Kisker lab: 5B5Q

How this page was createdHow 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.

Chlamydia trachomatis inhibits apoptosisChlamydia 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.

Protein ubiquitination and degradationProtein 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-1The 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.

StructureStructure

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. 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 . 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. 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 Cub1 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.

spinqualitylabelsall models Caption for this structure Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Relevant LinksRelevant 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