Why do cellular proteins linked to K63-polyubiquitin chains not associate with proteasomes?

Ubiquitination regulates the stability and/or activity of numerous cellular proteins. The corollary is that de-ubiquitinating enzymes, which ‘trim’ polyubiquitin chains from specific substrate proteins, play key roles in controlling fundamental cellular activities. Ubiquitin is essential at several stages during the activation of NF-κB (nuclear factor κB), a central co-ordinator of inflammation and other immune processes. Ubiquitination is known to cause degradation of the inhibitory molecule IκBα (inhibitor of κB). In addition, activation of TRAF (tumour-necrosis-factor-receptor-associated factor) and IKKγ (IκB kinase γ)/NEMO (NF-κB essential modifier) signal adaptors relies on their modification with ‘nonclassical’ forms of polyubiquitin chains. Ubiquitin also plays a key role in determining cell fate by modulating the stability of numerous pro-apoptotic or anti-apoptotic proteins. The zinc-finger protein A20 has dual functions in inhibiting NF-κB activation and suppressing apoptosis. The molecular mechanisms of these anti-inflammatory and cytoprotective effects are unknown. Here we demonstrate that A20 is a de-ubiquitinating enzyme. It contains an N-terminal catalytic domain that belongs to the ovarian-tumour superfamily of cysteine proteases. A20 cleaved ubiquitin monomers from branched polyubiquitin chains linked through Lys48 or Lys63 and bound covalently to a thiol-group-reactive, ubiquitin-derived probe. Mutation of a conserved cysteine residue in the catalytic site (Cys103) abolished these activities. A20 did not have a global effect on ubiquitinated cellular proteins, which indicates that its activity is target-specific. The biological significance of the catalytic domain is unknown.

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Ubiquitomics: An Overview and Future

Biomolecules ◽

10.3390/biom10101453 ◽

2020 ◽

Vol 10 (10) ◽

pp. 1453 ◽

Cited By ~ 1

Author(s):

George Vere ◽

Rachel Kealy ◽

Benedikt M. Kessler ◽

Adan Pinto-Fernandez

Keyword(s):

Chemical Biology ◽

Biological Diversity ◽

Analytical Techniques ◽

Cellular Proteins ◽

Covalent Attachment ◽

Post Translational Modification ◽

Polyubiquitin Chains ◽

Protein Substrates ◽

Protein Ubiquitination ◽

Amino Acid Side Chains

Covalent attachment of ubiquitin, a small globular polypeptide, to protein substrates is a key post-translational modification that determines the fate, function, and turnover of most cellular proteins. Ubiquitin modification exists as mono- or polyubiquitin chains involving multiple ways how ubiquitin C-termini are connected to lysine, perhaps other amino acid side chains, and N-termini of proteins, often including branching of the ubiquitin chains. Understanding this enormous complexity in protein ubiquitination, the so-called ‘ubiquitin code’, in combination with the ∼1000 enzymes involved in controlling ubiquitin recognition, conjugation, and deconjugation, calls for novel developments in analytical techniques. Here, we review different headways in the field mainly driven by mass spectrometry and chemical biology, referred to as “ubiquitomics”, aiming to understand this system’s biological diversity.

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Orchestra for assembly and fate of polyubiquitin chains

Essays in Biochemistry ◽

10.1042/eb0410001 ◽

2005 ◽

Vol 41 (1) ◽

pp. 1 ◽

Cited By ~ 10

Author(s):

Kuhlbrodt Kirsten ◽

Mouysset Julien ◽

Hoppe Thorsten

Keyword(s):

Polyubiquitin Chains

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PHOTACs Enable Optical Control of Protein Degradation

10.26434/chemrxiv.8206688 ◽

2019 ◽

Cited By ~ 2

Author(s):

Martin Reynders ◽

Bryan Matsuura ◽

Marleen Bérouti ◽

Daniele Simoneschi ◽

Antonio Marzio ◽

...

Keyword(s):

Protein Degradation ◽

E3 Ligase ◽

Optical Control ◽

Cellular Proteins ◽

Bifunctional Molecules ◽

Protein Levels ◽

Lead Compounds ◽

Subsequent Degradation ◽

Temporal And Spatial ◽

Precision Therapeutics

PROTACs (proteolysis targeting chimeras) are bifunctional molecules that tag proteins for ubiquitylation by an E3 ligase complex and subsequent degradation by the proteasome. They have emerged as powerful tools to control the levels of specific cellular proteins and are on the verge of being clinically used. We now introduce photoswitchable PROTACs that can be activated with the temporal and spatial precision that light provides. These trifunctional molecules, which we named PHOTACs, consist of a ligand for an E3 ligase, a photoswitch, and a ligand for a protein of interest. We demonstrate this concept by using PHOTACs that target either BET family proteins (BRD2,3,4) or FKBP12. Our lead compounds display little or no activity in the dark but can be reversibly activated to varying degrees with different wavelengths of light. Our modular and generalizable approach provides a method for the optical control of protein levels with photopharmacology and could lead to new types of precision therapeutics that avoid undesired systemic toxicity.

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