Post-Proline Cleaving Enzymes (PPCEs): Classification, Structure, Molecular Properties, and Applications

Abstract

Proteases or peptidases are hydrolases that catalyze the breakdown of polypeptide chains into smaller peptide subunits. Proteases exist in all life forms, including archaea, bacteria, protozoa, insects, animals, and plants due to their vital functions in cellular processing and regulation. There are several classes of proteases in the MEROPS database based on their catalytic mechanisms. This review focuses on post-proline cleaving enzymes (PPCEs) from different peptidase families, as well as prolyl endoprotease/oligopeptidase (PEP/POP) from the serine peptidase family. To date, most PPCEs studied are of microbial and animal origins. Recently, there have been reports of plant PPCEs. The most common PEP/POP are members of the S9 family that comprise two conserved domains. The substrate-limiting β-propeller domain prevents unwanted digestion, while the α/β hydrolase catalyzes the reaction at the carboxyl-terminal of proline residues. PPCEs display preferences towards the Pro-X bonds for hydrolysis. This level of selectivity is substantial and has benefited the brewing industry, therapeutics for celiac disease by targeting proline-rich substrates, drug targets for human diseases, and proteomics analysis. Protein engineering via mutagenesis has been performed to improve heat resistance, pepsin-resistant capability, specificity, and protein turnover of PPCEs for pharmacological applications. This review aims to synthesize recent structure–function studies of PPCEs from different families of peptidases to provide insights into the molecular mechanism of prolyl cleaving activity. Despite the non-exhaustive list of PPCEs, this is the first comprehensive review to cover the biochemical properties, biological functions, and biotechnological applications of PPCEs from the diverse taxa.

Identifying Candidate Genes for Sugar Accumulation in Sugarcane Cultivars: From a Syntenic Genomic Region to a Gene Coexpression Network

“…Gene 01 (Supplementary Table 3) shares similarities with POP, which belongs to the serine protease family (clan SC, family S9) that includes various peptidases. POP is a cytoplasmic enzyme that hydrolyzes peptide bonds at the C-terminal side of proline residues (Gutierrez et al, 2008; Baharin et al, 2022). The enzyme’s three-dimensional structure allows for the postproline cleavage of peptides containing up to 30 amino acid residues (Gutierrez et al, 2008; Baharin et al, 2022).…”

“…POP is a cytoplasmic enzyme that hydrolyzes peptide bonds at the C-terminal side of proline residues (Gutierrez et al, 2008; Baharin et al, 2022). The enzyme’s three-dimensional structure allows for the postproline cleavage of peptides containing up to 30 amino acid residues (Gutierrez et al, 2008; Baharin et al, 2022). Post- or preproline cleavage enzymes can belong to different peptidase families, including aminopeptidases, endopeptidases, or oligopeptidases (PAP/PEP/POP).…”

“…The interaction of proline accumulation with sucrose during salt stress has been reported in sugarcane (Ghosh et al, 2019). The enzyme prolyl oligopeptidase (POP—serine protease family clan SC, family S9) is a cytoplasmic enzyme that hydrolyzes oligopeptides up to 30 residues and occurs at the C-terminal side of proline residues (Gutierrez et al, 2008; Baharin et al, 2022). In plants, POP has been associated with responses to biotic and abiotic stresses (Gutierrez et al, 2008; Singh et al, 2011; Tan et al, 2013).…”

The Complex World of Emaraviruses – Challenges, Insights and Prospects

“…Both enzymes adopt the same predicted glucanase fold, and the two glutamates involved in catalysis in Glu2-Pro [137] are superposed to two conserved glutamates in the predicted 3D structure of Neprosin [141], suggesting that both enzymes have a similar catalytic mechanism. Emaravirus Glu2-Pro enzymes, which are shorter than other Glu2-Pro homologs (as short as 174 aa for ChMaV P5), may be of interest, since Prolyl endoproteases have biotechnological and biomedical applications [143].…”

Structural and time‐resolved mechanistic investigations of protein hydrolysis by the acidic proline‐specific endoprotease from Aspergillus niger

“…Some bacterial and fungal proline‐specific proteases have been developed into convenient tools for application in the food industry (Baharin et al, 2022 ; Mika et al, 2015 ). Still, most of them have a reaction specificity that limits their application.…”