Near-atomic resolution structural model of the yeast 26S proteasome

Beck, Florian; Unverdorben, Pia; Bohn, Stefan; Schweitzer, A.; Pfeifer, Günter; Sakata, Eri; Nickell, Stephan; Plitzko, Jürgen M.; Villa, Elizabeth; Baumeister, Wolfgang; Förster, Friedrich

doi:10.1073/pnas.1213333109

Cited by 243 publications

(347 citation statements)

References 49 publications

(75 reference statements)

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“…POH1 is adjacent to the ubiquitin receptor Adrm1/Rpn13 and positioned directly above the AAA-ATPase N-ring (16). The activity of POH1 is enigmatic.…”

Section: A Proteasomal Dubsmentioning

confidence: 99%

“…Although crystal structures of proteasomal complexes are unavailable, sub-nanometer resolution structures derived from electron microscopy single-particle analyses provide information on the organization of constituent proteins (16,53,137,141). POH1 is adjacent to the ubiquitin receptor Adrm1/Rpn13 and positioned directly above the AAA-ATPase N-ring (16).…”

Section: A Proteasomal Dubsmentioning

confidence: 99%

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Deubiquitylases From Genes to Organism

Clague

Barsukov

Coulson

et al. 2013

Physiological Reviews

359

384

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Ubiquitylation is a major posttranslational modification that controls most complex aspects of cell physiology. It is reversed through the action of a large family of deubiquitylating enzymes (DUBs) that are emerging as attractive therapeutic targets for a number of disease conditions. Here, we provide a comprehensive analysis of the complement of human DUBs, indicating structural motifs, typical cellular copy numbers, and tissue expression profiles. We discuss the means by which specificity is achieved and how DUB activity may be regulated. Generically DUB catalytic activity may be used to 1) maintain free ubiquitin levels, 2) rescue proteins from ubiquitin-mediated degradation, and 3) control the dynamics of ubiquitin-mediated signaling events. Functional roles of individual DUBs from each of five subfamilies in specific cellular processes are highlighted with an emphasis on those linked to pathological conditions where the association is supported by whole organism models. We then specifically consider the role of DUBs associated with protein degradative machineries and the influence of specific DUBs upon expression of receptors and channels at the plasma membrane.

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“…POH1 is adjacent to the ubiquitin receptor Adrm1/Rpn13 and positioned directly above the AAA-ATPase N-ring (16). The activity of POH1 is enigmatic.…”

Section: A Proteasomal Dubsmentioning

confidence: 99%

Section: A Proteasomal Dubsmentioning

confidence: 99%

Deubiquitylases From Genes to Organism

Clague

Barsukov

Coulson

et al. 2013

Physiological Reviews

359

384

View full text Add to dashboard Cite

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“…Previous analysis revealed that the conformational states of the RPs at the two CP ends are not correlated (6,13,15). Therefore, the following analysis was performed using the holocomplex cut into two halves (6, 13), i.e., the two RPs of the double-capped 26S proteasomes were treated as separate particles.…”

Section: Dmentioning

confidence: 99%

“…At least three distinct states, which we refer to as "s1-s3," can be distinguished (13). In ATP-containing buffer, purified 26S proteasomes primarily adopt the s1 state, which is characterized by pronounced off-axis positioning of the AAAATPase hexamer with respect to the CP and a staircase arrangement of the Rpts with Rpt3 in the most elevated position (6)(7)(8)(9). Under the same conditions a minority of particles (∼20%) adopts the s2 state, in which the axis of the AAA-ATPase is positioned closer to that of the CP and the Rpns concomitantly rotate largely en bloc by ∼25° (13).…”

mentioning

confidence: 99%

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Structural characterization of the interaction of Ubp6 with the 26S proteasome

Aufderheide

Beck

Stengel

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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135

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In eukaryotic cells, the 26S proteasome is responsible for the regulated degradation of intracellular proteins. Several cofactors interact transiently with this large macromolecular machine and modulate its function. The deubiquitylating enzyme ubiquitin C-terminal hydrolase 6 [Ubp6; ubiquitin-specific protease (USP) 14 in mammals] is the most abundant proteasome-interacting protein and has multiple roles in regulating proteasome function. Here, we investigate the structural basis of the interaction between Ubp6 and the 26S proteasome in the presence and absence of the inhibitor ubiquitin aldehyde. To this end we have used single-particle electron cryomicroscopy in combination with cross-linking and mass spectrometry. Ubp6 binds to the regulatory particle non-ATPase (Rpn) 1 via its N-terminal ubiquitin-like domain, whereas its catalytic USP domain is positioned variably. Addition of ubiquitin aldehyde stabilizes the binding of the USP domain in a position where it bridges the proteasome subunits Rpn1 and the regulatory particle triple-A ATPase (Rpt) 1. The USP domain binds to Rpt1 in the immediate vicinity of the Ubp6 active site, which may effect its activation. The catalytic triad is positioned in proximity to the mouth of the ATPase module and to the deubiquitylating enzyme Rpn11, strongly implying their functional linkage. On the proteasome side, binding of Ubp6 favors conformational switching of the 26S proteasome into an intermediateenergy conformational state, in particular upon the addition of ubiquitin aldehyde. This modulation of the conformational space of the 26S proteasome by Ubp6 explains the effects of Ubp6 on the kinetics of proteasomal degradation.conformational switching | proteolysis | proteostasis | quality control D egradation of proteins that are misfolded, damaged, or no longer needed is an essential element of cellular homeostasis. In eukaryotic cells, the ubiquitin-proteasome system (UPS) is the major pathway for regulated protein degradation (1). Proteins that are processed by the UPS are marked for destruction by polyubiquitin chains, which are recognized as a degradation signal by the 26S proteasome.The 26S proteasome consists of the core particle (CP), which degrades substrates into short peptides, and one or two 19S regulatory particles (RP), which associate with the ends of the cylinder-shaped CP to recruit substrates and prepare them for degradation (2, 3). Although the structure of the CP has been known for more than two decades (4, 5), the molecular architecture of the RP was unraveled by cryo-electron microscope (EM)-based approaches only recently (6-9). It comprises six RP triple A (AAA) ATPases (Rpt), 1-6, and 13 RP non-ATPases (Rpn), 1-3, 5-13, and 15. Similar to AAA-ATPases in prokaryotic ATP-dependent proteases, the Rpts form a hexameric ring that binds to the ends of the CP and is responsible for substrate unfolding and translocation into the CP. Unlike their prokaryotic counterparts, the Rpts are surrounded by non-ATPases. Apart from Rpn1, all Rpns form a cohesive struct...

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Mechanisms of cell regulation – proteolysis, the big surprise

Wolf

Menssen

2018

FEBS Letters

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Precise regulation of cellular processes is essential for life. Regarding proteins, many regulatory mechanisms were explored over the years, such as posttranslational modifications (e.g., phosphorylation), enzyme activation or inhibition by small molecules, and modulation of protein-protein interactions. Complete removal of a protein via proteolysis as a regulatory mechanism, however, was denied for a long time, mainly due to economical considerations. Scientists could not believe that a protein which is synthesized at the expense of a lot of energy could be destroyed again. Here, we discuss the landmark discoveries and the use of yeast as a eukaryotic model organism that finally paved the way for our current understanding of proteolysis as an essential regulatory principle in the cell.

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Near-atomic resolution structural model of the yeast 26S proteasome

Cited by 243 publications

References 49 publications

Deubiquitylases From Genes to Organism

Deubiquitylases From Genes to Organism

Structural characterization of the interaction of Ubp6 with the 26S proteasome

Mechanisms of cell regulation – proteolysis, the big surprise

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