General information on Peptidase C16 domain of PL-Pro
Papain-like proteases also known as PL-Pro, nonstructural protein 3 and nsp3 is an enzyme essential for the replication of coronavirus, CoV or COVID virus. CoV PLpro belongs to the CA peptidase clan (family C16). COVID virus contains the largest known RNA genome and is responsible for coronavirus disease (COVID-19) which is highly infectious. The replication of CoV virus is highly orchestrated process which involved replication machineries that protects virus genome and proteins from the defense mechanism of the host.
Nsp3 protein, similar to other nonstructural proteins, is derived from viral polyproteins, pp1 and pp1ab. It is believed that nsp3 protein, along with nsp4 and nsp6, regulates the replication site by recruiting the replicase proteins to the host membrane. Another main function of PLpro is to process the viral polyprotein and impair ubiquitin and ISG15 from host cells. As such, PL-Pro protein helps coronaviruses block the innate immune response of the host.
Nsp3 is the largest replicase subunit and numerous interactions with other nonstructural proteins especially nsp4 and nsp6. Furthermore, the protein contains several domains
A N-terminal region which consists of ubiquitin-like (Ubl) globular fold
An extended acidic domain (AS domain) which is rich in glutamic acid
A catalytically active ADP-ribose-1″-phosphatase (ADRP, app-1″-pase) also known as X domain or the macro domain.
SARS Unique Domain (SUD)
Nucleic acid-binding domain (NAB) which has a nucleic acid chaperone function
An uncharacterized domain also known as marker domain G2M
The catalytic domain is thought to be involved during the synthesis of viral subgenomic RNAs. Furthermore, catalytic domain contains numerous catalytically active enzymes as well as transmembrane domains and domains whose function remains unknown. The active site of the catalytic domain consists of a classic catalytic triad, composed of Cys112–His273–Asp287. During the catalytic mechanism, Cys112 functions as nucleophile, His273 acts as a general acid-base, and Asp287 promote deprotonation of Cys112 by pairing with histidine.