The ubiquitin proteasome system (UPS) controls protein concentrations in eukaryotic cells by setting protein degradation rates. Proteins are targeted to the proteasome by covalently attached ubiquitin tags; the proteasome recognizes these tags, unfolds the protein and translocates it in an ATP-dependent process into a proteolytic chamber, where it is hydrolysed into small peptides.
The 26S proteasome consists of ∼33 different subunits that form a cylindrical particle of a molecular weight of ∼2.5 MDa. In the past 2 years, the structure of the entire proteasome has been revealed at near-atomic resolution in a series of breakthrough studies.
The structures show that the biochemical activities of the proteasome are arranged in the order in which they act on a substrate: the two ubiquitin receptors are located near to the ends of the particle, followed by a protease that cleaves the ubiquitin tag from substrates, the ATPase motor that translocates substrates into the proteasome and finally the proteolytic sites in a chamber at the centre of the particle.
The arrangement of ubiquitin receptors, substrate channel and ATPase motor in the proteasome seems to form a versatile platform that allows substrates to be recognized in multiple ways and to be fed into the degradation machinery.
Proteasome structures in the presence and absence of substrate and ATP analogues show that the proteasome adopts distinct conformations under the different conditions, and the structures give insights into how it might be allosterically regulated. The binding of a substrate or ATP analogue switches the proteasome from a presumably inactive structure, in which parts of the substrate translocation channel are misaligned, into an active structure with an unobstructed channel.
Substrate binding affects the structure of the ATPase ring that forms the translocation motor of the proteasome and switches it from a spiral to a more planar ring. The rearrangements might represent resting and active states of the proteasome and suggest several models by which changes of the ATPase subunits could move substrate through the translocation channel.
The ubiquitin proteasome system (UPS) is the main ATP-dependent protein degradation pathway in the cytosol and nucleus of eukaryotic cells. At its centre is the 26S proteasome, which degrades regulatory proteins and misfolded or damaged proteins. In a major breakthrough, several groups have determined high-resolution structures of the entire 26S proteasome particle in different nucleotide conditions and with and without substrate using cryo-electron microscopy combined with other techniques. These structures provide some surprising insights into the functional mechanism of the proteasome and will give invaluable guidance for genetic and biochemical studies of this key regulatory system.
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The authors would like to thank A. Martin and M. Matyskiela for providing segmented electron density maps of their proteasome structures, and members of the Matouschek laboratory, especially J. Renn for critically reading this manuscript. Work in the authors' laboratory is supported by the Gates Foundation, the Welch Foundation and US National Institutes of Health grants R01 GM63004, R01 GM094479, U54 GM105816 and U54 CA143869.
The authors declare no competing financial interests.
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Bhattacharyya, S., Yu, H., Mim, C. et al. Regulated protein turnover: snapshots of the proteasome in action. Nat Rev Mol Cell Biol 15, 122–133 (2014). https://doi.org/10.1038/nrm3741
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