A Tetrahedral Transition State at the Active Sites of the 20S Proteasome Is Coupled to Opening of the α-Ring Channel (original) (raw)
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Atomic Force Microscopy Reveals Two Conformations of the 20 S Proteasome from Fission Yeast
Journal of Biological Chemistry, 2000
The proteasome is a major cytosolic proteolytic complex, indispensable in eukaryotic cells. The barrelshaped core of this enzyme, the 20 S proteasome, is built from 28 subunits forming four stacked rings. The two inner -rings harbor active centers, whereas the two outer ␣-rings play a structural role. Crystal structure of the yeast 20 S particle showed that the entrance to the central channel was sealed. Because of this result, the path of substrates into the catalytic chamber has remained enigmatic. We have used tapping mode atomic force microscopy (AFM) in liquid to address the dynamic aspects of the 20 S proteasomes from fission yeast. We present here evidence that, when observed with AFM, the proteasome particles in top view position have either open or closed entrance to the central channel. The preferred conformation depends on the ligands present. Apparently, the addition of a substrate to the uninhibited proteasome shifts the equilibrium toward the open conformation. These results shed new light on the possible path of the substrate into the proteolytic chamber.
Biochemistry, 2002
The proteasome is a major cytosolic proteolytic assembly, essential for the physiology of eukaryotic cells. Both the architecture and enzymatic properties of the 20S proteasome are relatively well understood. However, despite longstanding interest, the integration of structural and functional properties of the proteasome into a coherent model explaining the mechanism of its enzymatic actions has been difficult. Recently, we used tapping mode atomic force microscopy (AFM) in liquid to demonstrate that the R-rings of the proteasome imaged in a top-view position repeatedly switched between their open and closed conformations, apparently to control access to the central channel. Here, we show with AFM that the molecules in a side-view position acquired two stable conformations. The overall shapes of the 20S particles were classified as either barrel-like or cylinder-like. The relative abundance of the two conformers depended on the nature of their interactions with ligands. Similarly to the closed molecules in top view, the barrels predominated in control or inhibited molecules. The cylinders and open molecules prevailed when the proteasome was observed in the presence of peptide substrates. Based on these data, we developed the two-state model of allosteric transitions to explain the dynamics of proteasomal structure. This model helps to better understand the observed properties of the 20S molecule, and sets foundations for further studies of the structural dynamics of the proteasome.
Near-atomic resolution structural model of the yeast 26S proteasome
Proceedings of the National Academy of Sciences, 2012
The 26S proteasome operates at the executive end of the ubiquitinproteasome pathway. Here, we present a cryo-EM structure of the Saccharomyces cerevisiae 26S proteasome at a resolution of 7.4 Å or 6.7 Å (Fourier-Shell Correlation of 0.5 or 0.3, respectively). We used this map in conjunction with molecular dynamics-based flexible fitting to build a near-atomic resolution model of the holocomplex. The quality of the map allowed us to assign α-helices, the predominant secondary structure element of the regulatory particle subunits, throughout the entire map. We were able to determine the architecture of the Rpn8/Rpn11 heterodimer, which had hitherto remained elusive. The MPN domain of Rpn11 is positioned directly above the AAA-ATPase N-ring suggesting that Rpn11 deubiquitylates substrates immediately following commitment and prior to their unfolding by the AAA-ATPase module. The MPN domain of Rpn11 dimerizes with that of Rpn8 and the C-termini of both subunits form long helices, which are integral parts of a coiled-coil module. Together with the C-terminal helices of the six PCI-domain subunits they form a very large coiled-coil bundle, which appears to serve as a flexible anchoring device for all the lid subunits.
Atomic force microscopy of the proteasome
Methods in enzymology, 2005
The proteasome should be an ideal molecule for studies on large enzymatic complexes, given its multisubunit and modular structure, compartmentalized design, numerous activities, and its own means of regulation. Considering the recent increased interest in the ubiquitin-proteasome pathway, it is surprising that biophysical approaches to study this enzymatic assembly are applied with limited frequency. Methods including atomic force microscopy, fluorescence spectroscopy, surface plasmon resonance, and high-pressure procedures all have gained popularity in characterization of the proteasome. These methods provide significant and often unexpected insight regarding the structure and function of the enzyme. This chapter describes the use of atomic force microscopy for dynamic structural studies of the proteasome.
Conformational constraints for protein self-cleavage in the proteasome
Journal of Molecular Biology, 1998
The proteasome is the central enzyme of protein degradation in the cytosol and the nucleus. It is involved in the removal of abnormal, misfolded or incorrectly assembled proteins, in the processing or degradation of transcriptional regulators in stress response, in degradation of cyclins in cell-cycle control, in the destruction of transcription factors or metabolic enzymes in cell differentiation and metabolic response, and in MHC class I mediated cellular immune response. By the analysis of the crystal and molecular structures of the 20 S proteasomes from the archaeon Thermoplasma acidophilum and from yeast it was shown that the b-type subunits in which the proteolytic activities reside are members of the N-terminal nucleophile (Ntn) protein family. They are synthesized as proproteins and become active by autoprocessing at a Gly À 1 ±Thr1 bond.
Conformational constraints for protein self-cleavage in the proteasome1
Journal of Molecular Biology, 1998
The proteasome is the central enzyme of protein degradation in the cytosol and the nucleus. It is involved in the removal of abnormal, misfolded or incorrectly assembled proteins, in the processing or degradation of transcriptional regulators in stress response, in degradation of cyclins in cell-cycle control, in the destruction of transcription factors or metabolic enzymes in cell differentiation and metabolic response, and in MHC class I mediated cellular immune response. By the analysis of the crystal and molecular structures of the 20 S proteasomes from the archaeon Thermoplasma acidophilum and from yeast it was shown that the b-type subunits in which the proteolytic activities reside are members of the N-terminal nucleophile (Ntn) protein family. They are synthesized as proproteins and become active by autoprocessing at a Gly À 1 ±Thr1 bond.
Atomic force microscopy as a tool to study the proteasome assemblies
Methods in cell biology, 2008
Proteasome is an exceptional enzyme because of its essential physiological role, multiple activities, and structural complexity. It is, in fact, a family of enzymes sharing a common catalytic core and equipped with distinct protein attachments regulating the core and adding to its new functional capabilities. As a drug target and a major regulator of cellular processes, proteasome is extensively studied with tools of structural, biochemical, and molecular biology. Atomic force microscopy (AFM) besides X-ray crystallography and electron microscopy is one of the most attractive methods to study proteasome. The noninvasive nature of this method is particularly well suited for investigating the structure-function relationship within the core particle (CP) as well as in higher-order assemblies. Here we review, from the methodological point of view, AFM-based studies on the proteasome. First, we will present the application of height distribution analysis of proteasome complexes to dissec...
Mechanism of Gate Opening in the 20S Proteasome by the Proteasomal ATPases
Molecular Cell, 2008
Substrates enter the cylindrical 20S proteasome through a gated channel that is regulated by the ATPases in the 19S regulatory particle in eukaryotes or the homologous PAN ATPase complex in archaea. These ATPases contain a conserved C-terminal hydrophobic-tyrosine-X (HbYX) motif that triggers gate opening upon ATP binding. Using cryo-electron microscopy, we identified the sites in the archaeal 20S where PAN's C-terminal residues bind and determined the structures of the gate in its closed and open forms. Peptides containing the HbYX motif bind to 20S in the pockets between neighboring a subunits where they interact with conserved residues required for gate opening. This interaction induces a rotation in the a subunits and displacement of a reverse-turn loop that stabilizes the open-gate conformation. This mechanism differs from that of PA26/28, which lacks the HbYX motif and does not cause a subunit rotation. These findings demonstrated how the ATPases' C termini function to facilitate substrate entry.
Proteasome Channel Opening as a Rate-Limiting Step in the Ubiquitin-Proteasome System
Israel Journal of Chemistry, 2006
The 26S proteasome eliminates multiubiquitinated proteins in cytosol and nucleus, and from the secretory pathway by a mechanism known as ER-associ-ated degradation (ERAD). Access to the proteasomal 20S catalytic core particle is hindered by conserved N-terminal tails of α-subunits that form a gated pore into the central channel. Hence, the isolated 20S core particle possesses slower peptide hydrolysis rates and cannot degrade multiubiquitinated proteins. Purified catalytic particles from an α3α7dN open channel double mutant, in which the N-terminal tails of α-subunits from opposite sites of the α ring are deleted, showed significantly enhanced peptidase activity and proteolytic properties. Here we show that also in vivo the access of substrates to the proteasomal catalytic chamber partially limits the overall rate of protein elimination. This regulation applies to unstable cytosolic proteins of the N-end rule and ubiquitin fusion degradation (UFD) pathways, as well as to ERAD substrates that must dislocate from the ER back to the cytosol in order to become ubiquitinated and degraded by the proteasome. Hence, even for a complicated multistep process such as ERAD, traffic through the proteasome itself is partially rate limiting for the entire proteolytic process. However, proteasome gating can be added to a growing list of phenomena that distinguish membrane ERAD substrates from lumenal ones because while gating hinders access of lumenal substrates, it is less effective in controlling the entry of membrane substrates. The open channel mutant is a new class of proteasome mutant, which is unrelated to the catalytic protease active sites or to the "classical" regulatory particle mutants. Its improved performance at high temperatures is in stark contrast to the behavior of the "classical" mutants, suggesting that the α3α7dN mutant adapts better to mild stress conditions.