User:Ann Taylor/SARS-CoV2 MPro - Revision history

Ann Taylor at 16:00, 2 March 2023

Ann Taylor — Thu, 02 Mar 2023 16:00:54 GMT

←Older revision		Revision as of 16:00, 2 March 2023
Line 8:		Line 8:
	The main protease is a cysteine protease that is essential for the viral life cycle. It is forms a <scene name='95/952725/Dimer/1'>homodimer</scene> consisting of the perpendicular protomers A and B. One protomer consists of <scene name='86/866577/Domains/2'>three domains</scene>. Domains I and II 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> The substrate binds in a <scene name='95/952725/Substrate_binding_groove/1'>channel</scene> between Domains I and II. Most of the residues in the channel are neutral (shown in white) with a few acidic residues. S1 is the <scene name='95/952725/S1_with_peptide/1'>substrate binding site</scene> and consists of the side chains Phe 140, His 163 and the backbone atoms 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 interactions with the <scene name='95/952725/Oxyanion_w_substrate/1'>backbone amide</scene> 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>		The main protease is a cysteine protease that is essential for the viral life cycle. It is forms a <scene name='95/952725/Dimer/1'>homodimer</scene> consisting of the perpendicular protomers A and B. One protomer consists of <scene name='86/866577/Domains/2'>three domains</scene>. Domains I and II 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> The substrate binds in a <scene name='95/952725/Substrate_binding_groove/1'>channel</scene> between Domains I and II. Most of the residues in the channel are neutral (shown in white) with a few acidic residues. S1 is the <scene name='95/952725/S1_with_peptide/1'>substrate binding site</scene> and consists of the side chains Phe 140, His 163 and the backbone atoms 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 interactions with the <scene name='95/952725/Oxyanion_w_substrate/1'>backbone amide</scene> 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>

-	The active site involves a <scene name='86/866577/Active_site/2'>catalytic dyad</scene> consisting of the residues Cys145 and His41. It forms a covalent intermediate with the substrate in a similar fashion to ''serine ~~proteases''~~.	+	The active site involves a <scene name='86/866577/Active_site/2'>catalytic dyad</scene> consisting of the residues Cys145 and His41. It forms a covalent intermediate with the substrate in a similar fashion to a [[serine protease]].

	==Peptidic inhibitors==		==Peptidic inhibitors==

Ann Taylor at 15:53, 2 March 2023

Ann Taylor — Thu, 02 Mar 2023 15:53:59 GMT

←Older revision		Revision as of 15:53, 2 March 2023
Line 6:		Line 6:
	== Overall Structure and Active Site of M protease ==		== Overall Structure and Active Site of M protease ==

-	The main protease is a cysteine protease that is essential for the viral life cycle. It is forms a <scene name='95/952725/Dimer/1'>homodimer</scene> consisting of the perpendicular protomers A and B. One protomer consists of <scene name='86/866577/Domains/2'>three domains</scene>. Domains I and II 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> The substrate binds in a <scene name='95/952725/Substrate_binding_groove/1'>channel</scene> between Domains I and II. Most of the residues in the channel are neutral (shown in white) with a few acidic residues. S1 is the <scene name='95/952725/S1_with_peptide/1'>substrate binding site</scene> and consists of the side chains Phe 140, His 163 and the backbone atoms 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>	+	The main protease is a cysteine protease that is essential for the viral life cycle. It is forms a <scene name='95/952725/Dimer/1'>homodimer</scene> consisting of the perpendicular protomers A and B. One protomer consists of <scene name='86/866577/Domains/2'>three domains</scene>. Domains I and II 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> The substrate binds in a <scene name='95/952725/Substrate_binding_groove/1'>channel</scene> between Domains I and II. Most of the residues in the channel are neutral (shown in white) with a few acidic residues. S1 is the <scene name='95/952725/S1_with_peptide/1'>substrate binding site</scene> and consists of the side chains Phe 140, His 163 and the backbone atoms 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 interactions with the <scene name='95/952725/Oxyanion_w_substrate/1'>backbone amide</scene> 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>

	The active site involves a <scene name='86/866577/Active_site/2'>catalytic dyad</scene> consisting of the residues Cys145 and His41. It forms a covalent intermediate with the substrate in a similar fashion to ''serine proteases''.		The active site involves a <scene name='86/866577/Active_site/2'>catalytic dyad</scene> consisting of the residues Cys145 and His41. It forms a covalent intermediate with the substrate in a similar fashion to ''serine proteases''.

Ann Taylor at 14:50, 2 March 2023

Ann Taylor — Thu, 02 Mar 2023 14:50:53 GMT

←Older revision		Revision as of 14:50, 2 March 2023
Line 6:		Line 6:
	== Overall Structure and Active Site of M protease ==		== Overall Structure and Active Site of M protease ==

-	The main protease is a cysteine protease that is essential for the viral life cycle. It is forms a <scene name='95/952725/Dimer/1'>homodimer</scene> consisting of the perpendicular protomers A and B. One protomer consists of <scene name='86/866577/Domains/2'>three domains</scene>. Domains I and II 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> 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='95/952725/~~Substrate_binding_site~~/1'>substrate binding ~~pocket~~</scene> ~~which lies next to the catalytic dyad~~ and consists of the side chains Phe 140, His 163 and the backbone atoms 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>	+	The main protease is a cysteine protease that is essential for the viral life cycle. It is forms a <scene name='95/952725/Dimer/1'>homodimer</scene> consisting of the perpendicular protomers A and B. One protomer consists of <scene name='86/866577/Domains/2'>three domains</scene>. Domains I and II 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> The substrate binds in a <scene name='95/952725/Substrate_binding_groove/1'>channel</scene> between Domains I and II. Most of the residues in the channel are neutral (shown in white) with a few acidic residues. S1 is the <scene name='95/952725/S1_with_peptide/1'>substrate binding site</scene> and consists of the side chains Phe 140, His 163 and the backbone atoms 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>
		+
		+	The active site involves a <scene name='86/866577/Active_site/2'>catalytic dyad</scene> consisting of the residues Cys145 and His41. It forms a covalent intermediate with the substrate in a similar fashion to ''serine proteases''.

	==Peptidic inhibitors==		==Peptidic inhibitors==

Ann Taylor at 22:10, 20 February 2023

Ann Taylor — Mon, 20 Feb 2023 22:10:19 GMT

←Older revision		Revision as of 22:10, 20 February 2023
Line 8:		Line 8:
	The main protease is a cysteine protease that is essential for the viral life cycle. It is forms a <scene name='95/952725/Dimer/1'>homodimer</scene> consisting of the perpendicular protomers A and B. One protomer consists of <scene name='86/866577/Domains/2'>three domains</scene>. Domains I and II 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> 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='95/952725/Substrate_binding_site/1'>substrate binding pocket</scene> which lies next to the catalytic dyad and consists of the side chains Phe 140, His 163 and the backbone atoms 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>		The main protease is a cysteine protease that is essential for the viral life cycle. It is forms a <scene name='95/952725/Dimer/1'>homodimer</scene> consisting of the perpendicular protomers A and B. One protomer consists of <scene name='86/866577/Domains/2'>three domains</scene>. Domains I and II 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> 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='95/952725/Substrate_binding_site/1'>substrate binding pocket</scene> which lies next to the catalytic dyad and consists of the side chains Phe 140, His 163 and the backbone atoms 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>

-		+	==Peptidic inhibitors==
		+	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.

Ann Taylor at 21:53, 20 February 2023

Ann Taylor — Mon, 20 Feb 2023 21:53:12 GMT

←Older revision		Revision as of 21:53, 20 February 2023
Line 6:		Line 6:
	== Overall Structure and Active Site of M protease ==		== Overall Structure and Active Site of M protease ==

-	The main protease is a cysteine protease that is essential for the viral life cycle. It is forms a <scene name='95/952725/Dimer/1'>homodimer</scene> 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 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>	+	The main protease is a cysteine protease that is essential for the viral life cycle. It is forms a <scene name='95/952725/Dimer/1'>homodimer</scene> consisting of the perpendicular protomers A and B. One protomer consists of <scene name='86/866577/Domains/2'>three domains</scene>. Domains I and II 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> 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='95/952725/Substrate_binding_site/1'>substrate binding pocket</scene> which lies next to the catalytic dyad and consists of the side chains Phe 140, His 163 and the backbone atoms 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>

Ann Taylor at 21:39, 20 February 2023

Ann Taylor — Mon, 20 Feb 2023 21:39:28 GMT

←Older revision		Revision as of 21:39, 20 February 2023
Line 2:		Line 2:
	<StructureSection load='6y2e' size='340' side='right' caption='Main Protease from SARS-CoV2' scene=''>		<StructureSection load='6y2e' size='340' side='right' caption='Main Protease from SARS-CoV2' scene=''>

-	Like many viruses, SARS-CoV2 synthesizes its proteins in long, polypeptide chains that must be cleaved to form functional proteins. ~~The coronavirus ORF 1 polyprotein can be divided into an N~~-~~terminal region that is processed by one or~~ two ~~Papain~~-like ~~proteases~~ and ~~a C-terminal region which is processed by~~ the main protease. <ref> Enjuanes, L., (2005). Coronavirus replication and reverse genetics Berlin; New York: Springer, S. 69-78. </ref> While papain-like protease(s) cleave only three sites, the main protease cleaves 11 sites in the polyprotein to generate functional proteins~~. Additionally~~, ~~the main protease cleaves its own N-~~ and ~~C-terminal autoprocessing sites. The cleaved functional proteins include viral enzymes needed for replication such as~~ the ~~RNA-dependant RNA polymerase, a helicase and other non-structural or accessory proteins such as an exoribonuclease, an endoribonuclease, a ssRNA binding protein and a 2’-O-ribose methyltransferase~~. ~~<ref> 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. </ref>~~	+	Like many viruses, SARS-CoV2 synthesizes its proteins in long, polypeptide chains that must be cleaved to form functional proteins. SARS-CoV2 uses two different proteases, a papain-like protease and the main protease. <ref> Enjuanes, L., (2005). Coronavirus replication and reverse genetics Berlin; New York: Springer, S. 69-78. </ref> While papain-like protease(s) cleave only three sites, the main protease cleaves 11 sites in the polyprotein to generate functional proteins, and is the focus of this page.

	== Overall Structure and Active Site of M protease ==		== Overall Structure and Active Site of M protease ==

-	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>	+	The main protease is a cysteine protease that is essential for the viral life cycle. It is forms a <scene name='95/952725/Dimer/1'>homodimer</scene> 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 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>

Ann Taylor at 21:35, 20 February 2023

Ann Taylor — Mon, 20 Feb 2023 21:35:40 GMT

←Older revision		Revision as of 21:35, 20 February 2023
Line 1:		Line 1:
	==SARS-CoV2 MPro==		==SARS-CoV2 MPro==
-	<StructureSection load='6y2e' size='340' side='right' caption='Main Protease from SARS-CoV2' scene=''	+	<StructureSection load='6y2e' size='340' side='right' caption='Main Protease from SARS-CoV2' scene=''>

	Like many viruses, SARS-CoV2 synthesizes its proteins in long, polypeptide chains that must be cleaved to form functional proteins. The coronavirus ORF 1 polyprotein can be divided into an N-terminal region that is processed by one or two Papain-like proteases and a C-terminal region which is processed by the main protease. <ref> Enjuanes, L., (2005). Coronavirus replication and reverse genetics Berlin; New York: Springer, S. 69-78. </ref> While papain-like protease(s) cleave only three sites, the main protease cleaves 11 sites in the polyprotein to generate functional proteins. Additionally, the main protease cleaves its own N- and C-terminal autoprocessing sites. The cleaved functional proteins include viral enzymes needed for replication such as the RNA-dependant RNA polymerase, a helicase and other non-structural or accessory proteins such as an exoribonuclease, an endoribonuclease, a ssRNA binding protein and a 2’-O-ribose methyltransferase. <ref> 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. </ref>		Like many viruses, SARS-CoV2 synthesizes its proteins in long, polypeptide chains that must be cleaved to form functional proteins. The coronavirus ORF 1 polyprotein can be divided into an N-terminal region that is processed by one or two Papain-like proteases and a C-terminal region which is processed by the main protease. <ref> Enjuanes, L., (2005). Coronavirus replication and reverse genetics Berlin; New York: Springer, S. 69-78. </ref> While papain-like protease(s) cleave only three sites, the main protease cleaves 11 sites in the polyprotein to generate functional proteins. Additionally, the main protease cleaves its own N- and C-terminal autoprocessing sites. The cleaved functional proteins include viral enzymes needed for replication such as the RNA-dependant RNA polymerase, a helicase and other non-structural or accessory proteins such as an exoribonuclease, an endoribonuclease, a ssRNA binding protein and a 2’-O-ribose methyltransferase. <ref> 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. </ref>

Ann Taylor at 21:33, 20 February 2023

Ann Taylor — Mon, 20 Feb 2023 21:33:42 GMT

←Older revision		Revision as of 21:33, 20 February 2023
Line 1:		Line 1:
	==SARS-CoV2 MPro==		==SARS-CoV2 MPro==
-	<StructureSection load='6y2e' size='340' side='right' caption='Main Protease from SARS-CoV2' scene='~~<scene name=~~'~~95/952725/Dimer/1'>~~	+	<StructureSection load='6y2e' size='340' side='right' caption='Main Protease from SARS-CoV2' scene=''

	Like many viruses, SARS-CoV2 synthesizes its proteins in long, polypeptide chains that must be cleaved to form functional proteins. The coronavirus ORF 1 polyprotein can be divided into an N-terminal region that is processed by one or two Papain-like proteases and a C-terminal region which is processed by the main protease. <ref> Enjuanes, L., (2005). Coronavirus replication and reverse genetics Berlin; New York: Springer, S. 69-78. </ref> While papain-like protease(s) cleave only three sites, the main protease cleaves 11 sites in the polyprotein to generate functional proteins. Additionally, the main protease cleaves its own N- and C-terminal autoprocessing sites. The cleaved functional proteins include viral enzymes needed for replication such as the RNA-dependant RNA polymerase, a helicase and other non-structural or accessory proteins such as an exoribonuclease, an endoribonuclease, a ssRNA binding protein and a 2’-O-ribose methyltransferase. <ref> 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. </ref>		Like many viruses, SARS-CoV2 synthesizes its proteins in long, polypeptide chains that must be cleaved to form functional proteins. The coronavirus ORF 1 polyprotein can be divided into an N-terminal region that is processed by one or two Papain-like proteases and a C-terminal region which is processed by the main protease. <ref> Enjuanes, L., (2005). Coronavirus replication and reverse genetics Berlin; New York: Springer, S. 69-78. </ref> While papain-like protease(s) cleave only three sites, the main protease cleaves 11 sites in the polyprotein to generate functional proteins. Additionally, the main protease cleaves its own N- and C-terminal autoprocessing sites. The cleaved functional proteins include viral enzymes needed for replication such as the RNA-dependant RNA polymerase, a helicase and other non-structural or accessory proteins such as an exoribonuclease, an endoribonuclease, a ssRNA binding protein and a 2’-O-ribose methyltransferase. <ref> 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. </ref>

Ann Taylor at 21:32, 20 February 2023

Ann Taylor — Mon, 20 Feb 2023 21:32:53 GMT

←Older revision		Revision as of 21:32, 20 February 2023
Line 1:		Line 1:
	==SARS-CoV2 MPro==		==SARS-CoV2 MPro==
-	<StructureSection load='' size='340' side='right' caption='Main Protease from SARS-CoV2' scene='<scene name='95/952725/Dimer/1'>	+	<StructureSection load='6y2e' size='340' side='right' caption='Main Protease from SARS-CoV2' scene='<scene name='95/952725/Dimer/1'>

	Like many viruses, SARS-CoV2 synthesizes its proteins in long, polypeptide chains that must be cleaved to form functional proteins. The coronavirus ORF 1 polyprotein can be divided into an N-terminal region that is processed by one or two Papain-like proteases and a C-terminal region which is processed by the main protease. <ref> Enjuanes, L., (2005). Coronavirus replication and reverse genetics Berlin; New York: Springer, S. 69-78. </ref> While papain-like protease(s) cleave only three sites, the main protease cleaves 11 sites in the polyprotein to generate functional proteins. Additionally, the main protease cleaves its own N- and C-terminal autoprocessing sites. The cleaved functional proteins include viral enzymes needed for replication such as the RNA-dependant RNA polymerase, a helicase and other non-structural or accessory proteins such as an exoribonuclease, an endoribonuclease, a ssRNA binding protein and a 2’-O-ribose methyltransferase. <ref> 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. </ref>		Like many viruses, SARS-CoV2 synthesizes its proteins in long, polypeptide chains that must be cleaved to form functional proteins. The coronavirus ORF 1 polyprotein can be divided into an N-terminal region that is processed by one or two Papain-like proteases and a C-terminal region which is processed by the main protease. <ref> Enjuanes, L., (2005). Coronavirus replication and reverse genetics Berlin; New York: Springer, S. 69-78. </ref> While papain-like protease(s) cleave only three sites, the main protease cleaves 11 sites in the polyprotein to generate functional proteins. Additionally, the main protease cleaves its own N- and C-terminal autoprocessing sites. The cleaved functional proteins include viral enzymes needed for replication such as the RNA-dependant RNA polymerase, a helicase and other non-structural or accessory proteins such as an exoribonuclease, an endoribonuclease, a ssRNA binding protein and a 2’-O-ribose methyltransferase. <ref> 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. </ref>

Ann Taylor at 21:32, 20 February 2023

Ann Taylor — Mon, 20 Feb 2023 21:32:19 GMT

←Older revision		Revision as of 21:32, 20 February 2023
Line 1:		Line 1:
	==SARS-CoV2 MPro==		==SARS-CoV2 MPro==
-	<StructureSection load='' size='340' side='right' caption='Main Protease from SARS-CoV2' scene='<scene name='95/952725/Dimer/1'>'>	+	<StructureSection load='' size='340' side='right' caption='Main Protease from SARS-CoV2' scene='<scene name='95/952725/Dimer/1'>

	Like many viruses, SARS-CoV2 synthesizes its proteins in long, polypeptide chains that must be cleaved to form functional proteins. The coronavirus ORF 1 polyprotein can be divided into an N-terminal region that is processed by one or two Papain-like proteases and a C-terminal region which is processed by the main protease. <ref> Enjuanes, L., (2005). Coronavirus replication and reverse genetics Berlin; New York: Springer, S. 69-78. </ref> While papain-like protease(s) cleave only three sites, the main protease cleaves 11 sites in the polyprotein to generate functional proteins. Additionally, the main protease cleaves its own N- and C-terminal autoprocessing sites. The cleaved functional proteins include viral enzymes needed for replication such as the RNA-dependant RNA polymerase, a helicase and other non-structural or accessory proteins such as an exoribonuclease, an endoribonuclease, a ssRNA binding protein and a 2’-O-ribose methyltransferase. <ref> 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. </ref>		Like many viruses, SARS-CoV2 synthesizes its proteins in long, polypeptide chains that must be cleaved to form functional proteins. The coronavirus ORF 1 polyprotein can be divided into an N-terminal region that is processed by one or two Papain-like proteases and a C-terminal region which is processed by the main protease. <ref> Enjuanes, L., (2005). Coronavirus replication and reverse genetics Berlin; New York: Springer, S. 69-78. </ref> While papain-like protease(s) cleave only three sites, the main protease cleaves 11 sites in the polyprotein to generate functional proteins. Additionally, the main protease cleaves its own N- and C-terminal autoprocessing sites. The cleaved functional proteins include viral enzymes needed for replication such as the RNA-dependant RNA polymerase, a helicase and other non-structural or accessory proteins such as an exoribonuclease, an endoribonuclease, a ssRNA binding protein and a 2’-O-ribose methyltransferase. <ref> 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. </ref>