User:Ann Taylor/SARS-CoV2 MPro

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== Overall Structure and Active Site of M protease ==
== Overall Structure and Active Site of M protease ==
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The main protease is a cysteine protease that is essential for the viral life cycle. It is folded like an augmented serine-protease which forms a homodimer consisting of the perpendicular protomers A and B. One protomer consists of <scene name='86/866577/Domains/2'>three domains</scene>. Domain I and II (N-terminal domain) form an antiparallel chymotrypsin-like ß-barrel structure. Domain III (C-terminal end) consist of five alpha-helices arranged in an antiparallel cluster. <ref> Yang, H., Yang, M., Ding, Y., Liu, Y., Lou, Z., Zhou, Z., Sun, L., Mo, L., Ye, S., Pang, H., Gao, G. F., Anand, K., Bartlam, M., Hilgenfeld, R. & Rao, Z. (2003). Proc Natl Acad Sci U S A. 100, 13190–13195. </ref> <ref name=”Xu”> Xu, T., Ooi, A., Lee, H. C., Wilmouth, R., Liu, D. X. & Lescar, J. (2005). Acta Crystallogr Sect F Struct Biol Cryst Commun. 61, 964–966. </ref> For maximal protease activity, the protease forms a homodimer as the substrate binding site is located in a catalytic cleft between the two N-terminal ß-barrel structures (between domain I and II). The substrate binding site involves a <scene name='86/866577/Active_site/2'>catalytic dyad</scene> consisting of the residues Cys145 and His41. The N- and C-terminal domains are connected by a long loop. <ref> Anand, K., Ziebuhr, J., Wadhwani, P., Mesters, J. R. & Hilgenfeld, R. (2003). Science. 300, 1763–1767. </ref> N-terminal residues of each protomer which are called N-finger, make contact between the N- and C-terminal domains of the other protomer and thus are necessary for dimerization.
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The main protease is a cysteine protease that is essential for the viral life cycle. It is folded like an augmented serine-protease which forms a homodimer consisting of the perpendicular protomers A and B. One protomer consists of <scene name='86/866577/Domains/2'>three domains</scene>. Domain I and II (N-terminal domain) form an antiparallel chymotrypsin-like ß-barrel structure. Domain III (C-terminal end) consist of five alpha-helices arranged in an antiparallel cluster. <ref> Yang, H., Yang, M., Ding, Y., Liu, Y., Lou, Z., Zhou, Z., Sun, L., Mo, L., Ye, S., Pang, H., Gao, G. F., Anand, K., Bartlam, M., Hilgenfeld, R. & Rao, Z. (2003). Proc Natl Acad Sci U S A. 100, 13190–13195. </ref> <ref name=”Xu”> Xu, T., Ooi, A., Lee, H. C., Wilmouth, R., Liu, D. X. & Lescar, J. (2005). Acta Crystallogr Sect F Struct Biol Cryst Commun. 61, 964–966. </ref> For maximal protease activity, the protease forms a homodimer as the substrate binding site is located in a catalytic cleft between the two N-terminal ß-barrel structures (between domain I and II). The substrate binding site involves a <scene name='86/866577/Active_site/2'>catalytic dyad</scene> consisting of the residues Cys145 and His41. S1 is a <scene name='86/866577/Binding_pocket/1'>substrate binding subsite pocket</scene> which lies next to the catalytic dyad and consists of the side chains Phe 140, His 163 and the main chains of Glu166, Asn142, Gly 143 and His172. It confers absolute specificity for the Gln-P1 substrate residue on the enzyme as the carbonyl oxygen of Gln-P1 is stabilized by an <scene name='86/866577/Oxyanion_hole/1'>oxyanion hole</scene> which is formed by amide groups of Gly143 and the catalytic Cys145. <ref> Gorbalenya, A. E., Snijder, E. J. & Ziebuhr, J. (2000). Journal of General Virology. 81, 853–879. </ref> <ref> Xue, X., Yu, H., Yang, H., Xue, F., Wu, Z., Shen, W., Li, J., Zhou, Z., Ding, Y., Zhao, Q., Zhang, X. C., Liao, M., Bartlam, M. & Rao, Z. (2008). Journal of Virology. 82, 2515–2527. </ref> Hence, polyproteins are cleaved within the Leu-Gln↓(Ser, Ala, Gly) sequence. <ref> Rut, W., Groborz, K., Zhang, L., Sun, X., Zmudzinski, M., Hilgenfeld, R. & Drag, M. (2020). BioRxiv. 2020.03.07.981928. </ref>
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<ref> Yang, H., Xie, W., Xue, X., Yang, K., Ma, J., Liang, W., Zhao, Q., Zhou, Z., Pei, D., Ziebuhr, J., Hilgenfeld, R., Yuen, K. Y., Wong, L., Gao, G., Chen, S., Chen, Z., Ma, D., Bartlam, M. & Rao, Z. (2005). PLoS Biol. 3. </ref> S1 is a <scene name='86/866577/Binding_pocket/1'>substrate binding subsite pocket</scene> which lies next to the catalytic dyad and consists of the side chains Phe 140, His 163 and the main chains of Glu166, Asn142, Gly 143 and His172. It confers absolute specificity for the Gln-P1 substrate residue on the enzyme as the carbonyl oxygen of Gln-P1 is stabilized by an <scene name='86/866577/Oxyanion_hole/1'>oxyanion hole</scene> which is formed by amide groups of Gly143 and the catalytic Cys145. <ref> Gorbalenya, A. E., Snijder, E. J. & Ziebuhr, J. (2000). Journal of General Virology. 81, 853–879. </ref> <ref> Xue, X., Yu, H., Yang, H., Xue, F., Wu, Z., Shen, W., Li, J., Zhou, Z., Ding, Y., Zhao, Q., Zhang, X. C., Liao, M., Bartlam, M. & Rao, Z. (2008). Journal of Virology. 82, 2515–2527. </ref> Hence, polyproteins are cleaved within the Leu-Gln↓(Ser, Ala, Gly) sequence. <ref> Rut, W., Groborz, K., Zhang, L., Sun, X., Zmudzinski, M., Hilgenfeld, R. & Drag, M. (2020). BioRxiv. 2020.03.07.981928. </ref>
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<ref>PMID:35380892</ref>
 
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==Peptidic inhibitors==
 
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A number of structures of MPro with candidate inhibitors have been determined, including <scene name='42/426139/6xa4/1'>6XA4</scene>, <scene name='42/426139/6xfn/1'>6XFN</scene>, <scene name='42/426139/6xbg/1'>6XBG</scene>, <scene name='42/426139/6xbh/1'>6XBH</scene>, <scene name='42/426139/6xbi/1'>6XBI</scene>, and 6WTT.
 

Revision as of 21:17, 20 February 2023

SARS-CoV2 MPro

Main Protease from SARS-CoV2

Drag the structure with the mouse to rotate

References

  1. ↑ Enjuanes, L., (2005). Coronavirus replication and reverse genetics Berlin; New York: Springer, S. 69-78.
  2. ↑ Muramatsu, T., Takemoto, C., Kim, Y.-T., Wang, H., Nishii, W., Terada, T., Shirouzu, M. & Yokoyama, S. (2016). Proc Natl Acad Sci U S A. 113, 12997–13002.
  3. ↑ Yang, H., Yang, M., Ding, Y., Liu, Y., Lou, Z., Zhou, Z., Sun, L., Mo, L., Ye, S., Pang, H., Gao, G. F., Anand, K., Bartlam, M., Hilgenfeld, R. & Rao, Z. (2003). Proc Natl Acad Sci U S A. 100, 13190–13195.
  4. ↑ Xu, T., Ooi, A., Lee, H. C., Wilmouth, R., Liu, D. X. & Lescar, J. (2005). Acta Crystallogr Sect F Struct Biol Cryst Commun. 61, 964–966.
  5. ↑ Gorbalenya, A. E., Snijder, E. J. & Ziebuhr, J. (2000). Journal of General Virology. 81, 853–879.
  6. ↑ Xue, X., Yu, H., Yang, H., Xue, F., Wu, Z., Shen, W., Li, J., Zhou, Z., Ding, Y., Zhao, Q., Zhang, X. C., Liao, M., Bartlam, M. & Rao, Z. (2008). Journal of Virology. 82, 2515–2527.
  7. ↑ Rut, W., Groborz, K., Zhang, L., Sun, X., Zmudzinski, M., Hilgenfeld, R. & Drag, M. (2020). BioRxiv. 2020.03.07.981928.

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Ann Taylor

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