Site-specific ubiquitination: Deconstructing the degradation tag

Ubiquitin is a small eukaryotic protein so named for its cellular abundance and originally recognized for its role as the posttranslational modification (PTM) “tag” condemning substrates to degradation by the 26S proteasome. Since its discovery in the 1970s, protein ubiquitination has also been identified as a key regulatory feature in dozens of non-degradative cellular processes. This myriad of roles illustrates the versatility of ubiquitin as a PTM; however, understanding the cellular and molecular factors that enable discrimination between degradative versus non-degradative ubiquitination events has been a persistent challenge. Here, we discuss recent advances in uncovering how site-specificity — the exact residue that gets modified — modulates distinct protein fates and cellular outcomes with an emphasis on how ubiquitination site specificity regulates proteasomal degradation. We explore recent advances in structural biology, biophysics, and cell biology that have enabled a broader understanding of the role of ubiquitination in altering the dynamics of the target protein, including implications for the design of targeted protein degradation therapeutics. •Advances in purification of site-specific, ubiquitin-modified proteins enables structural/mechanistic studies.•Ubiquitin modifications communicate with their substrate proteins by modulating energetics, activity, and conformation.•New techniques for mapping ubiquitination will increase our resolution of ubiquitin’s effects on individual sites/proteins.•Degradation-targeting therapeutics can leverage discoveries in site-specific ubiquitination to promote desired cellular consequences.