mediates polar contacts between the catalytic His and a conserved Asp located in the domain II-III junction and is suitably positioned to stabilize the developing positive charge of the catalytic His in the transition state during catalysis. The study also reveals the structural basis for the distinct P2 Asn-specific substrate-binding pocket of mesonivirus 3CL pro s.

The SARS‐CoV‐2 main protease (Mpro): Structure, function, and emerging therapies for COVID‐19

“…[22][23][24][25][26] Because no homolog of 3CL pro has been identified in humans, it is feasible to develop efficacious and specific 3CL pro inhibitors with extremely weak inhibitory effects on human proteases, thereby reducing the side effects caused by 3CL pro inhibitors. As shown in Figure 1, the phylogenetic relationships of 14 kinds of 3CL pro s from coronaviruses show that the relatedness of the 3CL pro s for SARS-CoV-2 and SARS-CoV are extremely close [27][28][29][30][31][32][33][34][35][36][37] ; thus, most attempts to develop new SARS-CoV-2 3CL pro inhibitors are based on previously reported SARS-CoV 3CL pro inhibitor. As an attractive target for combating viral replication and pathogenesis to control various CoVs, 3CL pro has drawn much interest from both academics and industry.…”

Structural leitmotif and functional variations of the structural catalytic core in (chymo)trypsin-like serine/cysteine fold proteinases

“…A possible explanation for the need to lengthen the 214T-Zone in complement factor C2 (Tables S2, row numbered 58) is that, the Arg 696 residue, which located in the middle of the 214T-Zone, takes over the role of Ile 16 , which induces oxyanion-hole formation in trypsin [35]. The second example of a long 214T-Zone is observed in a 3CL Protease from Cavally virus (Tables S2, row numbered 169) [36]. This cysteine protease, like eleven coronavirus proteases, is part of the [Sm]102T&HOH Class (Table S1, rows numbered 159-169).…”

NBCZone: Universal three-dimensional construction of eleven amino acids near the catalytic nucleophile and base in the superfamily of (chymo)trypsin-like serine fold proteases

“…Instead of cysteine, glycine is located at position 42 T , with the exception of phenylalanine in the HCV NS3 protease (Table S1). Since the [KR]P group has lysine or arginine instead of threonine or serine at position [45][46][47][48]). Perhaps, to accommodate the cysteine nucleophile, the active site of the viral cysteine (chymo)trypsin-like fold proteases is larger than that of the serine proteases [49].…”

“…With one exception, the group of proteases with a catalytic dyad have cysteine and proline at positions 54 T and 55 T , respectively ( Table S1). The alignment of the primary structures of such proteases, given in the work of Kanitz et al [47], shows that the number of dyad proteases with the dipeptide Ile-Gln at positions 54 T and 55 T is approximately equal to the number of dyad proteases with the dipeptide Cys-Pro [47]. Table 1 lists the structural parameters of the 3Cl protease from Alphamesonivirus 1 with the participation of the dipeptide Ile-Gln in the active site (PDB ID: 5LAC, [47]).…”