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.

The active site of the SGNH hydrolase-like fold proteins: Nucleophile–oxyanion (Nuc-Oxy) and Acid–Base zones

“…Earlier, we have described catalytic cores in many catalytic triad-based proteins with the ABH, (chymo)trypsin-like, and papain-like folds, and showed the presence of unique structure/functional environments, or “zones”, around the catalytic sites in these proteins ( Denessiouk et al, 2020a ; Denesyuk et al, 2020a ; Denesyuk et al, 2020b ). Each zone incorporated a segment of the catalytic core, connected to their respective element of protein functional machinery.…”

New sources of papain: SEM and SDS‐PAGE analysis to determine the natural tenderizer from papaya latex and senesced leaves

“…This break down led to the soft properties observed after the treat ment with papain. The catalytic mechanism of papain is initiated by deprotonation of Cys25 by the His159 imi dazole ring, which is facilitated by Asp175 (Denessiouk et al 2020). Although the positions of these three amino acids in the peptide sequence of the enzymes are far apart, folding causes the formation of the active side, which has a single function.…”

Plant and Arthropod IgE-Binding Papain-like Cysteine Proteases: Multiple Contributions to Allergenicity

“…Clan CA of PLCPs includes proteins with a papain-like fold [ 40 , 41 , 42 ]. These proteases are usually sensitive to the small molecule inhibitor E64 [ 43 ], which is ineffective against peptidases from other clans of cysteine peptidases.…”

“…In addition to the catalytic cysteine, the mechanism of action involves also a His and a Asn residue. All together, they constitute a generally conserved catalytic Cys–His–Asn triad lying at the surface of the cleft between the two domains of the molecule [ 8 , 41 ].…”

“…Although all known allergenic PLCPs are reported to show a similar fold, namely the papain-like fold [ 41 ], a comparative analysis of the primary structure of plant food enzymes and a comparison between plants and arthropods homologs highlights a low conservation of the protein sequence [ 9 ]. Conversely, a fairly high level of identity between the two mite allergens belonging to the Dermatophagoides genus, Der p 1 and Der f 1, is reported.…”