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. 2010 Apr 1;1(4):371–383. doi: 10.1007/s13238-010-0044-8

Three-dimensional domain swapping as a mechanism to lock the active conformation in a super-active octamer of SARS-CoV main protease

Shengnan Zhang 1,2, Nan Zhong 1,2, Fei Xue 3, Xue Kang 1,2, Xiaobai Ren 1,2, Jiaxuan Chen 1,4, Changwen Jin 1,2,4, Zhiyong Lou 3,✉, Bin Xia 1,2,4,✉
PMCID: PMC4875095  PMID: 21203949

Abstract

Proteolytic processing of viral polyproteins is indispensible for the lifecycle of coronaviruses. The main protease (Mpro) of SARS-CoV is an attractive target for anti-SARS drug development as it is essential for the polyprotein processing. Mpro is initially produced as part of viral polyproteins and it is matured by autocleavage. Here, we report that, with the addition of an N-terminal extension peptide, Mpro can form a domain-swapped dimer. After complete removal of the extension peptide from the dimer, the mature Mpro self-assembles into a novel super-active octamer (AO-Mpro). The crystal structure of AO-Mpro adopts a novel fold with four domain-swapped dimers packing into four active units with nearly identical conformation to that of the previously reported Mpro active dimer, and 3D domain swapping serves as a mechanism to lock the active conformation due to entanglement of polypeptide chains. Compared with the previously well characterized form of Mpro, in equilibrium between inactive monomer and active dimer, the stable AO-Mpro exhibits much higher proteolytic activity at low concentration. As all eight active sites are bound with inhibitors, the polyvalent nature of the interaction between AO-Mpro and its polyprotein substrates with multiple cleavage sites, would make AO-Mpro functionally much more superior than the Mpro active dimer for polyprotein processing. Thus, during the initial period of SARS-CoV infection, this novel active form AOMpro should play a major role in cleaving polyproteins as the protein level is extremely low. The discovery of AOMpro provides new insights about the functional mechanism of Mpro and its maturation process.

Electronic Supplementary Material

Supplementary material is available for this article at 10.1007/s13238-010-0044-8 and is accessible for authorized users.

Keywords: SARS-CoV, main protease, crystal structure, 3D domain swapping, polyprotein processing

Electronic supplementary material

13238_2010_44_MOESM1_ESM.pdf (181.8KB, pdf)

Supplementary material, approximately 181 KB.

Footnotes

These authors contributed equally to the work.

Electronic Supplementary Material

Supplementary material is available for this article at 10.1007/s13238-010-0044-8 and is accessible for authorized users.

Contributor Information

Zhiyong Lou, Email: binxia@pku.edu.cn.

Bin Xia, Email: louzy@xtal.tsinghua.edu.cn.

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