ATR-mediated activation of S-phase checkpoint
ATR is activated during every S-phase and in response to many different types of damage, including double strand breaks (DSB), base adducts, crosslinks and replication stress. The structural requirement for ATR activation is a RPA-coated single-stranded DNA with a 5 double stranded primer junction. ATR recognition of the above DNA structure depends upon a protein co-factor, ATRIP (ATR-interacting protein), that regulates ATR localization and activation. The activity of ATR-ATRIP complex is directly stimulated by TOPBP1 (DNA topoisomerase II binding protein 1), which recruitment to DNA is facilitated by the 9-1-1 (Rad9-Rad1-Hus1) checkpoint clamp.
Activated ATR signals to coordinate cell cycle transitions and repair through the phosphorylation of numerous of substrates including RAD17, p53, TopBP1 (via a feed-forward signalling loop that amplifies ATR-mediated signals), the mediator protein CEP164 and the downstream effector Chk1 (checkpoint kinase 1), which is the best characterized target of the ATR activity. Recombination proteins BRCA1 (breast cancer susceptibility gene 1), WRN (Werners syndrome helicase), and BLM (Blooms syndrome helicase) are ATR sunstrates as well. ATR also phosphorylates the Fanconi-anemia protein FANCD2 to regulate inter-strand crosslink repair as well as the nucleotide excision repair protein XPA to regulate its intracellular localization. Moreover, ATR interacts with the mismatch repair protein MSH2 (mutS homolog 2) to form a signalling module and regulate the phosphorylation of Chk1 and SMC1 (structure maintenance of chromosome 1). Upon replication stress ATR also phosphorylates the Ser-139 of H2AX/H2AFX, while is associated with the tyrosine kinase oncogene BCR-ABL after genotoxic stress.

ATR-mediated stabilization of replication forks
ATR has a crucial role in the maintenance of functional replication forks independent of its function in the activation of Rad53 (yeast homolog of checkpoint kinase 2). Among substrates of ATR on the replication forks are the proteins RPA1, RPA2, MCM2-7 (minichromosome maintenance 2-7) complex, MCM10, PCNA, replication factor C, Tim (Timeless)-Tipin complex, SMARCAL1 (HARP)-a SNF2 ATP-dependent annealing helicase, and several polymerases, such as Pol alpha and Pol epsilon. Furthermore, a key target of ATR-ATRIP complex is Claspin, and is important both for S-phase checkpoint activation (via regulation of Chk1 phosphorylation) but also for replication forks stabilization (via interactions with Pol epsilon) even in normal cycling cells. ATR is found also associated with two components of the nucleosome remodelling and deacetylating complex, the chromodomain-helicase-DNA-binding protein 4 (CHD4) and the histone-deacetylase-2 (HDAC2).
ATR also functions to stabilize fragile sites. In effect of all the above, the ATRs essential function for cell viability may be to respond to abundant sources of replication stress in normal cycling cells as well as after exposure to DNA damage agents.

ATR implication in centrosomal function via:
(a) Direct interaction with NBS1 (Nijmegen breakage syndrome 1) and BRCA1 pathway.
(b) Signalling to Chk1 and control of centrosome overduplication after DNA damage.
(c) Direct phosphorylation and delocalization from centrosome of CEP63 in the presence of chromosomal breaks.