Mechanism of Activation of the Ubiquitin E3 Ligase, Parkin

Abstract

The Parkinson disease associated proteins, Parkin and PINK1, together comprise a mitochondrial quality control system that promotes neuronal survival through autophagy of damaged mitochondria. In the pathway, PINK1 acts as a sensor of depolarized mitochondria and phosphorylates ubiquitin to recruit and activate Parkin on the mitochondrial outer membrane. Parkin ubiquitinates mitochondrial proteins, which leads to the removal of the damaged mitochondria through mitophagy. We have carried out structural and functional studies of Parkin to understand its regulation and mechanism of activation 1– 3. Parkin exhibits low basal activity as a ubiquitin ligase and requires activation both in vitro and in cells. Multiple features inhibit Parkin activity: the E2‐binding site on RING1 is blocked, the catalytic site is partially occluded, and the incoming E2~Ub linkage is far from the parkin catalytic site (Fig. 1). In response to mitochondrial damage, Parkin is activated by PINK1 via a two‐step mechanism involving binding of Parkin to phosphorylated ubiquitin and a large‐scale conformational change induced by Parkin phosphorylation (Fig. 2). Positive feedback in the Parkin/PINK1 pathway generates a binary, all‐or‐nothing switch for the induction of mitophagy. These structural studies are critical for understanding how Parkin and PINK1 protect neurons and provide a framework for the design of small molecules for treating Parkinson disease.Support or Funding InformationSupported by the Michael J Fox Foundation, the Canadian Institutes of Health Research, and the Canada Research Chair program.Autoinhibited conformation of Parkin.The crystal structure of Parkin revealed that the catalytic and E2‐binding sites are occluded by interdomain contacts mediated by the ubiquitin‐like domain, Repressor Element of Parkin (REP) and RING0 domain 1. Disruption of the inhibitory contacts derepresses ligase activity.Figure 1Active complex of Parkin with ubiquitin‐charged E2 enzyme and phospho‐ubiquitin (Ub).The crystal structure of activated Parkin showed that phosphorylation of the Parkin Ubl domain induces a large conformational change allowing the catalytic RING2 domain to interact with the bound E2~Ub 3. Hydrogen‐deuterium exchange experiments confirm that the RING2 domain is released and accessible upon Ubl binding to RING0.Figure 2