Papain-like cysteine proteinase zone (PCP-zone) and PCP structural catalytic core (PCP-SCC) of enzymes with cysteine proteinase fold

Abstract

There are several families of cysteine proteinases with different folds - for example the (chymo)trypsin fold family and papain-like fold family - but in both families the hydrolase activity of cysteine proteinases requires a cysteine residue as the catalytic nucleophile. In this work, we have analyzed the topology of the active site regions in 146 three-dimensional structures of proteins belonging to the Papain-like Cysteine Proteinase (PCP) superfamily, which includes papain as a typical representative of this protein superfamily. All analyzed enzymes contain a unique structurally closed conformation - a "PCP-Zone" - which can be divided into two groups, Class A and Class B. Eight structurally conserved amino acids of the PCP-Zone form a common Structural Core. The Structural Core, catalytic nucleophile, catalytic base and residue Xaa - which stabilizes the side-chain conformation of the catalytic base - make up a PCP Structural Catalytic Core (PCP-SCC). The PCP-SCC of Class A and Class B are divided into 5 and 2 types, respectively. Seven variants of the mutual arrangement of the amino-acid side chains of the catalytic triad - nucleophile, base and residue Xaa - within the same fold clearly demonstrate how enzymes with the papain-like fold adapt to the need to perform diverse functions in spite of their limited structural diversity. The roles of both the PCP-Zone of SARS-CoV-2-PLpro described in this study and the NBCZone of SARS-CoV-2-3CLpro presented in our earlier article (Denesyuk AI, Johnson MS, Salo-Ahen OMH, Uversky VN, Denessiouk K. Int J Biol Macromol. 2020;153:399-411) that are in contacts with inhibitors are discussed.

Keywords: COVID-19; Catalytic triad; Cysteine proteinases; Fold; Papain; SARC-CoV-2; Structural catalytic core; Zone.

Graphical abstract

Fig. 1

PCP-Zone Class A as a structural union of the N-Zone and C-Zone. A) A schematic representation of a PCP-Zone Class A using papain three-dimensional structure as an example. Two dashed lines connect the amino acids that define the boundaries of the N- and C-Zones. Positions of the catalytic triad (Nucleophile, Base and residue Xaa) are also shown. B), C), D) Contact schemes of ten amino acids of PCP-SCC of three types: C(H)X, C(X)H and CXH, respectively.

Fig. 2

PCP-Zone Class B. A. A schematic representation of a PCP-Zone Class B using three-dimensional structure of papain-like protease 2 as an example (for the designation of the details of the figure, see the legend to Fig. 1A) B. and C. Contact schemes of ten amino acids of PCP-SCC of two types: XC(H) and C(HX), respectively.

Fig. 3

VCP-Zone Class C. A. A schematic representation of a VCP-Zone Class C using three-dimensional structure of papain-like cysteine protease as an example (for the designation of the details of the figure, see the legend to Fig. 1A) B. Contact scheme of eleven amino acids of VCP-SCC, Type C(H)X.

Fig. 4

Structural characterization of the SARS-CoV-2 proteases. A. Crystal structure of SARS-CoV-2-PLpro complexed with the inhibitor (PDB ID: 6WX4; [30]). B. Crystal structure of SARS-CoV-2-3CLpro complexed with the inhibitor (PDB ID: 7BQY [31]). Positions of the residues belonging to the N-Zone and the NBCZone are shown in yellow. Closer look at the complexes of the N-Zone of SARS-CoV-2-PLpro (C) and the NBCZone of SARS-CoV-2-3CLpro (D) with inhibitors. The color of carbon atoms in proteinases is gray, and in inhibitors, green. Contacts (potential hydrogen bonds) between proteinases and inhibitors are shown by dotted lines.