7OTP

DNA-PKcs in complex with ATPgammaS-Mg

7OTP の概要

• エントリーDOI: 10.2210/pdb7otp/pdb
• EMDBエントリー: 13064
• 分子名称: DNA-dependent protein kinase catalytic subunit,DNA-PKcs, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER, MAGNESIUM ION (3 entities in total)
• 機能のキーワード: complex, inhibitor, dna repair, dna binding protein
• 由来する生物種: Homo sapiens (Human); 詳細
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 471947.26

構造登録者

Liang, S.,Thomas, S.E.,Blundell, T.L. (登録日: 2021-06-10, 公開日: 2022-01-12, 最終更新日: 2025-07-02)

主引用文献

Liang, S.,Thomas, S.E.,Chaplin, A.K.,Hardwick, S.W.,Chirgadze, D.Y.,Blundell, T.L.
Structural insights into inhibitor regulation of the DNA repair protein DNA-PKcs.
Nature, 601:643-648, 2022

PubMed Abstract: The DNA-dependent protein kinase catalytic subunit (DNA-PKcs) has a central role in non-homologous end joining, one of the two main pathways that detect and repair DNA double-strand breaks (DSBs) in humans. DNA-PKcs is of great importance in repairing pathological DSBs, making DNA-PKcs inhibitors attractive therapeutic agents for cancer in combination with DSB-inducing radiotherapy and chemotherapy. Many of the selective inhibitors of DNA-PKcs that have been developed exhibit potential as treatment for various cancers. Here we report cryo-electron microscopy (cryo-EM) structures of human DNA-PKcs natively purified from HeLa cell nuclear extracts, in complex with adenosine-5'-(γ-thio)-triphosphate (ATPγS) and four inhibitors (wortmannin, NU7441, AZD7648 and M3814), including drug candidates undergoing clinical trials. The structures reveal molecular details of ATP binding at the active site before catalysis and provide insights into the modes of action and specificities of the competitive inhibitors. Of note, binding of the ligands causes movement of the PIKK regulatory domain (PRD), revealing a connection between the p-loop and PRD conformations. Electrophoretic mobility shift assay and cryo-EM studies on the DNA-dependent protein kinase holoenzyme further show that ligand binding does not have a negative allosteric or inhibitory effect on assembly of the holoenzyme complex and that inhibitors function through direct competition with ATP. Overall, the structures described in this study should greatly assist future efforts in rational drug design targeting DNA-PKcs, demonstrating the potential of cryo-EM in structure-guided drug development for large and challenging targets.

PubMed: 34987222
DOI: 10.1038/s41586-021-04274-9

実験手法

ELECTRON MICROSCOPY (3.4 Å)