Related Experiment Video

Updated: Aug 15, 2025

Amide Hydrogen/Deuterium Exchange & MALDI-TOF Mass Spectrometry Analysis of Pak2 Activation
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Amide Hydrogen/Deuterium Exchange & MALDI-TOF Mass Spectrometry Analysis of Pak2 Activation

Published on: November 26, 2011

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Human DNA-dependent protein kinase activation mechanism

Shikang Liang1,2, Tom L Blundell3,4

  • 1Department of Biochemistry, University of Cambridge, Cambridge, UK. sl744@cam.ac.uk.

Nature Structural & Molecular Biology
|January 5, 2023
PubMed

Insights

DNA-dependent protein kinase (DNA-PK) activation involves conformational changes regulated by ligand binding and specific protein regions interacting with DNA. This research clarifies DNA-PK

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • DNA-dependent protein kinase (DNA-PK) is crucial for DNA damage response and repair in humans.
  • The DNA-PK complex consists of the catalytic subunit and the Ku70/80 heterodimer, requiring DNA for its function.

Purpose of the Study:

  • To elucidate the molecular mechanisms regulating human DNA-PK complex activation.
  • To understand the role of ligand binding and specific protein domains in DNA-PK kinase activity.

Main Methods:

  • Utilized a DNA-PK-selective inhibitor (M3814).
  • Determined two cryo-electron microscopy (cryo-EM) structures of the human DNA-PK complex (intermediate and active states).

Main Results:

  • Identified conformational changes in DNA-PK upon ligand binding and interaction with its string region (residues 802-846), including the helix-hairpin-helix motif (residues 816-836).
  • Demonstrated the regulatory role of the ligand and the DNA-binding motif in kinase activation.
  • Highlighted the contribution of protein-protein interactions and flexible regions to kinase modulation.

Conclusions:

  • Ligand binding and specific DNA-interacting regions are key regulators of DNA-PK activation.
  • The findings explain the DNA-dependent nature of DNA-PK.
  • Provides enhanced molecular insights into DNA-PK catalysis and its role in DNA repair.

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