Kisker lab: 5B5Q: Difference between revisions
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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 == | ||
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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 | (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=== | ||
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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>. | ||
===Superposition with product complex of SENP8=== | ===Superposition with product complex of SENP8=== | ||
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===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 (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> | ||