Proteasome
Protein complexes that degrade proteins via ubiquitin tagging.
Proteasomes are large protein complexes that break down other proteins through a process called proteolysis, which involves the chemical splitting of peptide bonds. The enzymes that carry out this reaction are known as proteases. These complexes are present in all eukaryotes and archaea, as well as in certain bacteria. Within eukaryotic cells, proteasomes can be found in both the nucleus and the cytoplasm. This degradation pathway is crucial for numerous cellular functions, such as controlling the cell cycle, regulating gene expression, and managing oxidative stress.
The core of the proteasome, known as the 20S particle, has a cylindrical shape made of four stacked rings that create a central channel. Each ring consists of seven individual protein subunits. The two inner rings are formed from seven β subunits, which contain between three and seven active sites for proteolysis, all located inside the central chamber. Access to these active sites is controlled by gates at the top of the 20S particle, and this access is regulated by several large protein complexes, including the 19S Regulatory Particle. Together, the 20S core and the 19S particle form the 26S proteasome. In eukaryotes, proteins marked with a small tag called ubiquitin are directed to the 26S proteasome for destruction, which is the final step in the ubiquitin-proteasome system (UPS). This system is a major way cells control the levels of specific proteins and eliminate misfolded ones.
For a protein to be degraded by the 26S proteasome, two key features are required: first, the attachment of ubiquitin, and second, an unstructured region of about 25 amino acids. If a protein lacks this unstructured region, another motor protein—Cdc48 in yeast or p97 in humans—can create it by unfolding the ubiquitin tag with the help of cofactors Npl4 and Ufd1. The process of attaching ubiquitin to a target protein involves a cascade of three enzymes: a ubiquitin-activating enzyme (E1), a ubiquitin-conjugating enzyme (E2), and a ubiquitin ligase (E3). Once a single ubiquitin is attached, other ligases add more ubiquitin molecules, forming a polyubiquitin chain. This chain is recognized by the proteasome, which then degrades the tagged protein in a process that requires ATP. The degradation itself produces peptides roughly seven to eight amino acids long, which can later be broken down further into shorter sequences and reused to build new proteins.
**Discovery**
Before the ubiquitin-proteasome system was identified, scientists believed that cells mainly relied on lysosomes—membrane-bound compartments filled with acidic proteases—to degrade proteins, particularly those from outside the cell or damaged organelles. However, in 1977, Joseph Etlinger and Alfred L. Goldberg observed ATP-dependent protein degradation in reticulocytes, which lack lysosomes, hinting at another degradation mechanism. The following year, this mechanism was shown to consist of several distinct protein chains, which was unusual for proteases at the time. Later research on histone modification revealed an unexpected covalent bond between a lysine side chain of histone and the C-terminal glycine of ubiquitin, a protein with no known function at that point. It was then discovered that a previously identified factor involved in proteolysis, called ATP-dependent proteolysis factor 1 (APF-1), was actually the same as ubiquitin. The proteolytic activities of this system were isolated as a multi-protein complex, originally named the multi-catalytic proteinase complex by Sherwin Wilk and Marion Orlowski. Later, the ATP-dependent complex responsible for ubiquitin-tagged protein degradation was identified and named the 26S proteasome.
Much of the foundational work on the ubiquitin-proteasome system took place in the late 1970s and early 1980s at the Technion, in Avram Hershko’s laboratory, where Aaron Ciechanover was a graduate student. A year-long sabbatical by Hershko in Irwin Rose’s lab at the Fox Chase Cancer Center provided key conceptual advances, though Rose later minimized his own role. The three researchers shared the 2004 Nobel Prize in Chemistry for their discovery. While electron microscopy data revealing the stacked-ring structure of the proteasome appeared in the mid-1980s, the first X-ray crystallography structure of the core particle was not solved until 1994. Wolfgang Baumeister’s group later used cryo-electron microscopy to reveal the overall architecture of the 26S proteasome, which enabled biochemical experiments to outline a general mechanism for ubiquitin-dependent degradation. In 2018, the first structure of the yeast 26S proteasome was solved, followed by the first atomic structures of the human 26S proteasome holoenzyme bound to a polyubiquitylated substrate. These structures confirmed the steps of substrate recognition, deubiquitylation, unfolding, and degradation. Detailed biochemistry has since provided a general mechanism: the substrate binds to the proteasome, an unstructured region engages the AAA motor, triggering a major conformational change, followed by deubiquitylation by Rpn11 during translocation, and finally unfolding and proteolysis by the 20S core. Cryo-electron tomography has also offered unique views of proteasomes inside cells, showing that in neurons, proteasomes exist in the same ground state and process.
- type
- Protein complex
- location
- Eukaryotes, archaea, some bacteria
- subunits
- 20S core (four stacked rings of seven subunits each), 19S regulatory particle, 26S proteasome
- function
- Degradation of proteins by proteolysis
Lore & Background
Before the discovery of the ubiquitin–proteasome system, protein degradation in cells was thought to rely mainly on lysosomes. However, work by Joseph Etlinger and Alfred L. Later work on modification of histones led to the identification of an unexpected covalent modification of the histone protein by ubiquitin, a protein that had no known function. It was then discovered that a previously identified protein associated with proteolytic degradation, known as ATP-dependent proteolysis factor 1 (APF-1), was the same protein as ubiquitin. The proteolytic activities of this system were isolated as a multi-protein complex originally called the multi-catalytic proteinase complex by Sherwin Wilk and Marion Orlowski. Later, the ATP-dependent proteolytic complex responsible for ubiquitin-dependent protein degradation was discovered and called the 26S proteasome.
Reader's Guide
Proteasomes are part of a major mechanism by which cells regulate the concentration of particular proteins and degrade misfolded proteins. The core 20S proteasome is a cylindrical, compartmental protein complex of four stacked rings forming a central pore. Access to its protease active sites is gated and regulated by several large protein complexes, including the 19S Regulatory Particle forming the 26S Proteasome. In eukaryotes, proteins tagged with ubiquitin are targeted to the 26S proteasome, which is the penultimate step of the Ubiquitin Proteasome System (UPS). The degradation process yields peptides of about seven to eight amino acids long, which can then be further degraded into shorter amino acid sequences and used in synthesizing new proteins. Cryo-electron tomography has provided unique insight into proteasomes within cells, showing that in neurons most proteasomes are in a ground state ready to start working when a cell undergoes proteotoxic stress.
Did You Know?
- Proteasomes are found inside all eukaryotes and archaea, and in some bacteria.
- The 20S core particle consists of four stacked heptameric ring structures, with outer rings of α subunits and inner rings of β subunits containing protease active sites.
- The tagging of a target protein by ubiquitin is catalyzed by a cascade of enzymes: Ubiquitin-activating enzyme (E1), Ubiquitin-conjugating enzyme (E2), and ubiquitin ligases (E3).
- Cryo-ET of green algae Chlamydomonas reinhardtii found that 26S proteasomes within the nucleus cluster around the Nuclear pore complex and are specifically attached to the membrane.
Architecture and Catalytic Core
The proteasome is a cylindrical, compartmentalized protein complex built from four stacked rings that enclose a central pore. Each ring is assembled from seven individual subunits, and the two innermost rings are composed of β subunits bearing between three and seven protease active sites within the central chamber. This inner 20S core is the catalytic heart of the machine, yet direct access to its active sites is restricted by a gating mechanism at the top of the complex. In eukaryotic cells, this gating is controlled by large protein assemblies, most notably the 19S Regulatory Particle, which together with the 20S core forms the 26S proteasome. These complexes are not confined to a single cellular compartment; they reside in both the nucleus and the cytoplasm. Beyond eukaryotes, proteasomes are also present in archaea and certain bacterial species, underscoring their ancient evolutionary origin. The overall architecture—stacked rings, a sealed central chamber, and regulated entry—reflects a design optimized for controlled proteolysis rather than indiscriminate protein destruction.
The Ubiquitin Tagging Cascade
For a protein to be recognized and destroyed by the 26S proteasome, it must first receive a molecular tag. This tagging is carried out by a three-enzyme cascade: an ubiquitin-activating enzyme (E1) primes the process, an ubiquitin-conjugating enzyme (E2) transfers the small ubiquitin molecule, and a family of ubiquitin ligases (E3) recognize the specific substrate and catalyze the final attachment. A single ubiquitin molecule attached to a target protein serves as a signal that prompts additional ligases to append more ubiquitin molecules, ultimately generating a polyubiquitin chain. The proteasome binds this chain and, in an ATP-dependent manner, unfolds and degrades the tagged protein. In addition to the ubiquitin tag, the substrate generally requires an unstructured region of roughly twenty-five amino acids; when this region is absent, motor proteins such as cdc48 in yeast or P97 in humans, working with cofactors Npl4 and Ufd1, can forcibly generate the necessary disorder by unfolding ubiquitin itself. The end products of proteolysis are peptides approximately seven to eight residues long, which can be further broken down and recycled into new proteins.
From Lysosome Dogma to Nobel Recognition
For decades, the prevailing view held that lysosomes were the primary intracellular site of protein breakdown. Goldberg demonstrated ATP-dependent protein degradation in reticulocytes—cells that lack lysosomes entirely—pointing to a second, previously unrecognized degradation pathway. A pivotal clue emerged from studies of histone modification, revealing that a then-functionless protein called ubiquitin was covalently attached to histones via a bond between a lysine side chain and ubiquitin's C-terminal glycine. It was subsequently established that ubiquitin was identical to ATP-dependent proteolysis factor 1 (APF-1), linking it directly to proteolytic activity. Much of the foundational work was carried out in the late 1970s and early 1980s in Avram Hershko's laboratory at the Technion, where Aaron Ciechanover was a graduate student. Hershko's sabbatical with Irwin Rose at Fox Chase Cancer Center contributed key conceptual insights.
Structural Milestones and In Vivo Behavior
Wolfgang Baumeister's group then made groundbreaking advances with cryo-electron microscopy, revealing the overall architecture of the 26S proteasome and enabling biochemical studies that clarified the general mechanism of ubiquitin-dependent degradation. More recently, cryo-electron tomography has offered a glimpse of proteasomes in their native cellular context. In neurons, most proteasomes were observed in a ground state, poised to respond when proteotoxic stress strikes. In other experiments, proteasomes were captured stalled on overexpressed poly-Gly-Ala aggregates. In the green alga Chlamydomonas reinhardtii, 26S proteasomes within the nucleus were found clustering around the nuclear pore complex.
Frequently Asked Questions
What is Proteasome?
Proteasome is a large multi-subunit protein complex that serves as the cell's primary protein-recycling machine. It is found in all eukaryotes and archaea, as well as in certain bacterial species.
What does Proteasome actually do?
Proteasome destroys proteins that have been flagged with ubiquitin tags by severing their peptide bonds in a process called proteolysis. This degradation pathway is essential for driving the cell cycle, tuning gene expression, and helping cells manage oxidative stress.
What is Proteasome's structure?
The core of the proteasome is a 20S barrel composed of four stacked rings, each ring holding seven subunits. One or two 19S regulatory particles cap the ends, and together the assembly is called the 26S proteasome.
Why is Proteasome important?
Without proteasome-mediated degradation, cells could not properly regulate the cell cycle, control gene expression, or cope with oxidative damage. It is therefore indispensable for virtually every eukaryotic and archaeal cell.
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