A Structural Comparison of SARS-CoV-2 Main Protease and Animal Coronaviral Main Protease Reveals Species-Specific Ligand Binding and Dimerization Mechanism
Abstract
:1. Introduction
2. Results
2.1. GC376 Is a Potential Lead Compound against CCoV Mpro
2.2. Overall Structure of CCoV Mpro in Complex with GC376
2.3. GC376 Covalently Linked to Catalytic Cys144 of CCoV Mpro, Forming an (R)- or (S)-Hemithioacetal
2.4. Three Conserved Structural Features Dictate the Substrate-Binding Pocket of CoV Mpros
2.5. Species-Specific Dimerization of CoV Mpros
3. Discussion
4. Materials and Methods
4.1. Cloning, Expression, and Purification of CCoV Mpro
4.2. Fluorescence Resonance Energy Transfer (FRET)-Based Assay
4.3. Protein Thermal Shift Assay
4.4. Crystallization and Structural Determination of CCoV Mpro in Complex with GC376
4.5. Bioinformatic Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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GC376 Bound CCoV Mpro | |
---|---|
PDB Code | 7XJW |
Data collection | |
Diffraction source | TPS 05A, 3 GeV TPS, NSRRC |
Wavelength (Å) | 0.99984 |
Detector | MX300-HS |
Crystal-detector distance (mm) | 300 |
Space group | C2 |
a, b, c (Å) | 156.975, 125.749, 160.418 |
α, β, γ (°) | 90, 97.467, 90 |
Resolution range (Å) | 30.0–2.75 (2.85–2.75) |
Total no. of reflections | 295,387 (28,408) |
No. of unique reflections | 79,392 (7891) |
Completeness (%) | 99.3 (99.7) |
Multiplicity | 3.7 (3.6) |
〈I/σ(I)〉 | 20.39 (3.39) |
Rmerge | 0.062 (0.386) |
Rp.i.m. | 0.036 (0.234) |
CC1/2 | (0.914) |
Refinement | |
Resolution range (Å) | 27.83–2.75 (2.82–2.75) |
Final Rwork (%) | 21.0 (27.2) |
Final Rfree (%) | 25.7 (28.0) |
No. of non-H atoms | 18,564 |
No. of atoms | |
Protein | 18,224 |
Ligand | 232 |
Water | 108 |
B factors (Å2) | 54.4 |
Protein | 54.6 |
Ligand | 48.6 |
Water | 31.9 |
R.m.s. deviations | |
Bonds (Å) | 0.015 |
Angles (°) | 1.72 |
Ramachandran plot | |
Most favoured (%) | 92.44 |
Allowed (%) | 7.22 |
Outliers (%) | 0.34 |
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Ho, C.-Y.; Yu, J.-X.; Wang, Y.-C.; Lin, Y.-C.; Chiu, Y.-F.; Gao, J.-Y.; Lai, S.-J.; Chen, M.-J.; Huang, W.-C.; Tien, N.; et al. A Structural Comparison of SARS-CoV-2 Main Protease and Animal Coronaviral Main Protease Reveals Species-Specific Ligand Binding and Dimerization Mechanism. Int. J. Mol. Sci. 2022, 23, 5669. https://doi.org/10.3390/ijms23105669
Ho C-Y, Yu J-X, Wang Y-C, Lin Y-C, Chiu Y-F, Gao J-Y, Lai S-J, Chen M-J, Huang W-C, Tien N, et al. A Structural Comparison of SARS-CoV-2 Main Protease and Animal Coronaviral Main Protease Reveals Species-Specific Ligand Binding and Dimerization Mechanism. International Journal of Molecular Sciences. 2022; 23(10):5669. https://doi.org/10.3390/ijms23105669
Chicago/Turabian StyleHo, Chien-Yi, Jia-Xin Yu, Yu-Chuan Wang, Yu-Chuan Lin, Yi-Fang Chiu, Jing-Yan Gao, Shu-Jung Lai, Ming-Jen Chen, Wei-Chien Huang, Ni Tien, and et al. 2022. "A Structural Comparison of SARS-CoV-2 Main Protease and Animal Coronaviral Main Protease Reveals Species-Specific Ligand Binding and Dimerization Mechanism" International Journal of Molecular Sciences 23, no. 10: 5669. https://doi.org/10.3390/ijms23105669