Kisker lab: 5B5Q
How this page was createdHow this page was created
The goal of this page is to make the figures found in the primary citation of the 5B5Q structure three-dimensional and interactive. The figures are closely modeled on Figure 2 panels A-E of the paper. Biochemistry students from Westfield State University have made drafts of the figures, and will revise them after getting feedback from the researchers working on this protein.
Chlamydia inhibits apoptosisChlamydia inhibits apoptosis
Chlamydia 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 that is attached to other proteins as a signal. 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 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
FoldThe 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 proteinsFor 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 triadBefore 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 . 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. A all-atom view of the (catalytic triad in yellow, blue, red for Cys, His, Asp, respectively, with hydrophobic side chains in black) shows how inaccessible the active site cysteine is. Same as . 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.
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