Cryo-EM Structure of Nucleotide-Bound Tel1ATM Unravels the Molecular Basis of Inhibition and Structural Rationale for Disease-Associated Mutations

Abstract

Highlights d cryo-EM structure of Tel1 in complex with Mg 2+-AMP-PNP at 3.7 Å resolution d Key residues of the active site are in productive conformation for catalysis d PIKK regulatory domain insert (PRD-I) restricts peptide substrate access d Structural rational for mutations found in ataxiatelangiectasia and cancer

ATM-Deficient Cancers Provide New Opportunities for Precision Oncology

“…Apart from R337H/C, a hotspot mutation prevalent in colorectal cancer, other individual mutations are seen less frequently and their effects on ATM function is not known. Recently, three papers describe cryo-electron microscopy structures of Tel1, the well-conserved ATM homolog in lower eukaryotes, showing that ATM forms an autoinhibited dimer [78][79][80], providing insight into the conformational changes necessary for ATM activation. Three of these structures provide atomic models of the C-terminal kinase domain, and one, from a thermophilic fungus, also provides an atomic model of the majority of the N-terminal heat repeat domain in open and closed conformations.…”

“…These structures provide the molecular basis to begin to understand cancer-associated ATM mutations. Initial analyses predict many cancer-associated mutations in the kinase domain are likely to impact ATM activity or protein folding [78,79], and the equivalent residue to R337 appears to stabilize the packing of two helices in the N-terminal domain, with the R337C/H mutation possibly destabilizing this region of ATM [78]. The methods developed to purify wildtype ATM homologs pave the way for more comprehensive studies to test the effect of cancer-associated mutations on ATM activities and stability.…”

Structures and regulations of ATM and ATR, master kinases in genome integrity

“…This supports the role of the PRD in regulating kinase activity across PIKKs. Structural and sequence comparisons reveal that the PRD consists of highly conserved Ka9 and Ka10 helices, and a variable region (both in length and amino acid composition), which is referred to as the PRD-Insert [13 ] ( Figure 2g-k). ATR and Mec1 contain a minimal length of PRD-I (9 residues for Mec1, 16 residues for ATR) (Figure 2i-j), sufficient to connect Ka9 and Ka10 while ATM and Tel1 possess a conserved short helix and an unstructured loop totalling 50 and 43 residues, respectively (Figure 2g-h).…”

“…A mechanism for PRD-I eviction from the active site for the human ATM dimer has been suggested [11 ], which involves a 24 motion of one protomer that causes the PRD-I to become disordered. In Tel1, the PRD-I interacts with the long helical FLAP-BE domains of the adjacent protomer via charged residues [13 ]. Upon activator binding, movement between the two protomers due to conformational changes in FAT and kinase domains could cause PRD-I to be expelled from the active site through movement of the FLAP-BE from the adjacent protomer (Figure 3c).…”

“…The activation loop plays key roles in catalysis due to its dual roles in binding peptide-substrate, a second Mg 2+ via its DFG motif, and coordination of the catalytic loop [20,22,34]. In nucleotide-bound Tel1, the activation loop makes extensive interactions with the PRD-I [13 ]. In apo-Tel1, a positive correlation between the extent of disorder in the PRD-I and the structural flexibility of the activation loop is observed [12 ], suggesting that substrate access and active site remodelling might be coupled during activation (Figure 2).…”