Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography
SARS-CoV-2 emerged at the end of 2019 to cause an unprecedented pandemic of the deadly respiratory disease COVID-19 that continues to date. The viral main protease (Mpro) is essential for SARS-CoV-2 replication and is therefore an important drug target. Understanding the catalytic mechanism of Mpro,...
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| Format: | Article |
| Language: | English |
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International Union of Crystallography
2021-11-01
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| Series: | IUCrJ |
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| Online Access: | http://scripts.iucr.org/cgi-bin/paper?S2052252521010113 |
| _version_ | 1818333702728450048 |
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| author | Daniel W. Kneller Qiu Zhang Leighton Coates John M. Louis Andrey Kovalevsky |
| author_facet | Daniel W. Kneller Qiu Zhang Leighton Coates John M. Louis Andrey Kovalevsky |
| author_sort | Daniel W. Kneller |
| collection | DOAJ |
| description | SARS-CoV-2 emerged at the end of 2019 to cause an unprecedented pandemic of the deadly respiratory disease COVID-19 that continues to date. The viral main protease (Mpro) is essential for SARS-CoV-2 replication and is therefore an important drug target. Understanding the catalytic mechanism of Mpro, a cysteine protease with a catalytic site comprising the noncanonical Cys145–His41 dyad, can help in guiding drug design. Here, a 2.0 Å resolution room-temperature X-ray crystal structure is reported of a Michaelis-like complex of Mpro harboring a single inactivating mutation C145A bound to the octapeptide Ac-SAVLQSGF-CONH2 corresponding to the nsp4/nsp5 autocleavage site. The peptide substrate is unambiguously defined in subsites S5 to S3′ by strong electron density. Superposition of the Michaelis-like complex with the neutron structure of substrate-free Mpro demonstrates that the catalytic site is inherently pre-organized for catalysis prior to substrate binding. Induced fit to the substrate is driven by P1 Gln binding in the predetermined subsite S1 and rearrangement of subsite S2 to accommodate P2 Leu. The Michaelis-like complex structure is ideal for in silico modeling of the SARS-CoV-2 Mpro catalytic mechanism. |
| first_indexed | 2024-12-13T13:55:50Z |
| format | Article |
| id | doaj.art-53704c447e1746098f45e3c77c49f7ca |
| institution | Directory Open Access Journal |
| issn | 2052-2525 |
| language | English |
| last_indexed | 2024-12-13T13:55:50Z |
| publishDate | 2021-11-01 |
| publisher | International Union of Crystallography |
| record_format | Article |
| series | IUCrJ |
| spelling | doaj.art-53704c447e1746098f45e3c77c49f7ca2022-12-21T23:42:54ZengInternational Union of CrystallographyIUCrJ2052-25252021-11-018697397910.1107/S2052252521010113mf5056Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallographyDaniel W. Kneller0Qiu Zhang1Leighton Coates2John M. Louis3Andrey Kovalevsky4Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USANeutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USANational Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC 20585, USALaboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, USANeutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USASARS-CoV-2 emerged at the end of 2019 to cause an unprecedented pandemic of the deadly respiratory disease COVID-19 that continues to date. The viral main protease (Mpro) is essential for SARS-CoV-2 replication and is therefore an important drug target. Understanding the catalytic mechanism of Mpro, a cysteine protease with a catalytic site comprising the noncanonical Cys145–His41 dyad, can help in guiding drug design. Here, a 2.0 Å resolution room-temperature X-ray crystal structure is reported of a Michaelis-like complex of Mpro harboring a single inactivating mutation C145A bound to the octapeptide Ac-SAVLQSGF-CONH2 corresponding to the nsp4/nsp5 autocleavage site. The peptide substrate is unambiguously defined in subsites S5 to S3′ by strong electron density. Superposition of the Michaelis-like complex with the neutron structure of substrate-free Mpro demonstrates that the catalytic site is inherently pre-organized for catalysis prior to substrate binding. Induced fit to the substrate is driven by P1 Gln binding in the predetermined subsite S1 and rearrangement of subsite S2 to accommodate P2 Leu. The Michaelis-like complex structure is ideal for in silico modeling of the SARS-CoV-2 Mpro catalytic mechanism.http://scripts.iucr.org/cgi-bin/paper?S2052252521010113sars-cov-23cl proteasemain proteasecatalytic mechanismc145a mutantenzyme–substrate complexroom-temperature x-ray crystallography |
| spellingShingle | Daniel W. Kneller Qiu Zhang Leighton Coates John M. Louis Andrey Kovalevsky Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography IUCrJ sars-cov-2 3cl protease main protease catalytic mechanism c145a mutant enzyme–substrate complex room-temperature x-ray crystallography |
| title | Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography |
| title_full | Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography |
| title_fullStr | Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography |
| title_full_unstemmed | Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography |
| title_short | Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography |
| title_sort | michaelis like complex of sars cov 2 main protease visualized by room temperature x ray crystallography |
| topic | sars-cov-2 3cl protease main protease catalytic mechanism c145a mutant enzyme–substrate complex room-temperature x-ray crystallography |
| url | http://scripts.iucr.org/cgi-bin/paper?S2052252521010113 |
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