Protein Name

SARS coronavirus main proteinase


Severe acute respiratory syndrome coronavirus(SARS-CoV)

Biological Context

Severe acute respiratory syndrome (SARS) was reported as an atypical pneumonia on November 2002, and spread among 32 countries between January and February in 2003. About 8500 people had been infected and more than 900 people had died when the WHO declared the end of the epidemic on July 2003. The rapid transmission and high mortality ratio made SARS a global threat. After two to seven days of incubation period, patients develop the disease with sudden fever exceeding 38 degrees C, and display respiratory symptoms of cough or dyspnea. In serious cases intubation and mechanical ventilation are required. The main route of infection is supposed to be droplet infection from a patients cough or sneeze. The pathogen of this disease is a new type of coronavirus named SARS coronavirus (SARS-CoV). CoVs are positive-sense (in host cells proteins are translated from genome RNA, which plays a role of mRNA), single-stranded RNA viruses featuring the largest RNA genome known to date. The replicase, which deals with RNA replication and the transcription of SARS-CoV, encodes two overlapping polyproteins pp1a (486 kDa) and pp1ab (790 kDa). In each polyprotein several different proteins are connected in parallel, and then functional proteins are cut out from this precursor by proteases in the site-specific manner. Cleavage is primarily achieved by the main proteinase (Mpro) (also known as 3C proteinase; 3CLpro). This protease itself also included in the polyprotein and is, therefore, an attractive target for the development of drugs directed against SARS and other coronavirus infections. SARS-CoV Mpro has the fold of an augmented serine-protease, which is homologous to the enzymes from human CoV, bovine CoV and porcine transmissible gastroenteritis.

Structure Description


It forms a dimer in the crystal, and each monomer is composed of three domains. Each of the two N-terminal domains (domain I; domain II) has an antiparallel b-barrel structure, which is similar to those in other CoV proteases. The C-terminal third domain (domain III) has a globular form containing five antiparallel a-helices, and is connected with domain II through a long loop region. The substrate-binding site is located in a cleft between domains I and II. In contrast to serine proteases, which use a Ser-His-Asp catalytic triad, here a Cys-His catalytic dyad is responsible for the activity. SARS-CoV Mpro exhibits maximal protease activity in the pH range between 7.3 and 8.5 whereas it shows only half of that activity at pH 6.0. As if to support this, the structure shown here, which is solved at pH 6.0, has only one monomer (Protomer A) of the dimer in its active form structure that is similar to the structure at pH 7.6 and pH 8.0 (xPSSS:1UK3 and xPSSS:1UK2, respectively) determined at the same time. The other monomer (Protomer B) has an inactive structure in which the substrate-binding domain is partly collapsed. Furthermore, in the complex crystal structure at pH 6.0 in which a substrate-analogue was soaked in (xPSSS:1UK4), the inhibitor binds to the B protomer as well as the A protomer but cannot enter the substrate-binding pocket of the former. This information about pH-dependent structural changes and unexpected inhibitor binding modes may provide a structural basis for rational drug design.

Protein Data Bank (PDB)



  • Yang, H. Yang, M. Ding, Y. Liu, Y. Lou, Z. Zhou, Z. Sun, L. Mo, L. Ye, S. Pang, H. Gao, G.F. Anand, K. Bartlam, M. Hilgenfeld, R. Rao, Z.; "The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor"; Proc.Natl.Acad.Sci.USA; (2003) 100:13190-13195 PubMed:14585926.


author: Tomoki Matsuda

Japanese version:PDB:1UJ1