ubiquitin-proteasome

**Mechanism** 1. **Ubiquitin**: a 76-amino-acid, highly conserved protein. 2. **E1 (ubiquitin-activating enzyme)**: uses ATP to activate ubiquitin and forms a high-energy thioester bond with it. 3. **E2 (ubiquitin-conjugating enzyme)**: accepts ubiquitin from E1. 4. **E3 (ubiquitin ligase)**: recognizes the specific substrate and transfers ubiquitin from E2 to a lysine on the target. E3s confer substrate specificity, and there are hundreds of them. 5. **Polyubiquitination**: a chain of ≥4 ubiquitins linked through **lysine 48 (K48)** marks the protein for proteasomal degradation. Monoubiquitination or K63-linked chains instead function in signaling, endocytosis, and DNA repair. 6. **26S proteasome**: a barrel-shaped complex made of a 20S core catalytic particle and 19S regulatory caps. - The 19S cap recognizes the ubiquitin tag, removes the ubiquitin (deubiquitinases), unfolds the substrate (ATPase activity), and feeds it into the core. - The 20S core has protease activity (chymotrypsin-like, trypsin-like, and caspase-like) and cleaves the protein into small peptides, typically 7–9 amino acids. - Ubiquitin is recycled.

**Physiologic roles** - **Cell cycle control**: degradation of cyclins (via the APC/C and SCF complexes) and CDK inhibitors (p27) drives cell-cycle progression. - **Tumor suppressor regulation**: MDM2 is an E3 ligase that ubiquitinates **p53** and keeps its levels low. DNA damage inhibits MDM2 and stabilizes p53. - **NF-κB activation**: IκB is phosphorylated, ubiquitinated, and degraded, which frees NF-κB to enter the nucleus. - **MHC class I antigen presentation**: cytosolic proteins are degraded by the proteasome (the **immunoproteasome**, induced by IFN-γ). The peptides are transported by **TAP** into the ER and loaded onto MHC I. - **ER-associated degradation (ERAD)**: misfolded ER proteins are retrotranslocated to the cytosol and degraded. Example: misfolded **CFTR ΔF508** in cystic fibrosis is destroyed by this pathway. - **HIF-1α regulation**: under normoxia, prolyl hydroxylation lets **VHL** (an E3 ligase) ubiquitinate HIF-1α for degradation. Loss of VHL in **von Hippel-Lindau disease** stabilizes HIF-1α and causes overproduction of VEGF and EPO (hemangioblastomas, clear cell RCC, pheochromocytoma).

**Clinical correlations** - **Parkinson disease**: *parkin* (PARK2) is an E3 ligase. Mutations cause autosomal recessive early-onset Parkinson disease. Lewy bodies contain ubiquitinated α-synuclein. - **Neurodegeneration in general**: ubiquitin-positive inclusions are seen in Alzheimer disease (neurofibrillary tangles), Pick disease, ALS, and Huntington disease. - **Angelman syndrome**: loss of the maternal **UBE3A** (an E3 ligase) gene. Features include happy demeanor, ataxia, seizures, and intellectual disability. - **HPV**: E6 protein recruits the E3 ligase E6-AP to degrade **p53**, and E7 inactivates Rb. Together they promote cervical cancer. - **Cystic fibrosis**: ΔF508 CFTR is degraded prematurely by the proteasome. - **Cachexia/muscle wasting**: upregulated UPS activity (atrogin-1, MuRF1) causes muscle atrophy.

**Pharmacology** - **Bortezomib, carfilzomib, ixazomib**: proteasome inhibitors used in **multiple myeloma** and mantle cell lymphoma. - Mechanism: they block the 20S proteolytic activity. Accumulated IκB and pro-apoptotic proteins inhibit NF-κB and induce apoptosis. Myeloma cells are especially sensitive because they make large amounts of immunoglobulin and rely on the proteasome to clear misfolded protein. - Adverse effects: **peripheral neuropathy** (bortezomib), herpes zoster reactivation (give acyclovir prophylaxis), thrombocytopenia, and cardiotoxicity (carfilzomib). - **Thalidomide/lenalidomide/pomalidomide** (IMiDs): bind **cereblon**, a component of an E3 ligase, and redirect it to degrade the transcription factors Ikaros and Aiolos. Teratogenic (phocomelia). - **PROTACs**: emerging drugs that recruit an E3 ligase to a target protein to induce its degradation.

**High-yield contrast** - The UPS degrades **individual, tagged cytosolic/nuclear proteins**. - **Lysosomal/autophagy pathways** degrade bulk cytoplasm, organelles, and extracellular or endocytosed proteins. Ubiquitin is also used there (e.g., p62 adaptors in selective autophagy). - The 2004 Nobel Prize in Chemistry went to Ciechanover, Hershko, and Rose for discovering ubiquitin-mediated protein degradation.