Journal Article

Mechanism of phospho-ubiquitin-induced PARKIN activation

Simicek, Michal, Wauer, Tobias, Komander, David, Schubert, Alexander

2015

Overview

This study provides insights into conformational changes that lead to phospho-ubiquitin-induced PARKIN activation and how PARKIN is recruited to phospho-ubiquitin chains on mitochondria; the crystal structure of PARKIN in complex with phospho-ubiquitin also indicates that the pocket within PARKIN where phospho-ubiquitin binds carries amino acid residues that are mutated in patients with autosomal-recessive juvenile Parkinsonism. PARKIN activation mechanism revealed The enzymatic duo PARKIN and PINK1 are notable not only because they regulate the process of mitophagy, whereby the cell degrades its damaged mitochondria, but also because they are mutated in autosomal-recessive juvenile Parkinson disease (AR-JP). At a molecular level, PINK1 activates PARKIN by phosphorylating both the ubiquitin (Ub)-like (Ubl) domain of PARKIN and Ub molecules. David Komander and colleagues provide insights into conformational changes that lead to phosphoUb-induced PARKIN activation and how PARKIN recruits phosphoUb chains on mitochondria. The crystal structure of PARKIN in complex with phosphoUb also indicates that the pocket within PARKIN where phosphoUb binds carries amino acid residues that are mutated in patients with AR-JP. The E3 ubiquitin ligase PARKIN (encoded by PARK2 ) and the protein kinase PINK1 (encoded by PARK6 ) are mutated in autosomal-recessive juvenile Parkinsonism (AR-JP) and work together in the disposal of damaged mitochondria by mitophagy 1 , 2 , 3 . PINK1 is stabilized on the outside of depolarized mitochondria and phosphorylates polyubiquitin 4 , 5 , 6 , 7 , 8 as well as the PARKIN ubiquitin-like (Ubl) domain 9 , 10 . These phosphorylation events lead to PARKIN recruitment to mitochondria, and activation by an unknown allosteric mechanism 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 . Here we present the crystal structure of Pediculus humanus PARKIN in complex with Ser65-phosphorylated ubiquitin (phosphoUb), revealing the molecular basis for PARKIN recruitment and activation. The phosphoUb binding site on PARKIN comprises a conserved phosphate pocket and harbours residues mutated in patients with AR-JP. PhosphoUb binding leads to straightening of a helix in the RING1 domain, and the resulting conformational changes release the Ubl domain from the PARKIN core; this activates PARKIN. Moreover, phosphoUb-mediated Ubl release enhances Ubl phosphorylation by PINK1, leading to conformational changes within the Ubl domain and stabilization of an open, active conformation of PARKIN. We redefine the role of the Ubl domain not only as an inhibitory 13 but also as an activating element that is restrained in inactive PARKIN and released by phosphoUb. Our work opens up new avenues to identify small-molecule PARKIN activators.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 101/6 / 631/45/173 / 631/535/1266 / 631/80/458/582 / 82/1 / 82/80 / 82/83 / 96/63 / 96/95 / Analysis / Animals / Binding sites / Binding Sites - genetics / Conserved Sequence - genetics / Crystal structure / Crystallography, X-Ray / Enzyme Activation / Humanities and Social Sciences / Humans / Kinases / letter / Ligases / Mitochondria / Mitochondrial DNA / Models, Molecular / multidisciplinary / Mutation / Mutation - genetics / Parkinsonian Disorders - genetics / Pediculus - chemistry / Phosphates - metabolism / Phosphoproteins - chemistry / Phosphoproteins - metabolism / Phosphorylation / Protein Binding / Protein Kinases - metabolism / Protein Structure, Tertiary / Science / Structure-Activity Relationship / Ubiquitin - chemistry / Ubiquitin - metabolism / Ubiquitin-proteasome system / Ubiquitin-Protein Ligases - chemistry / Ubiquitin-Protein Ligases - genetics / Ubiquitin-Protein Ligases - metabolism