SAP domain forms a flexible part of DNA aperture in Ku70/80

• DOI: 10.1111/febs.15732
• Publication Date: 2021-01-29T08:27:28Z
• Authors: Aleš Hnízda; Petr Tesina; Thanh‐Binh Nguyen; Zdeněk Kukačka; Lukas Kater; Amanda K. Chaplin; Roland Beckmann; David B. Ascher; Petr Novák; Tom L. Blundell
• Keywords: 0301 basic medicine; 570; 0303 health sciences; DNA End-Joining Repair; Protein Conformation; Original Articles; DNA; SAP domain; nonhomologous end joining; Ku70/80; 03 medical and health sciences; Protein Domains; DNA double-strand break; Humans; DNA Breaks, Double-Stranded; Ku Autoantigen; integrative structural biology

Nonhomologous end joining (NHEJ) is a DNA repair mechanism that religates double‐strand DNA breaks to maintain genomic integrity during the entire cell cycle. The Ku70/80 complex recognizes DNA breaks and serves as an essential hub for recruitment of NHEJ components. Here, we describe intramolecular interactions of the Ku70 C‐terminal domain, known as the SAP domain. Using single‐particle cryo‐electron microscopy, mass spectrometric analysis of intermolecular cross‐linking and molecular modelling simulations, we captured variable positions of the SAP domain depending on DNA binding. The first position was localized at the DNA aperture in the Ku70/80 apo form but was not observed in the DNA‐bound state. The second position, which was observed in both apo and DNA‐bound states, was found below the DNA aperture, close to the helical arm of Ku70. The localization of the SAP domain in the DNA aperture suggests a function as a flexible entry gate for broken DNA.DatabasesEM maps have been deposited in EMDB (EMD‐11933). Coordinates have been deposited in Protein Data Bank (PDB 7AXZ). Other data are available from corresponding authors upon a request.