Kisker lab: 5B5Q - Revision history

Karsten Theis at 17:51, 29 June 2018

Karsten Theis — Fri, 29 Jun 2018 17:51:44 GMT

←Older revision		Revision as of 17:51, 29 June 2018
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	Before you look at the shape of the binding site of Cdu1, you probably will want to show the overall view of again: <scene name='78/781027/Panela/3'>Panel A</scene>.		Before you look at the shape of the binding site of Cdu1, you probably will want to show the overall view of again: <scene name='78/781027/Panela/3'>Panel A</scene>.

-	<scene name='78/781027/Bonus/5'>Bonus figure:</scene> The active-site cysteine sidechain acting as a nucleophile in the hydrolysis reaction is buried surprisingly deeply, barely visible in the surface view (yellow patches on the gray surface). The alpha helix ~~inserted between strand 1 and two~~ (also shown in yellow) is above the substrate binding cavity, with Val 271 blocking access to the active site.	+	<scene name='78/781027/Bonus/5'>Bonus figure:</scene> The active-site cysteine sidechain acting as a nucleophile in the hydrolysis reaction is buried surprisingly deeply, barely visible in the surface view (yellow patches on the gray surface). The alpha helix (also shown in yellow) inserted between strand 1 and 2 is above the substrate binding cavity, with Val 271 blocking access to the active site.

	</StructureSection>		</StructureSection>

Karsten Theis at 17:50, 29 June 2018

Karsten Theis — Fri, 29 Jun 2018 17:50:12 GMT

←Older revision		Revision as of 17:50, 29 June 2018
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	===Substrate binding site===		===Substrate binding site===
		+	Before you look at the shape of the binding site of Cdu1, you probably will want to show the overall view of again: <scene name='78/781027/Panela/3'>Panel A</scene>.

	<scene name='78/781027/Bonus/5'>Bonus figure:</scene> The active-site cysteine sidechain acting as a nucleophile in the hydrolysis reaction is buried surprisingly deeply, barely visible in the surface view (yellow patches on the gray surface). The alpha helix inserted between strand 1 and two (also shown in yellow) is above the substrate binding cavity, with Val 271 blocking access to the active site.		<scene name='78/781027/Bonus/5'>Bonus figure:</scene> The active-site cysteine sidechain acting as a nucleophile in the hydrolysis reaction is buried surprisingly deeply, barely visible in the surface view (yellow patches on the gray surface). The alpha helix inserted between strand 1 and two (also shown in yellow) is above the substrate binding cavity, with Val 271 blocking access to the active site.

Karsten Theis: /* Structure */

Karsten Theis — Tue, 26 Jun 2018 14:42:58 GMT

Structure

←Older revision		Revision as of 14:42, 26 June 2018
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	===Substrate binding site===		===Substrate binding site===

-	<scene name='78/781027/Bonus/5'>Bonus figure:</scene> The active-site cysteine sidechain acting as a nucleophile in the hydrolysis reaction is buried surprisingly deeply, barely visible in the surface view (yellow). The alpha helix inserted between strand 1 and two (shown in yellow) is above the substrate binding cavity, with Val 271 blocking access to the active site.	+	<scene name='78/781027/Bonus/5'>Bonus figure:</scene> The active-site cysteine sidechain acting as a nucleophile in the hydrolysis reaction is buried surprisingly deeply, barely visible in the surface view (yellow patches on the gray surface). The alpha helix inserted between strand 1 and two (also shown in yellow) is above the substrate binding cavity, with Val 271 blocking access to the active site.

	</StructureSection>		</StructureSection>

Karsten Theis: /* Structure */

Karsten Theis — Tue, 26 Jun 2018 14:37:16 GMT

Structure

←Older revision		Revision as of 14:37, 26 June 2018
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	<scene name='78/781027/Paneld/3'>Panel D:</scene> The active site residues Cys 345, His, and Asp form the catalytic triad. Instead of showing omit density like in the paper, we are showing 2Fo-Fc <jmol><jmollink><text>density</text><script>isosurface s_one color silver "http://proteopedia.org/wiki/images/6/61/Map.jvxl" mesh</script></jmollink></jmol>. Center on <jmol><jmollink><text>His 275</text><script>zoom *3; select 275 and sidechain; center selected; background black</script></jmollink></jmol>.		<scene name='78/781027/Paneld/3'>Panel D:</scene> The active site residues Cys 345, His, and Asp form the catalytic triad. Instead of showing omit density like in the paper, we are showing 2Fo-Fc <jmol><jmollink><text>density</text><script>isosurface s_one color silver "http://proteopedia.org/wiki/images/6/61/Map.jvxl" mesh</script></jmollink></jmol>. Center on <jmol><jmollink><text>His 275</text><script>zoom *3; select 275 and sidechain; center selected; background black</script></jmollink></jmol>.
-
-	===Substrate binding site===
-
-	<scene name='78/781027/Bonus/5'>Bonus figure:</scene> The active-site cysteine sidechain acting as a nucleophile in the hydrolysis reaction is buried surprisingly deeply, barely visible in the surface view (yellow). The alpha helix inserted between strand 1 and two (shown in yellow) is above the substrate binding cavity, with Val 271 blocking access to the active site.

	===Superposition with product complex of SENP8===		===Superposition with product complex of SENP8===
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		+	===Substrate binding site===
		+
		+	<scene name='78/781027/Bonus/5'>Bonus figure:</scene> The active-site cysteine sidechain acting as a nucleophile in the hydrolysis reaction is buried surprisingly deeply, barely visible in the surface view (yellow). The alpha helix inserted between strand 1 and two (shown in yellow) is above the substrate binding cavity, with Val 271 blocking access to the active site.

	</StructureSection>		</StructureSection>

Karsten Theis: /* Chlamydia trachomatis inhibits apoptosis */

Karsten Theis — Tue, 26 Jun 2018 14:18:32 GMT

Chlamydia trachomatis inhibits apoptosis

←Older revision		Revision as of 14:18, 26 June 2018
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	== Chlamydia trachomatis inhibits apoptosis ==		== Chlamydia trachomatis inhibits apoptosis ==
-	''Chlamydia trachomatis'' is a bacterium that reproduces inside human cells. One defense of the human body against Chlamydia is to kill affected cells before Chlamydia reproduces. This is done through a process called apoptosis, programmed cell death. One player in apoptosis is the human protein Mcl-1. High Mcl-1 levels inhibit one of the signalling pathways that lead to apoptosis. Chlamydia inhibits Mcl-1 degradation so that Mcl-1 levels remain high.	+	''Chlamydia trachomatis'' is a bacterium that reproduces inside human cells. One defense of the human body against Chlamydia is to kill affected human cells before Chlamydia reproduces and infects more human cells. This is done through a process called apoptosis, programmed cell death. One player in apoptosis is the human protein Mcl-1. High Mcl-1 levels inhibit one of the signalling pathways that lead to apoptosis. Chlamydia inhibits Mcl-1 degradation so that Mcl-1 levels remain high.

	== Protein ubiquitination and degradation ==		== Protein ubiquitination and degradation ==

Karsten Theis: /* Structure */

Karsten Theis — Tue, 26 Jun 2018 00:14:39 GMT

Structure

←Older revision		Revision as of 00:14, 26 June 2018
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	<scene name='78/781027/Panela/3'>Panel A:</scene> The overall structure, shown as cartoon, has a fold common to other deubiquitinases (green) with a helix inserted between strand 1 and 2 (yellow). The protein belongs to the family of cysteine proteases, in which an active-site cysteine initiates hydrolysis by acting as a nucleophile. Just like serine proteases, cystein proteases have a catalytic triad (i.e. three highly conserved residues in the active site). The catalytic triad is shown in all-bonds representation.		<scene name='78/781027/Panela/3'>Panel A:</scene> The overall structure, shown as cartoon, has a fold common to other deubiquitinases (green) with a helix inserted between strand 1 and 2 (yellow). The protein belongs to the family of cysteine proteases, in which an active-site cysteine initiates hydrolysis by acting as a nucleophile. Just like serine proteases, cystein proteases have a catalytic triad (i.e. three highly conserved residues in the active site). The catalytic triad is shown in all-bonds representation.

-	(If you are new to proteopedia: Click on the green links in the text to see the scene in the 3D browser on the right. Use the mouse to change the view of the scene. Click on the controls on the bottom of the 3D browser to automatically spin the molecule, to make the rendering fancier (and perhaps slower), to resize the 3D browser window or to open a pop-up window with the same content. More controls become visible when you right-click inside the 3D browser area, and you can even remove parts of the scene or add to it using these controls.)	+	(If you are new to proteopedia: Click on the green links in the text to see the scene in the 3D browser on the right. Use the mouse to change the view of the scene. Hover over structural elements to see a temporary label. Click on the controls on the bottom of the 3D browser to automatically spin the molecule, to make the rendering fancier (and perhaps slower), to resize the 3D browser window or to open a pop-up window with the same content. More controls become visible when you right-click inside the 3D browser area, and you can even remove parts of the scene or add to it using these controls.)

	===Related proteins===		===Related proteins===

Karsten Theis: /* Structure */

Karsten Theis — Tue, 26 Jun 2018 00:13:26 GMT

Structure

←Older revision		Revision as of 00:13, 26 June 2018
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	<scene name='78/781027/Panela/3'>Panel A:</scene> The overall structure, shown as cartoon, has a fold common to other deubiquitinases (green) with a helix inserted between strand 1 and 2 (yellow). The protein belongs to the family of cysteine proteases, in which an active-site cysteine initiates hydrolysis by acting as a nucleophile. Just like serine proteases, cystein proteases have a catalytic triad (i.e. three highly conserved residues in the active site). The catalytic triad is shown in all-bonds representation.		<scene name='78/781027/Panela/3'>Panel A:</scene> The overall structure, shown as cartoon, has a fold common to other deubiquitinases (green) with a helix inserted between strand 1 and 2 (yellow). The protein belongs to the family of cysteine proteases, in which an active-site cysteine initiates hydrolysis by acting as a nucleophile. Just like serine proteases, cystein proteases have a catalytic triad (i.e. three highly conserved residues in the active site). The catalytic triad is shown in all-bonds representation.

-	(If you are new to proteopedia: Click on the green links in the text to see the scene in the 3D browser on the right. Use the mouse to change the view of the scene. Click on the controls on the bottom of the 3D browser to automatically spin the molecule, to resize the 3D browser window ~~and~~ to open a pop-up window with the same content. More controls become visible when you right-click inside the 3D browser area, and you can even remove parts of the scene or add to it using these controls.)	+	(If you are new to proteopedia: Click on the green links in the text to see the scene in the 3D browser on the right. Use the mouse to change the view of the scene. Click on the controls on the bottom of the 3D browser to automatically spin the molecule, to make the rendering fancier (and perhaps slower), to resize the 3D browser window or to open a pop-up window with the same content. More controls become visible when you right-click inside the 3D browser area, and you can even remove parts of the scene or add to it using these controls.)

	===Related proteins===		===Related proteins===

Karsten Theis: /* Structure */

Karsten Theis — Tue, 26 Jun 2018 00:10:33 GMT

Structure

←Older revision		Revision as of 00:10, 26 June 2018
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	===Superposition with product complex of SENP8===		===Superposition with product complex of SENP8===

-	<scene name='78/781027/Panele/3'>Panel E:</scene> Detail of the active site of Cdu1 with the SENP8-Nedd8 complex superposed. The superposition shows where substrate would bind in relation to catalytic triad. The color scheme is like Panel A for ~~Cub1~~ and like Panel C for the product complex of SENP8.	+	<scene name='78/781027/Panele/3'>Panel E:</scene> Detail of the active site of Cdu1 with the SENP8-Nedd8 complex superposed. The superposition shows where substrate would bind in relation to catalytic triad. The color scheme is like Panel A for Cdu1 and like Panel C for the product complex of SENP8.

	If this figure is to busy for you, you can use the buttons below to show one protein structure at a time first. Or, you can click on the popup control at the bottom of the browser, maximize the popup window to full screen, and use right click->style->stereographic->your preference for a interactive 3D stereographic figure.		If this figure is to busy for you, you can use the buttons below to show one protein structure at a time first. Or, you can click on the popup control at the bottom of the browser, maximize the popup window to full screen, and use right click->style->stereographic->your preference for a interactive 3D stereographic figure.

Karsten Theis at 19:24, 25 June 2018

Karsten Theis — Mon, 25 Jun 2018 19:24:38 GMT

←Older revision		Revision as of 19:24, 25 June 2018
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	[[Ubiquitin chains]] : Proteopedia article on Ubiquitin Chains		[[Ubiquitin chains]] : Proteopedia article on Ubiquitin Chains

-	[[Category:Kisker%2C_C]] : list of structures associated with the Kisker lab	+	[http://proteopedia.org/wiki/index.php/Category:Kisker%2C_C Category: Kisker C] : list of structures associated with the Kisker lab

	<references/>		<references/>

Karsten Theis at 19:22, 25 June 2018

Karsten Theis — Mon, 25 Jun 2018 19:22:50 GMT

←Older revision		Revision as of 19:22, 25 June 2018
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	[[Ubiquitin chains]] : Proteopedia article on Ubiquitin Chains		[[Ubiquitin chains]] : Proteopedia article on Ubiquitin Chains

-	[[Category:Kisker~~, C~~]] : list of structures associated with the Kisker lab	+	[[Category:Kisker%2C_C]] : list of structures associated with the Kisker lab
		+
	<references/>		<references/>