Molecule of the Month: ATM and ATR Kinases

As cells divide, they must ensure that their DNA is completely and accurately copied. Environmental dangers like UV radiation and toxic chemicals can damage DNA, and even normal cellular processes like DNA replication can have problems that lead to damage. Altogether, each cell has tens of thousands of sites of DNA damage every day. Failure to find and fix this DNA damage often leads to cancer. Our cells have checkpoints for recognizing broken DNA and pausing cell division until it is repaired. The protein kinases ATM (Ataxia-telangiectasia mutated) and ATR (Ataxia telangiectasia and Rad3-related protein) are crucial regulators of these DNA repair checkpoints. These proteins were identified while studying Ataxia telangiectasia, a complex neurodegenerative disease with immune system dysfunction, increased sensitivity to radiations, and predisposition to cancer. When DNA damage is identified, ATM and ATR work together to temporarily arrest the cell cycle and recruit proteins to repair it.

ATM and ATR notify the cell about different common types of DNA damage. While ATM focuses on double-strand breaks, which pose grave dangers to cells, ATR identifies single-stranded DNA, where a single unrepaired break may be enough to kill a cell. Single-stranded regions are normally formed during DNA replication, but if DNA polymerase stalls, helicases can continue unwinding the double helix, forming dangerously long single-stranded segments. Single-stranded DNA is also created at the ends of broken DNA during the process of repair, as the ends are trimmed before they are reconnected. When ATM and ATR find DNA damage, they phosphorylate and activate hundreds of proteins involved in management of the cell cycle and DNA repair. These include proteins such as p53 tumor suppressor and proteins such as RAD51 of the homologous recombination pathway, a high-fidelity DNA repair process that uses an intact copy of the chromosome to repair and restore the damaged chromosome.

The basis of ATM and ATR signaling is now being revealed by cryoelectron microscopy. The 3D structure of human ATM is seen in PDB ID 5np0 and that of ATR is seen in PDB ID 5yz0, bound to ATRIP, a protein that helps mediate the interaction of ATR with proteins that bind to single-stranded DNA. ATM and ATR are members of the same protein family and both form huge butterfly-shaped complexes with several functional parts. The kinase domains (shown here in magenta) perform the phosphorylation reaction. The rest of the protein has several domains that are thought to mediate interactions with both specific sensors of damaged DNA and with the diverse proteins that are activated by phosphorylation.

ATM and ATR are key messengers in the DNA damage response. They rely on other proteins to find and recognize damaged DNA. Two examples are included here: a complex of Mre11 and Rad50 (PDB ID 5dny and 5gox) binds to double-strand breaks, and replication protein A (RPA, PDB ID 4gnx) binds to single-stranded DNA. These proteins then interact with ATM and ATR respectively, activating their kinase domains and allowing them to activate, in turn, the many proteins downstream in the cell cycle and repair pathways.