Two adjacent mutations on the dimer interface of SARS coronavirus 3C-like protease cause different conformational changes in crystal structure

Hu, Tiancen; Zhang, Yu; Li, Lianwei; Wang, Kuifeng; Chen, Shuai; Chen, Jing; Ding, Jianping; Jiang, Hualiang; Shen, Xu

doi:10.1016/j.virol.2009.03.034

Cited by 94 publications

(129 citation statements)

References 51 publications

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“…By use of overlapped residues such as Tyr126, dimerization becomes elegantly coupled to catalysis of the SARS-CoV 3C-like protease. Indeed, despite having mutation residues at very different locations, three monomeric mutants G11A , S139A (Hu et al, 2009) and R298A (Shi et al, 2008) available so far all share highly-superimposable backbone structures, in which the characteristic short 3 10 -helix forms within the region Ile136-Gly143 of all three mutants ( Fig. 3D).…”

Section: Inactivation Of the Catalytic Machinery By Structurally-drivmentioning

confidence: 99%

“…It is also surprised to find that although the dimeric SARS-CoV 3C-like protease has a very large dimeric interface area of over 1000 Å 2 , one single interfacial mutation such as Gl1A within the chymotrypsin fold (Chen et al, 2016;Hu et al, 2009), and R298A within the extra domain is sufficient to eliminate the dimerization. Most amazingly, it has been also shown that the residues for controlling dimerization are not just limited to the interfacial ones, because residues located away from the dimerization interface was also identified to be crucial for dimerization (Barrila et al, 2006(Barrila et al, , 2010.…”

Section: Inactivation Of the Catalytic Machinery By Structurally-drivmentioning

confidence: 99%

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Structurally- and dynamically-driven allostery of the chymotrypsin-like proteases of SARS, Dengue and Zika viruses

Lim

Gupta

Roy

et al. 2019

Progress in Biophysics and Molecular Biology

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Coronavirus 3C-like and Flavivirus NS2B-NS3 proteases utilize the chymotrypsin fold to harbor their catalytic machineries but also contain additional domains/co-factors. Over the past decade, we aimed to decipher how the extra domains/co-factors mediate the catalytic machineries of SARS 3C-like, Dengue and Zika NS2B-NS3 proteases by characterizing their folding, structures, dynamics and inhibition with NMR, X-ray crystallography and MD simulations, and the results revealed: 1) the chymotrypsin fold of the SARS 3C-like protease can independently fold, while, by contrast, those of Dengue and Zika proteases lack the intrinsic capacity to fold without co-factors. 2) Mutations on the extra domain of SARS 3C-like protease can transform the active catalytic machinery into the inactive collapsed state by structurally-driven allostery. 3) Amazingly, even without detectable structural changes, mutations on the extra domain are sufficient to either inactivate or enhance the catalytic machinery of SARS 3C-like protease by dynamically-driven allostery. 4) Global networks of correlated motions have been identified: for SARS 3C-like protease, N214A inactivates the catalytic machinery by decoupling the network, while STI/A and STIF/A enhance by altering the patterns of the network. The global networks of Dengue and Zika proteases are coordinated by their NS2B-cofactors. 5) Natural products were identified to allosterically inhibit Zika and Dengue proteases through binding a pocket on the back of the active site. Therefore, by introducing extra domains/cofactors, nature develops diverse strategies to regulate the catalytic machinery embedded on the chymotrypsin fold through folding, structurally- and dynamically-driven allostery, all of which might be exploited to develop antiviral drugs.

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Section: Inactivation Of the Catalytic Machinery By Structurally-drivmentioning

confidence: 99%

Section: Inactivation Of the Catalytic Machinery By Structurally-drivmentioning

confidence: 99%

Structurally- and dynamically-driven allostery of the chymotrypsin-like proteases of SARS, Dengue and Zika viruses

Lim

Gupta

Roy

et al. 2019

Progress in Biophysics and Molecular Biology

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show abstract

“…Critical N-terminal amino acid residues up to Arg-4 and C-terminal residues up to Gln-299 have been identified as involved in dimerization and thus in generating the correct conformation of the active site (17,18). In addition, the interactions between the two helices A 0 (residues [11][12][13][14][15] and the S1 substrate-binding subsite, consisting of Phe-140, His-163, Met-165, Glu-166, and His-172, are also regarded as major components of the dimer interface (19,20).…”

Section: Introductionmentioning

confidence: 99%

“…Compared with functional dimeric Mpro, the crystal structures of monomeric Mpro (G11A, S139A, and R298A) have provided direct structural evidence for the catalytic incompetence of the dissociated monomer (19)(20)(21). In the monomer mutants, the oxyanion loop (Ser-139 to Leu-141) is converted into a short 3 10 -helix and completely collapses inward, as exemplified by the large movement of Asn-142 and Leu-141.…”

Section: Introductionmentioning

confidence: 99%

Mutation of Glu-166 Blocks the Substrate-Induced Dimerization of SARS Coronavirus Main Protease

Cheng¹,

Chang²,

Chou³

2010

Biophysical Journal

126

153

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The maturation of SARS coronavirus involves the autocleavage of polyproteins 1a and 1ab by the main protease (Mpro) and a papain-like protease; these represent attractive targets for the development of anti-SARS drugs. The functional unit of Mpro is a homodimer, and each subunit has a His-41cdots, three dots, centeredCys-145 catalytic dyad. Current thinking in this area is that Mpro dimerization is essential for catalysis, although the influence of the substrate binding on the dimer formation has never been explored. Here, we delineate the contributions of the peptide substrate to Mpro dimerization. Enzyme kinetic assays indicate that the monomeric mutant R298A/L exhibits lower activity but in a cooperative manner. Analytical ultracentrifugation analyses indicate that in the presence of substrates, the major species of R298A/L shows a significant size shift toward the dimeric form and the monomer-dimer dissociation constant of R298A/L decreases by 12- to 17-fold, approaching that for wild-type. Furthermore, this substrate-induced dimerization was found to be reversible after substrates were removed. Based on the crystal structures, a key residue, Glu-166, which is responsible for recognizing the Gln-P1 of the substrate and binding to Ser-1 of another protomer, will interact with Asn-142 and block the S1 subsite entrance in the monomer. Our studies indicate that mutation of Glu-166 in the R298A mutant indeed blocks the substrate-induced dimerization. This demonstrates that Glu-166 plays a pivotal role in connecting the substrate binding site with the dimer interface. We conclude that protein-ligand and protein-protein interactions are closely correlated in Mpro.

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“…[23] Other vital component of S1 subsite is the oxyanion hole, formed by the interaction of carboxylate anion of the conserved Gln with Gly143, Ser144 and Cys145, which stabilizes the transition state during proteolysis. [24,25] Glu166 at the entrance of the pocket interacts via H-bond with Nɛ2 of the conserved 7 Gln. [24] The S2 and S4 subsites contain hydrophobic and bulky side chains like Val, Leu or Phe.…”

Section: Resultsmentioning

confidence: 99%

Identification, synthesis and evaluation of SARS-CoV and MERS-CoV 3C-like protease inhibitors

Kumar

Tan

Wang

et al. 2016

Bioorganic & Medicinal Chemistry

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Severe acute respiratory syndrome (SARS) led to a life-threatening form of atypical pneumonia in late 2002. Following that, Middle East Respiratory Syndrome (MERS-CoV) has recently emerged, killing about 36% of patients infected globally, mainly in Saudi Arabia and South Korea. Based on a scaffold we reported for inhibiting neuraminidase (NA), we synthesized the analogues and identified compounds with low micromolar inhibitory activity against 3CL(pro) of SARS-CoV and MERS-CoV. Docking studies show that a carboxylate present at either R(1) or R(4) destabilizes the oxyanion hole in the 3CL(pro). Interestingly, 3f, 3g and 3m could inhibit both NA and 3CL(pro) and serve as a starting point to develop broad-spectrum antiviral agents.

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Two adjacent mutations on the dimer interface of SARS coronavirus 3C-like protease cause different conformational changes in crystal structure

Cited by 94 publications

References 51 publications

Structurally- and dynamically-driven allostery of the chymotrypsin-like proteases of SARS, Dengue and Zika viruses

Structurally- and dynamically-driven allostery of the chymotrypsin-like proteases of SARS, Dengue and Zika viruses

Mutation of Glu-166 Blocks the Substrate-Induced Dimerization of SARS Coronavirus Main Protease

Identification, synthesis and evaluation of SARS-CoV and MERS-CoV 3C-like protease inhibitors

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