Kisker lab: 5B5Q

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Revision as of 14:37, 26 June 2018

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1 How this page was created
2 Chlamydia trachomatis inhibits apoptosis
3 Protein ubiquitination and degradation
4 The deubiquitinase activity of Cdu1 stabilizes Mcl-1
5 Structure
6 Relevant Links

How this page was created

The goal of this page is to provide three-dimensional and interactive figures to explore the structure of a protein involved in bacterial infections (PDB code 5B5Q). The starting point are the figures found in the paper describing the 5B5Q structure. Biochemistry students from Westfield State University recreated these figures as best as possible in jmol, and revised them after getting feedback from researchers who authored the primary citation (Kisker lab in Würzburg, Germany). A special thank you goes to Ose Aimua, Nina Aldabayeva, Faiqa Ashraf, Kaleigh Florek, Ellie Hoeg, Aya Maytham, Christian Mikule, Brigid Murray, Kevin Pelletier, Brandon Reder, Erin Riley, Brian Schuler, and Jakob Wyman for the revisions of figures and for working on the links to other proteopedia pages.

If you are interested to see the jmol scripts used to make these figures, take a look at the discussion page (2nd tab above).

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 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

Human cells have a protein assembly called the proteasome, which specializes in degrading proteins. Ubiquitin is a small, highly soluble protein; when ubiquitin chains are attached to other proteins in a certain way, it acts as a signal for protein degradation. The proteasome only degrades proteins that are poly-ubiquitinated, i.e. are covalently linked to a linear chain of ubiquitins. The covalent link is between the amino group of a lysine side chain and the carboxylic acid of a glycine at the C-terminus of ubiquitin.

The deubiquitinase activity of Cdu1 stabilizes Mcl-1

The Chlamydia protein Cdu1 is a protease that catalyzes the hydrolysis of ubiquitin chains from Mcl-1. When polyubiquitinated, Mcl-1 is destined to be degraded by the proteasome, lowering the level of Mcl-1 and subsequently leading to apoptosis. The activity of Cdu1 counteracts this by removing the ubiquitin, thus leading to higher levels of Mcl-1 in the cell.

Structure

1 Fold
2 Related proteins
3 Catalytic triad
4 Superposition with product complex of SENP8
5 Substrate binding site

Fold

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. 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

For comparison, this is panel A.

Structure of the Ulp1 (cyan)-SMT3 (orange) complex (PDB 1EUV). The loop between β-strands 1 and 2 is shown in yellow.

Structure of the SENP8 (gray) – Nedd8 (purple) complex (PDB 1XT9). The loop between β-strands 1 and 2 is shown in yellow. If you want to see Panel B and C at the same time, click on "popup" below the browser to make a pop-up copy, and then click on the other green link to show the second structure in the main viewer window.

Catalytic triad

Before you look at the details of the active site, you probably will want to show the overall view of Cdu1 again: .

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 . Center on .

Superposition with product complex of SENP8

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.

Substrate binding site

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.

Relevant Links

5b5q : autogenerated Proteopedia page on coordinates

Ubiquitin Structure & Function : Proteopedia article on Ubiquitin Structure, function and conjugation

Ubiquitin chains : Proteopedia article on Ubiquitin Chains

Category: Kisker C : list of structures associated with the Kisker lab

Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis

Retrieved from "http://52.214.119.220/wiki/index.php/Kisker_lab:_5B5Q"

@@ Line 34: / Line 34: @@
 <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===
@@ Line 63: / Line 59: @@
+===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>