3c-like Proteinase

SARS-CoV-2 3C-like Proteinase

3C-like proteinase (3CL^pro) 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 ^[1].

3C-like proteinase (3CL^pro) 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 ^[2]. All of these features of 3CL^pro 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 ^[3]. 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 ^[4].

A protomer of the SARS-CoV 3CL^pro 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 3CL^pro has a Cys-His catalytic dyad, and the substrate-binding site is located in a cleft between domains I and II ^[5].

2019-nCoV 3C-like Proteinase Protein (His Tag)

Reference

1.Perlman, S. & Netland, J. (2009).Coronaviruses post-SARS: update on replication and pathogenesis. Nature reviews Microbiology 7, 439-450.
2.Yang, H., Yang, M., Ding, Y., et al. (2003). The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor. Proceedings of the National Academy of Sciences of Sciences, 100(23), 13190–13195.
3.Fan K, Wei P, Feng Q, et al. Biosynthesis, Purification, and Substrate Specificity of Severe Acute Respiratory Syndrome Coronavirus 3C-like Proteinase[J]. Journal of Biological Chemistry, 2004, 279(3): 1637-1642.
4.Matthews, D. A., Smith, W. W., Ferre, R. A., Condon, B., Budahazi, G., Sisson, W., Villafranca, J. E., Janson, C. A., McElroy, H. E., Gribskov, C. L., and Worland, S. (1994) Cell 77, 761–771.
5.Yang, H., Yang, M., Ding, Yet al. (2003). The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor. Proceedings of the National Academy of Sciences of Sciences, 100(23), 13190–13195.