How to Inactivate Human Ubiquitin E3 Ligases by Mutation

E3 ubiquitin ligases are the ultimate enzymes involved in the transfer of ubiquitin to substrate proteins, a process that determines the fate of the modified protein. Numerous diseases are caused by defects in the ubiquitin-proteasome machinery, including when the activity of a given E3 ligase is hampered. Thus, inactivation of E3 ligases and the resulting effects at molecular or cellular level have been the focus of many studies during the last few years. For this purpose, site-specific mutation of key residues involved in either protein interaction, substrate recognition or ubiquitin transfer have been reported to successfully inactivate E3 ligases. Nevertheless, it is not always trivial to predict which mutation(s) will block the catalytic activity of a ligase. Here we review over 250 site-specific inactivating mutations that have been carried out in 120 human E3 ubiquitin ligases. We foresee that the information gathered here will be helpful for the design of future experimental strategies.

• Publication year

  2020

• Venue

  Frontiers in Cell and Developmental Biology

• Publication date

  2020-02-04

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.3389/fcell.2020.00039PMID 32117970PMCID 7010608
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2017cited by this paper
• Ubiquitin Ligases: Structure, Function, and Regulation.

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• RING-type E3 ligases: master manipulators of E2 ubiquitin-conjugating enzymes and ubiquitination.

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  2012cited by this paper
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