title: Three-dimensional domain swapping as a mechanism to lock the active conformation in a super-active octamer of SARS-CoV main protease.
abstract: Proteolytic processing of viral polyproteins is indispensible for the lifecycle of coronaviruses. The main protease (M(pro)) of SARS-CoV is an attractive target for anti-SARS drug development as it is essential for the polyprotein processing. M(pro) 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, M(pro) can form a domain-swapped dimer. After complete removal of the extension peptide from the dimer, the mature M(pro) self-assembles into a novel super-active octamer (AO-M(pro)). The crystal structure of AO-M(pro) adopts a novel fold with four domain-swapped dimers packing into four active units with nearly identical conformation to that of the previously reported M(pro) 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 M(pro), in equilibrium between inactive monomer and active dimer, the stable AO-M(pro) 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-M(pro) and its polyprotein substrates with multiple cleavage sites, would make AO-M(pro) functionally much more superior than the M(pro) active dimer for polyprotein processing. Thus, during the initial period of SARS-CoV infection, this novel active form AOM(pro) should play a major role in cleaving polyproteins as the protein level is extremely low. The discovery of AOM(pro) provides new insights about the functional mechanism of M(pro) and its maturation process.
authors.affiliation: Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China.|College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
authors.forename: Shengnan
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China.|College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
authors.forename: Nan
authors.initials: N
authors.lastname: Zhong
authors.affiliation: Structural Biology Laboratory, Tsinghua University, Beijing, 100084, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Xue
authors.affiliation: Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China.|College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
authors.forename: Xue
authors.initials: X
authors.lastname: Kang
authors.affiliation: Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China.|College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
authors.forename: Xiaobai
authors.initials: X
authors.lastname: Ren
authors.affiliation: Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China.|College of Life Sciences, Peking University, Beijing, 100871, China.
authors.forename: Jiaxuan
authors.initials: J
authors.lastname: Chen
authors.affiliation: Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China.|College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.|College of Life Sciences, Peking University, Beijing, 100871, China.
authors.forename: Changwen
authors.initials: C
authors.lastname: Jin
authors.affiliation: Structural Biology Laboratory, Tsinghua University, Beijing, 100084, China. binxia@pku.edu.cn.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Lou
authors.affiliation: Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China. louzy@xtal.tsinghua.edu.cn.|College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China. louzy@xtal.tsinghua.edu.cn.|College of Life Sciences, Peking University, Beijing, 100871, China. louzy@xtal.tsinghua.edu.cn.
authors.forename: Bin
authors.initials: B
authors.lastname: Xia
mesh_terms: D017934:Coronavirus / Q000378:metabolism; D000086782:Coronavirus 3C Proteases; D003546:Cysteine Endopeptidases; D010450:Endopeptidases / Q000378:metabolism*; D006801:Humans; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D020815:Polyproteins / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D045473:Severe acute respiratory syndrome-related coronavirus / Q000737:chemistry / Q000378:metabolism; D014764:Viral Proteins
chemical_list: D010455:Peptides; D020815:Polyproteins; D014764:Viral Proteins; D010450:Endopeptidases; D003546:Cysteine Endopeptidases; D000086782:Coronavirus 3C Proteases