Complex Conformational Interplay for Parkin Activation is Revealed by 19F NMR Spectroscopy

Parkin is a 52 kDa RING-Between-RING E3 ligase that ubiquitinates proteins at the outer mitochondrial membrane in response to oxidative stress. Part of a neuroprotective pathway, over 100 mutations in the PRKN gene have been associated with Early Onset Parkinson's Disease. To be fully active parkin requires interaction with phosphorylated ubiquitin and phosphorylation of its N-terminal Ubl domain, both dependent on the PINK1 kinase. Along with recruitment of an E2 ∼ Ubiquitin conjugate these events form a ∼90 kDa complex, undergoing a series of conformational changes that regulate transthiolation of ubiquitin from the E2 enzyme to the catalytic domain in parkin (Rcat) prior to substrate labeling. Numerous crystal and NMR structures have captured snapshots of parkin activation and its catalytic mechanism, yet questions surrounding the relative abundance, timing and interplay of parkin conformations remain. Further, most studies use truncated versions of the E3 ligase that may hide details of conformational dependencies. To examine parkin through its activation cycle from inactive (autoinhibited) to E2 ∼ Ubiquitin binding states we incorporated 5-¹⁹F-tryptophan into the full-length enzyme and used ¹⁹F NMR spectroscopy to identify structural and dynamics changes. Using chemical shift perturbation and T2 analysis, we show that phosphorylation of parkin leads to a population of unbound and bound forms of the phosphorylated Ubl domain and that release of the catalytic Rcat domain is dependent upon E2 ∼ Ub conjugate binding. This study shows the unique abilities of ¹⁹F NMR spectroscopy to provide details of the structural rearrangements required for catalysis for the large E3 ligase parkin.