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Structure of PINK1 in complex with its substrate ubiquitin
Structure of PINK1 in complex with its substrate ubiquitin
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Structure of PINK1 in complex with its substrate ubiquitin
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Structure of PINK1 in complex with its substrate ubiquitin
Structure of PINK1 in complex with its substrate ubiquitin

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Structure of PINK1 in complex with its substrate ubiquitin
Structure of PINK1 in complex with its substrate ubiquitin
Journal Article

Structure of PINK1 in complex with its substrate ubiquitin

2017
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Overview
Autosomal-recessive juvenile Parkinsonism (AR-JP) is caused by mutations in a number of PARK genes, in particular the genes encoding the E3 ubiquitin ligase Parkin ( PARK2 , also known as PRKN ) and its upstream protein kinase PINK1 (also known as PARK6 ). PINK1 phosphorylates both ubiquitin and the ubiquitin-like domain of Parkin on structurally protected Ser65 residues, triggering mitophagy. Here we report a crystal structure of a nanobody-stabilized complex containing Pediculus humanus corporis ( Ph )PINK1 bound to ubiquitin in the ‘C-terminally retracted’ (Ub-CR) conformation. The structure reveals many peculiarities of PINK1, including the architecture of the C-terminal region, and reveals how the N lobe of PINK1 binds ubiquitin via a unique insertion. The flexible Ser65 loop in the Ub-CR conformation contacts the activation segment, facilitating placement of Ser65 in a phosphate-accepting position. The structure also explains how autophosphorylation in the N lobe stabilizes structurally and functionally important insertions, and reveals the molecular basis of AR-JP-causing mutations, some of which disrupt ubiquitin binding. Stabilization of a transient protein kinase–substrate complex using a nanobody provides molecular details about how the Parkinson’s disease-linked protein kinase PINK1 phosphorylates ubiquitin, and suggests new pharmacological strategies. A study in PINK1 The kinase enzyme PINK1 is known mainly for two reasons. At an organism level, mutations of PINK1 have been associated with autosomal-recessive juvenile Parkinsonism (AR-JP). At a cellular level, PINK1 phosphorylates both ubiquitin and a ubiquitin-like domain within its partner enzyme Parkin to trigger mitophagy, the process by which cells get rid of dysfunctional mitochondria. David Komander and co-authors report the structure of a complex between louse PINK1 and ubiquitin, which they obtained using nanobody-based stabilization. The structure provides molecular insights not only into PINK1–ubiquitin interactions and therefore the mechanism of PINK1 activity, but also into AR-JP-associated mutations, some of which disrupt ubiquitin binding.