SARS-CoV-2 3C-like Proteinase
3C-like proteinase (3CLpro) is a cysteine protease present in the Coronavirus replicase polyprotein, it is also called the main protease (Mpro). This protease plays a central role in viral replication and transcription functions through extensive proteolysis of two replicase polyproteins, pp1a and pp1ab which will be processed into 16 unstructured proteins (nsp1-nsp16).The functional unit of 3C-like proteinase is located in the non-structural protein 5 (nsp5) of the Coronavirus .
3C-like proteinase (3CLpro) cleaves at least 11 inter-domain sites on the pp1a and pp1ab polyproteins to generate individual functional proteins, including an RNA-directed RNA polymerase, a helicase, an exoribonuclease, an endoribonuclease and a 2′-O-ribose methyltransferase. Also, it is excised from polyproteins by its proteolytic activity and forms a homodimer with one active site per subunit . All of these features of 3CLpro makes it a principal drug target for SARS-CoV-2.
The SARS 3C-like proteinase is fully conserved among all of the released SARS coronavirus genome sequences and is highly homologous with other coronavirus 3C-like proteinase . The resolved crystal structures of 3C-like proteinases of coronaviruses show that 3C-like proteinase contains three domains. The first two domains form a chymotrypsin fold, which is responsible for the catalytic reaction, and the third domain is α-helical with unclear biological function. Coronavirus 3C-like proteinase shares the chymotrypsin fold part with the 3C proteinases from other viruses like rhinovirus called picornavirus, and that’s the reason why it gets the name .
A protomer of the SARS-CoV 3CLpro crystal structure is composed of three domains. Domains I (residues 8-101) and II (residues 102-184) have an antiparallel β-barrel structure, which is similar to other CoV proteases and reminiscent of the trypsin-like serine proteases. Domain III (residues 201-303) contains five α-helices arranged into a largely antiparallel globular cluster, and is connected with domain II by means of a long loop region (residues 185-200). SARS-CoV 3CLpro has a Cys-His catalytic dyad, and the substrate-binding site is located in a cleft between domains I and II .
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