Subunit–subunit interactions in the human 26S proteasome

Chen, Chuan; Huang, Caoxin; Chen, Shouhui; Liang, Jie; Lin, Weiyi; Ke, Guifen; Wang, Bing; Huang, Jian; Han, Ze‐Guang; Ma, Lixin; Huo, Keke; Yang, Xiaoming; Yang, Pengyuan; He, Fuchu; Tao, Tao

doi:10.1002/pmic.200700588

Cited by 28 publications

(19 citation statements)

References 70 publications

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“…4B) can fulfill these restraints. Thus, our cross-linking data derived from the fully assembled 26S pro- teasome comply with the published protein-protein interaction data, such as Rpt2 binding to α4 (35,36), as well as genetic data suggesting Rpt2-α3 interaction (37), but they do conflict with the interactions reported for the synthetic C-terminal Rpt peptides (e.g., Rpt5-α3 and Rpt5-α4) (33,34). This discrepancy might be explained by different binding specificities of the full-length proteins as compared to the short C-terminal peptides.…”

Section: Resultssupporting

confidence: 83%

Structure of the 26S proteasome from Schizosaccharomyces pombe at subnanometer resolution

Bohn

Beck

Sakata

et al. 2010

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

130

158

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The structure of the 26S proteasome from Schizosaccharomyces pombe has been determined to a resolution of 9.1 Å by cryoelectron microscopy and single particle analysis. In addition, chemical cross-linking in conjunction with mass spectrometry has been used to identify numerous residue pairs in close proximity to each other, providing an array of spatial restraints. Taken together these data clarify the topology of the AAA-ATPase module in the 19S regulatory particle and its spatial relationship to the α-ring of the 20S core particle. Image classification and variance analysis reveal a belt of high "activity" surrounding the AAA-ATPase module which is tentatively assigned to the reversible association of proteasome interacting proteins and the conformational heterogeneity among the particles. An integrated model is presented which sheds light on the early steps of protein degradation by the 26S complex.deubiquitylating enzymes | macromolecular complex | ubiquitinproteasome pathway | ubiquitin receptor | single particle classification I n eukaryotic cells, most proteins in the cytosol and the nucleus are regulated via the ubiquitin-proteasome pathway and malfunctions of this pathway have been implicated in a wide variety of diseases (1). The 26S proteasome is the most downstream element of this pathway, executing protein degradation (2-4). Unlike constitutively active proteases, the proteasome has the capacity to degrade almost any protein, yet it acts with exquisite specificity. The key stratagem is self-compartmentalization: The active sites of the proteolytic 20S core particles (CPs) are sequestered from the cellular environment in the interior of this barrelshaped subcomplex (5). Proteins destined for degradation are marked by a polyubiquitin chain, a degradation signal that is recognized by the 19S regulatory particles (RPs) that bind to either one or both ends of the CP to form the 26S holocomplex. The RPs (i) recognize the polyubiquitylated substrates, (ii) trim and recycle the polyubiquitin chains, (iii) unfold substrates to be degraded, and (iv) open the gate to the CP and assist in substrate translocation into the interior of the CP. These tasks are performed by a complex machinery involving at least 19 different subunits, 6 AAA-ATPases (Rpt1-6), and 13 non-ATPases (Rpn1-3, Rpn5-13, Rpn15/Sem1p).Although the structure of the CP has been elucidated in great detail by X-ray crystallography (6, 7), the structure of the RP is only dimly understood at present. Best characterized are the AAA-ATPases which form a heterohexameric subcomplex situated at the base of the RP in close proximity to the α-rings of the CP (8, 9). The C-terminal residues of Rpt2 and Rpt5 were shown to be involved in opening the gate in the α-rings, allowing substrates to enter the CP. A similar mechanism has been postulated for proteasome-activating nucleotidase (PAN), the archaeal homohexameric homolog of the eukaryotic AAA-ATPase module (10). Crystal structures of the two major fragments of PAN suggest that the N-and C-terminal domains...

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Section: Resultssupporting

confidence: 83%

Structure of the 26S proteasome from Schizosaccharomyces pombe at subnanometer resolution

Bohn

Beck

Sakata

et al. 2010

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

130

158

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“…Rpt3 and Rpt6 are nearest neighbors in the base complex, 11 and the Rpt3-Rpt6 association has been observed before. 23,[29][30][31][32][33] The following interactions have also been found: Rpn13 with Rpn2, 12,[34][35][36] Rpn2 with Rpn10, 37 Rpn11 with Rpn10, 38 Txnl1 with Rpn11, 13 and Txnl1 with Rpn2. 16 Isono et al found an intact lid complex in yeast cells.…”

Section: Discussionmentioning

confidence: 77%

The 20S Proteasome as an Assembly Platform for the 19S Regulatory Complex

Hendil

Kriegenburg

Tanaka

et al. 2009

Journal of Molecular Biology

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“…To obtain a most accurate model, it will be important to remove erroneous protein-protein interaction data. For example, recent in vitro redesign of the CP-AAA-ATPase interface suggests that Rpt5 binds to the ␣ 3 /␣ 4 CP pocket (86), whereas the data underlying our CP-AAA-ATPase model suggest that Rpt2 binds to ␣ 4 (87,88), and genetic data indicate interaction of Rpt2 with ␣ 3 (89). Thus, taking into account the data from Yu et al (86), two conflicting models are possible where either Rpt2 or Rpt5 interact with the ␣ 3 /␣ 4 CP pocket.…”

Section: Integrative Structure Determination Of the Rpmentioning

confidence: 88%

Toward an Integrated Structural Model of the 26S Proteasome

Förster

Lasker

Nickell

et al. 2010

Molecular & Cellular Proteomics

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The 26S proteasome is the end point of the ubiquitinproteasome pathway and degrades ubiquitylated substrates. It is composed of the 20S core particle (CP), where degradation occurs, and the 19S regulatory particle (RP), which ensures substrate specificity of degradation. Whereas the CP is resolved to atomic resolution, the architecture of the RP is largely unknown. We provide a comprehensive analysis of the current structural knowledge on the RP, including structures of the RP subunits, physical protein-protein interactions, and cryoelectron microscopy data. These data allowed us to compute an atomic model for the CP-AAA-ATPase subcomplex. In addition to this atomic model, further subunits can be mapped approximately, which lets us hypothesize on the substrate path during its degradation. Molecular & Cellular Proteomics 9:1666 -1677, 2010.The ubiquitin-proteasome pathway is the major route used by eukaryotic cells for the disposal of misfolded or damaged proteins and for controlling the lifespan of proteins (1-3). As a consequence, the ubiquitin-proteasome pathway regulates a plethora of fundamental cellular processes, such as protein quality control, DNA repair, and signal transduction (4). The 26S proteasome is a molecular machine of ϳ2.5 MDa that targets polyubiquitylated proteins. It comprises two subcomplexes, the 20S core particle (CP) 1 and one or two copies of asymmetric 19S regulatory particles (RPs), which bind to the end(s) of the barrel-shaped CP.The active sites of the proteasome are located in the CP cavity where proteolytic cleavage of substrates takes place. Electron microscopy (EM) and x-ray crystallography have revealed that the CP is a cylinder consisting of four concentrically stacked rings (5-7): two identical "␣"-rings, each assembled of seven homologous proteins, form the outer rings, and two identical "␤"-rings, also assembled of seven homologs, form the two inner rings. Proteolysis is confined to the cavity formed by the ␤-rings, a nanocompartment sequestered from the cytosol.The RPs regulate substrate degradation by (i) binding polyubiquitylated substrates, (ii) subsequently deubiquitylating them, (iii) substrate unfolding, and (iv) opening the "gate" to the CP (8). The RPs consists of six AAA-ATPase subunits and at least 13 non-ATPase subunits. In contrast to the CP, the architecture of the RP subunits remains largely unknown. The problems that hamper structural characterization of the RP are manifold. It has proven difficult to obtain homogeneous, concentrated preparations of 26S proteasomes or RPs because the RP tends to disassociate into heterogeneous subcomplexes during purification and concentration. Moreover, many of the RP subunits likely exhibit a significant degree of structural variability. As a consequence, x-ray crystallographic analysis of the entire RP has not been accomplished to date, and only a few subunit fragments have been amenable to high resolution structure determination.For cryo-EM and protein-protein interaction experiments, the requirements for sample homogene...

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Subunit–subunit interactions in the human 26S proteasome

Cited by 28 publications

References 70 publications

Structure of the 26S proteasome from Schizosaccharomyces pombe at subnanometer resolution

Structure of the 26S proteasome from Schizosaccharomyces pombe at subnanometer resolution

The 20S Proteasome as an Assembly Platform for the 19S Regulatory Complex

Toward an Integrated Structural Model of the 26S Proteasome

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