ArticleThe journal of physical chemistry. B2025
The Lysine Deprotonation Mechanism in a Ubiquitin Conjugating Enzyme.
Article in The journal of physical chemistry. B, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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1 citing paper in PubMed.
- MechFind: a computational framework for de novo prediction of enzyme mechanisms.Nature communications · 2026Article
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4 authors.
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Abstract
Ubiquitination is a biochemical reaction in which a small protein, ubiquitin (Ub), is covalently linked to a lysine on a target protein. This type of post-translational modification can signal for protein degradation, DNA repair, or inflammation response. Ubiquitination is catalyzed by three families of enzymes: ubiquitin activating enzymes (E1), ubiquitin conjugating enzymes (E2), and ubiquitin ligases (E3). In this study, we focus on the chemical mechanism used by the E2 enzyme, Ubc13, which forms polyubiquitin chains by linking a substrate Ub to Lys63 on a target ubiquitin (Ub*). Initially, Ubc13 is covalently linked to the substrate Ub. Next, Lys63 in the Ub* is deprotonated, becomes an active nucleophile, and attacks the thioester bond in the Ubc13∼Ub conjugate. The deprotonation mechanism is not well understood. There are two, conserved nearby residues that may act as conjugate bases (Asp119 on Ubc13 and Glu64 on Ub*.) It is also hypothesized that the active site environment suppresses the lysine's p
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