Allosteric network of dynamic coupling within BAP1-UCH revealed by methyl NMR

BRCA1-associated protein 1 (BAP1) is a tumor suppressor whose deubiquitinase (DUB) activity is essential for transcriptional regulation and is frequently compromised in cancer by mutations clustered in its ubiquitin carboxyl-terminal hydrolase (UCH) domain. The structural and dynamic bases of these oncogenic mutations remain elusive. Here, we introduce 22 cancer mutations and additional methyl mutations on the other 22 cancer mutation sites of BAP1-UCH to map their effects on the methyl chemical shifts. This analysis reveals an allosteric coupling network centered on a conserved leucine (L49) shared across human UCH paralogs. Strikingly, a single-carbon side-chain truncation in the L49V variant abolishes DUB activity, coinciding with disruption of correlated μs–ms timescale motions within a phenylalanine cluster that undergoes concerted motions within the L49 hub. These findings uncover how BAP1-UCH sustains its catalytic competence through a delicately tuned dynamic network and how minute alterations can collapse this allosteric balance, providing a mechanistic link between subtle structural perturbations and oncogenesis. BAP1 is a tumor-suppressor deubiquitinase that helps control how genes are switched on and off. In this study, the authors use NMR spectroscopy to examine how more than 40 cancer associated and related mutations perturb the BAP1-UCH domain.