DNA-dependent protein kinase

Two proteins are initially involved in the nonho-mologous rejoining of a ds break. Ku, a heterodimer of 70 kDa and 86 kDa subunits, binds to free DNA ends and has latent ATP-dependent helicase activity. The DNA-bound Ku heterodimer recruits a unique protein kinase, DNA-dependent protein kinase (DNA-PK). DNA-PK has a binding site for DNA free ends and another for dsDNA just inside these ends. It therefore allows for the approximation of the two separated ends. The free end DNA-Ku-DNA-PK complex activates the kinase activity in the latter. DNA-PK reciprocally phos-phorylates Ku and the other DNA-PK molecule, on the opposing strand, in trans. DNA-PK then dissociates from the DNA and Ku, resulting in activation of the Ku helicase. This results in unwinding of the two ends. The unwound, approximated DNA forms base pairs the extra nucleotide tails are removed by an exonucle-... 

Figure 36-25. Double-strand break repair of DNA. The proteins Ku and DNA-dependent protein kinase combine to approximate the two strands and unwind them. The aligned fragments form base pairs the extra ends are removed, probably by a DNA-PK-associated endo- or exonuclease, and the gaps are filled in and continuity is restored by ligation.

Ataxia telangiectasia mutated (ATM), poly(ADP ribose) polymerase (PARP), DNA-dependent protein kinase, DNA replication factor C, DNA topoisomerase I, DNA fragmentation factor (DFF)45, inhibitor of caspase-activated DNAse (ICAD), lamins A, Bl, and C TRAF-1, Rafl, Ras, GAP, GDP dissociation inhibitor of Rho family GTPases, phospholipase A2, Statl... 

Ku (subunit of PARP) Homo sapiens SKBR3 cell line chromosome condensation, subunit of DNA-dependent protein kinase PARP... 

Smith GC, Jackson SP (1999) The DNA-dependent protein kinase. Genes Dev 13(8) 916-934... 

SI39 (for mammals). The responsible kinases are members from phosphatidyli-nositol 3-kinase (PI3K)-like family kinases, which include ataxia telangiectasia mutated (ATM), AT-related (ATR), and DNA dependent protein kinase (DNA-PK) (Burma et al, 2001 Stiff et al, 2004 van Attikum and Gasser, 2005). Histone H2AX phosphorylation is directly related to repair of damaged chromatin (for details see chapter on Role of histone phosphorylation in chromatin dynamics and its implication in diseases ). 

Yumoto, Y., Shirakawa, H., Yoshida, M., Suwa, A., Watanabe, F, and Teraoka, H. (1998) High mobility group proteins 1 and 2 can function as DNA-binding regulatory components for DNA-dependent protein kinase in vitro. J. Biochem. 124, 519-527. 

G. C. Selective benzopyranone and pyrimido[2,l-a]isoquinolin-4-one inhibitors of DNA-dependent protein kinase synthesis, structure-activity studies, and radiosensitization of a... 

Ataxia telangiectasia is an autosomal recessive disease characterized by neurologic, endocrine, and hepatic abnormalities, as well as a predisposition to malignancy (119). The defect has been traced to a gene on chromosome 11, the ATM gene that codes for a phosphatidylinositol 3-kinase-like protein which is related to the catalytic subunit of DNA-dependent protein kinase. This protein has a role in signal transduction, DNA repair, and control of the cell cycle (120). Affected patients have a defect in cell-mediated immunity. A decrease in semm IgA is seen in a majority of affected patients. IgG2 or total IgG and IgE levels may be decreased, with an increase in IgM. Patients are susceptible to chronic respiratory... 

Hartley, K. O., Gell, D., Smith, G. C., et al., DNA-dependent protein kinase catalytic subunit A relative of phosphatidylinositol 3-kinase and the ataxia telangiectasia gene product. Cell 82, 849-856 (1995). 

D Silva, I., Pelletier, J.D., Lagueux, J., D Amours, D., Chaudhry, M.A., Weinfeld, M. etal. (1999) Relative affinities of poly(ADP-ribose) polymerase and DNA-dependent protein kinase for DNA strand interruptions. Biochim. Biophys. Acta., 1430, 119-126. 

Song, S., Laipis, P. J., Berns, K. I. and Flotte, T. R. (2001a). Effect of DNA-dependent protein kinase on the molecular fate of the rAAV2 genome in skeletal muscle. Proc. Natl. Acad. Sci. USA 98, 4084—4088. 

Chakravarthy BR, Walker T, Rasquinha I, Hill IE, MacManus JP. 1999. Activation of DNA-dependent protein kinase may play a role in apoptosis of human neuroblastoma cells. J... 

Chechlacz M, Vemuri MC, Naegele JR. 2001. Role of DNA-dependent protein kinase in neuronal survival. J Neurochem 78 141-154. 

Culmsee C, Bondada S, Mattson MP. 2001. Hippocampal neurons of mice deficient in DNA-dependent protein kinase exhibit increased vulnerability to DNA damage, oxidative stress and excitotoxicity. Mol Brain Res 87 ... 

Oka A, Takashima S, Abe M, Araki R, Takeshita K. 2000. Expression of DNA-dependent protein kinase catalytic subunit and Ku80 in developing human brains Implications of DNA-repair in neurogenesis. Neurosci Lett 292 167-170. Okabe S. 2007. Molecular anatomy of the postsynaptic density. Mol Cell Neurosci 34 503-518. 

Oyama S, Yamakawa H, Sasagawa N, Hosoi Y, Futai E, et al. 2009. Dysbindin-1, a schizophrenia-related protein, functionally interacts with the DNA-dependent protein kinase in an isoform-dependent manner. PLoS One 4, e4199. Padmakumar VC, Abraham S, Braune S, Noegel AA, Tunggal B, et al. 2004. Enaptin, a giant actin-binding protein, is an element of the nuclear membrane and the actin cytoskele-ton. Exp Cell Res 295 330-339. 

Woo RA, Jack MT, Xu Y, Burma S, Chen DJ, et al. 2002. DNA damage-induced apoptosis requires the DNA-dependent protein kinase, and is mediated by the latent population of P53. EMBO J 21 3000-3008. 

Rg. 13.8 When damaged DNA is sensed, the Mdm-2 proteins receive a signal from a DNA-dependent protein kinase. DNA[Pg.241]

Gottlieb TM, Jackson SP. The DNA-dependent protein kinase requirement for DNA ends and association with Ku antigen. Cell 1993 72(1) 131-142. 

Hammarsten O, DeFazio LG, Chu G. Activation of DNA-dependent protein kinase by single-stranded DNA ends. J. Biol Chem. 2000 275 1541-1550. 

Ma Y, Pannicke U, Schwarz K, Lieber MR. Hairpin opening and overhang processing by an Artemis/DNA-dependent protein kinase complex in nonhomologous end joining and V(D)J recombination. Cell. 2002 108 781-794. 

Celine Cano-Soumillac was born in Angouleme, France, in 1977. She studied Organic Chemistry at the University of Poitiers, France. In 1999, she went to Paris as a predoctoral fellow and worked on asymmetric synthesis of substituted piperazines from phenylglycinol derivatives, under the supervision of Prof. H.-P. Husson. In 2000, she moved back to Poitiers, where she worked on the synthesis of biomolecules by 1,3-dipolar cycloadditions with carbohydrates and received her Ph.D. degree in 2004. She then joined the group of Prof John A. Joule at the University of Manchester, UK as a postdoctoral fellow and worked on the synthesis of analogues of cofactors of oxomolybdoenzymes. She now holds a research associate position in the Northern Institute for Cancer Research, at Newcastle University, UK, where she works on the synthesis of inhibitors of DNA-dependent protein kinase. Her research interests include heterocyclic chemistry, carbohydrates chemistry, asymmetric synthesis, and development of new synthetic methodologies. 

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