title: Site-specific Interaction Mapping of Phosphorylated Ubiquitin to Uncover Parkin Activation.
abstract: Damaged mitochondria are eliminated through autophagy machinery. A cytosolic E3 ubiquitin ligase Parkin, a gene product mutated in familial Parkinsonism, is essential for this pathway. Recent progress has revealed that phosphorylation of both Parkin and ubiquitin at Ser(65) by PINK1 are crucial for activation and recruitment of Parkin to the damaged mitochondria. However, the mechanism by which phosphorylated ubiquitin associates with and activates phosphorylated Parkin E3 ligase activity remains largely unknown. Here, we analyze interactions between phosphorylated forms of both Parkin and ubiquitin at a spatial resolution of the amino acid residue by site-specific photo-crosslinking. We reveal that the in-between-RING (IBR) domain along with RING1 domain of Parkin preferentially binds to ubiquitin in a phosphorylation-dependent manner. Furthermore, another approach, the Fluoppi (fluorescent-based technology detecting protein-protein interaction) assay, also showed that pathogenic mutations in these domains blocked interactions with phosphomimetic ubiquitin in mammalian cells. Molecular modeling based on the site-specific photo-crosslinking interaction map combined with mass spectrometry strongly suggests that a novel binding mechanism between Parkin and ubiquitin leads to a Parkin conformational change with subsequent activation of Parkin E3 ligase activity.
authors.affiliation: From the Ubiquitin Project and yamano-kj@igakuken.or.jp.
authors.forename: Koji
authors.initials: K
authors.lastname: Yamano
authors.affiliation: Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506 and.
authors.forename: Bruno B
authors.initials: BB
authors.lastname: Queliconi
authors.affiliation: From the Ubiquitin Project and.
authors.forename: Fumika
authors.initials: F
authors.lastname: Koyano
authors.affiliation: Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506 and.
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Saeki
authors.affiliation: the Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.
authors.forename: Takatsugu
authors.initials: T
authors.lastname: Hirokawa
authors.affiliation: Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506 and.
authors.forename: Keiji
authors.initials: K
authors.lastname: Tanaka
authors.affiliation: From the Ubiquitin Project and matsuda-nr@igakuken.or.jp.
authors.forename: Noriyuki
authors.initials: N
authors.lastname: Matsuda
mesh_terms: D001665:Binding Sites; D006367:HeLa Cells; D006801:Humans; D010766:Phosphorylation; D011494:Protein Kinases / Q000378:metabolism; D025801:Ubiquitin / Q000378:metabolism*; D044767:Ubiquitin-Protein Ligases / Q000737:chemistry / Q000378:metabolism*; D000099202:PTEN-Induced Putative Kinase
chemical_list: D011494:Protein Kinases; D025801:Ubiquitin; D044767:Ubiquitin-Protein Ligases; D000099202:PTEN-Induced Putative Kinase; C111567:parkin protein
keywords: E3 ubiquitin ligase; PTEN-induced putative kinase 1 (PINK1); Parkinson disease; mitochondria; mitophagy