Structural basis of allosteric regulation of Tel1/ATM kinase

Jiyu Xin,Yanhua Tian,Gang Cai,Xuejuan Wang,Zhu Xu,Zhihui Zhang

doi:10.1038/s41422-019-0176-1

Abstract

ATM/Tel1 is an apical kinase that orchestrates the multifaceted DNA damage response. Mutations of ATM/Tel1 are associated with ataxia telangiectasia syndrome. Here, we report cryo-EM structures of symmetric dimer (4.1 Å) and asymmetric dimer (4.3 Å) of Saccharomyces cerevisiae Tel1. In the symmetric state, the side chains in Tel1 C-terminus (residues 1129–2787) are discernible and an atomic model is built. The substrate binding groove is completely embedded in the symmetric dimer by the intramolecular PRD and intermolecular LID domains. Point mutations in these domains sensitize the S. cerevisiae cells to DNA damage agents and hinder Tel1 activation due to reduced binding affinity for its activator Xrs2/Nbs1. In the asymmetric state, one monomer becomes more compact in two ways: the kinase N-lobe moves down and the Spiral of α-solenoid moves upwards, which resemble the conformational changes observed in active mTOR. The accessibility of the activation loop correlates with the synergistic conformational disorders in the TRD1-TRD2 linker, FATC and PRD domains, where critical post-translational modifications and activating mutations are coincidently condensed. This study reveals a tunable allosteric network in ATM/Tel1, which is important for substrate recognition, recruitment and efficient phosphorylation.

Highlights

The genome is constantly under assault by environmental agents, such as exposure to irradiation, chemical agents and ultraviolet light (UV), as well as endogenous agents, such as free radicals generated during normal metabolic processes
The checkpoint signals are initiated through two critical protein kinases: ataxia-telangiectasia mutated (ATM) and ATM-Rad3-related (ATR)[1,2]
Overall structure of symmetric Tel[1] dimer The endogenously purified S. cerevisiae Tel[1] displays basal kinase activity, which could be stimulated by incubation with specific activator Xrs[2], the homolog of human Nbs[1] (Supplementary information, Fig. S1)

Summary

Introduction

The genome is constantly under assault by environmental agents, such as exposure to irradiation, chemical agents and ultraviolet light (UV), as well as endogenous agents, such as free radicals generated during normal metabolic processes. Cells have evolved surveillance mechanisms that monitor genomic lesions and activate various DNA damage responses, including cell cycle arrest and transcriptional induction of DNA repair genes[1]. In eukaryotes, this surveillance mechanism is called the DNA damage checkpoint. The checkpoint signals are initiated through two critical protein kinases: ataxia-telangiectasia mutated (ATM) and ATM-Rad3-related (ATR)[1,2]. ATM and ATR, master regulators of the DNA damage response, are highly conserved among eukaryotes. Tel[1] and Mec[1] correspond to ATM and ATR, respectively[3]

Methods

Results

Conclusion