The Ubiquitin-Proteasome System

Summary

The ubiquitin-proteasome system (UPS) is the major pathway for regulated protein degradation in eukaryotes. Proteins are tagged with ubiquitin chains and then degraded by the 26S proteasome, controlling protein quality, cell cycle progression, and signal transduction.

Key Points

1E1-E2-E3 cascade attaches ubiquitin to substrate proteins
2K48 polyubiquitin chains target proteins for proteasomal degradation
326S proteasome: 19S cap recognizes substrates, 20S core degrades them
4Controls protein quality, cell cycle, signaling, and immune function

The ubiquitin-proteasome system represents the primary mechanism for controlled protein degradation in eukaryotic cells, with profound implications for virtually every cellular process.

Ubiquitin: The Molecular Tag

Structure and Properties

Ubiquitin is a highly conserved 76-amino acid protein:

- Compact β-grasp fold: Extremely stable structure

- C-terminal glycine: Forms isopeptide bond with substrates

- Seven lysine residues: K6, K11, K27, K29, K33, K48, K63

- N-terminal methionine (M1): Also serves as attachment point

Ubiquitin Chain Types

Different chain linkages encode different signals:

- K48 chains: Classical degradation signal

- K11 chains: Cell cycle regulation, degradation

- K63 chains: Non-degradative signaling, DNA repair, autophagy

- M1 (linear) chains: NF-κB signaling, inflammation

- Mixed/branched chains: Complex regulatory outcomes

The Ubiquitination Cascade

E1: Ubiquitin-Activating Enzyme

Activates ubiquitin's C-terminus using ATP

Forms high-energy thioester intermediate

Only 2 E1 enzymes in humans (UBA1, UBA6)

E2: Ubiquitin-Conjugating Enzyme

Receives ubiquitin from E1 via transthioesterification

~40 E2 enzymes in humans

Determines chain topology in many cases

E3: Ubiquitin Ligase

Provides substrate specificity

- ~600-700 E3 ligases in humans

Two major classes:

#### RING E3 Ligases

Catalyze direct transfer from E2 to substrate

Function as scaffolds bringing E2 and substrate together

Examples: SCF complexes, APC/C

#### HECT E3 Ligases

Form thioester intermediate with ubiquitin

Ubiquitin transfers from E2 to E3 to substrate

Examples: NEDD4 family, E6AP

E4: Chain Elongation Factors

Specialized factors that extend ubiquitin chains

Example: UFD2

The 26S Proteasome

Overall Architecture

The 26S proteasome is a 2.5 MDa complex comprising:

- 20S core particle (CP): Proteolytic chamber

- 19S regulatory particle (RP): Recognition and unfolding

20S Core Particle

Barrel-shaped structure: α₇β₇β₇α₇

- Catalytic sites: Located on β1, β2, β5 subunits

- Caspase-like (β1)

- Trypsin-like (β2)

- Chymotrypsin-like (β5)

Products: Peptides of 3-25 amino acids

19S Regulatory Particle

- Base: ATPase ring (Rpt1-6), unfolds substrates

- Lid: Deubiquitinases (Rpn11), removes ubiquitin for recycling

Recognizes ubiquitinated substrates

Translocates unfolded proteins into 20S

Biological Functions

Protein Quality Control

Degrades misfolded and damaged proteins

- ERAD: ER-associated degradation of secretory proteins

Prevents accumulation of toxic aggregates

Cell Cycle Regulation

- Cyclin degradation: Controls cell cycle transitions

- APC/C: Anaphase-promoting complex

- SCF complexes: G1/S transition control

Signal Transduction

- NF-κB pathway: IκB degradation activates NF-κB

- Wnt signaling: β-catenin regulation

- Hypoxia response: HIF-1α degradation

Immune Function

- Antigen presentation: Generates peptides for MHC class I

- Immunoproteasome: Altered subunits in immune cells

Disease and Therapeutics

Proteasome Inhibitors

- Bortezomib: First FDA-approved proteasome inhibitor

Used in multiple myeloma treatment

Causes accumulation of pro-apoptotic factors

Neurodegenerative Disease

UPS dysfunction implicated in:

- Parkinson's disease

- Alzheimer's disease

- Huntington's disease

Aggregates can impair proteasome function

References

Quaternary Structure and Allostery

Aminoacyl-tRNA Synthetases