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Solids in which the atoms, ions, or molecules are arranged in a definite repeating pattern are known as crystalline solids. Metals and ionic compounds typically form ordered, crystalline solids. A crystalline solid has a precise melting temperature because each atom or molecule of the same type is held in place with the same forces or energy. Amorphous solids or non-crystalline solids (or, sometimes, glasses) which lack an ordered internal structure and are randomly arranged. Substances that...
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Updated: Feb 8, 2026

siRNA Screening to Identify Ubiquitin and Ubiquitin-like System Regulators of Biological Pathways in Cultured Mammalian Cells
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Structural insights into ubiquitin phosphorylation by PINK1.

Kei Okatsu1,2, Yusuke Sato1,2,3, Koji Yamano4

  • 1Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.

Scientific Reports
|July 12, 2018
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Summary

Mutations in PTEN-induced putative kinase 1 (PINK1) and parkin cause Parkinsonism. This study reveals the crystal structure of PINK1, uncovering a unique binding groove for ubiquitin and its UBL domain, crucial for mitochondrial repair.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Neuroscience

Background:

  • Mutations in PTEN-induced putative kinase 1 (PINK1) and parkin are linked to familial Parkinsonism.
  • PINK1 and parkin are critical for degrading damaged mitochondria via ubiquitylation.
  • PINK1 phosphorylates ubiquitin and parkin to regulate parkin activity.

Purpose of the Study:

  • To elucidate the structural mechanism of ubiquitin/UBL phosphorylation by PINK1.
  • To understand how PINK1 interacts with ubiquitin and parkin at a molecular level.

Main Methods:

  • Determined the crystal structure of Tribolium castaneum PINK1 kinase domain (TcPINK1) complexed with an ATP analogue.
  • Utilized crosslinking analyses to identify PINK1-ubiquitin interaction sites.
  • Performed structure-guided mutational analyses.

Main Results:

  • The crystal structure of TcPINK1 revealed its N- and C-terminal lobes and a PINK1-specific extension.
  • A nonhydrolyzable ATP analogue was observed bound in the cleft between the lobes.
  • A wider Ub/UBL-binding groove compared to other kinases was identified, suggesting specific accommodation for ubiquitin or UBL.
  • Crosslinking identified a specific surface on ubiquitin interacting with PINK1.

Conclusions:

  • The determined structure provides insights into the mechanism of PINK1-mediated phosphorylation of ubiquitin and parkin.
  • The unique binding groove facilitates PINK1's role in mitochondrial quality control.
  • Structure-guided mutations validated the proposed interaction model.