Cooperative Substructure and Energetics of Allosteric Regulation of the Catalytic Core of the E3 Ubiquitin Ligase Parkin by Phosphorylated Ubiquitin

• Published in: Biomolecules (Basel, Switzerland) Switzerland), 2024-10, Vol.14 (10), p.1338
• Main Authors: Ye, Xiang, Kotaru, Sravya, Lopes, Rosana, Cravens, Shannen, Lasagna, Mauricio, Wand, A Joshua
• Format: Article
• Language: English
• Subjects: Allosteric enzymes; Allosteric properties; Allosteric Regulation; allostery; Basal ganglia; Catalysis; Catalytic Domain; Central nervous system diseases; Chemical properties; Chromatography; Crystallography; Development and progression; E coli; Gene mutations; Genetic aspects; Glycerol; Health aspects; Humans; Hydrogen; Hydrogen exchange; Ligases; Mass spectrometry; Mass spectroscopy; Medical research; Medicine, Experimental; Mitophagy; Models, Molecular; Movement disorders; Parkin E3 ubiquitin ligase; Parkin protein; Parkinsonism; Peptides; Phosphorylation; Protein Binding; protein ensemble; protein stability; Protein structure; Proteins; Scientific imaging; Structure; Ubiquitin; Ubiquitin - chemistry; Ubiquitin - metabolism; Ubiquitin-protein ligase; Ubiquitin-Protein Ligases - chemistry; Ubiquitin-Protein Ligases - metabolism
• ISSN: 2218-273X; 2218-273X
• DOI: 10.3390/biom14101338

Mutations in the parkin gene product Parkin give rise to autosomal recessive juvenile parkinsonism. Parkin is an E3 ubiquitin ligase that is a critical participant in the process of mitophagy. Parkin has a complex structure that integrates several allosteric signals to maintain precise control of its catalytic activity. Though its allosterically controlled structural reorganization has been extensively characterized by crystallography, the energetics and mechanisms of allosteric regulation of Parkin are much less well understood. Allostery is fundamentally linked to the energetics of the cooperative (sub)structure of the protein. Herein, we examine the mechanism of allosteric activation by phosphorylated ubiquitin binding to the enzymatic core of Parkin, which lacks the antagonistic Ubl domain. In this way, the allosteric effects of the agonist phosphorylated ubiquitin can be isolated. Using native-state hydrogen exchange monitored by mass spectrometry, we find that the five structural domains of the core of Parkin are energetically distinct. Nevertheless, association of phosphorylated ubiquitin destabilizes structural elements that bind the ubiquitin-like domain antagonist while promoting the dissociation of the catalytic domain and energetically poises the protein for transition to the fully activated structure.