Ku (protein)

Ku is a protein that binds to DNA double-strand break ends and is required for the non-homologous end joining (NHEJ) pathway of DNA repair. Ku is evolutionarily conserved from bacteria to human. The ancestral bacterial Ku is a homodimer (two copies of the same protein bound to each other). [Doherty AJ, Jackson SP, Weller GR. Identification of bacterial homologues of the Ku DNA repair proteins. FEBS Lett. 2001 Jul 6;500(3):186-8. PMID 11445083.] Eukaryotic Ku is a heterodimer of two polypeptides, Ku70 and Ku80, so named because the molecular weight of the human Ku proteins is around 70 kDa and 80 kDa. The two Ku subunits form a basket-shaped structure that threads onto the DNA end. [Walker JR, Corpina RA, Goldberg J. Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. Nature. 2001 Aug 9;412(6847):607-14. PMID 11493912] Once bound, Ku can slide down the DNA strand, allowing more Ku molecules to thread onto the end. In higher eukaryotes, Ku forms a complex with the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) to form the full DNA-dependent protein kinase (DNA-PK). [Carter T, Vancurova I, Sun I, Lou W, DeLeon S. A DNA-activated protein kinase from HeLa cell nuclei. Mol Cell Biol. 1990 Dec;10(12):6460-71. PMID 2247066] Ku is thought to function as a molecular scaffold to which other proteins involved in NHEJ can bind.

Both subunits of Ku have been knocked out in mouse. These mice exhibit chromosomal instability, indicating that NHEJ is important for genome maintenance. [Difilippantonio MJ, Zhu J, Chen HT, Meffre E, Nussenzweig MC, Max EE, Ried T, Nussenzweig A. DNA repair protein Ku80 suppresses chromosomal aberrations and malignant transformation. Nature. 2000 Mar 30;404(6777):510-4. PMID 1076192] [Ferguson DO, Sekiguchi JM, Chang S, Frank KM, Gao Y, DePinho RA, Alt FW. The nonhomologous end-joining pathway of DNA repair is required for genomic stability and the suppression of translocations. Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6630-3. PMID 10823907]

In many organisms, Ku has additional functions at telomeres in addition to its role in DNA repair. [Boulton SJ, Jackson SP. 1998. Components of the Ku-dependent non-homologous endjoining pathway are involved in telomeric length maintenance and telomeric silencing. EMBO J. 17:1819–28 PMID 9501103]

Unresolved double stranded breaks (DSB) in DNA lead to chromosomal abnormalities and associated pathologies, like cancer. Through the many years of evolution, cells have survived because of 2 main repair pathways. NHEJ involving Ku, DNApk, and DNA ligase 4 complex, repairs the DSB with high fidelity at the site of damage, without needing the matching sequence. The other is called homologous recombination (HR) because it does involve the use of the homologous sequence of DNA. The multifunctional protein complex that initiates HR is composed of Mre11-Rad50-Nbs1 (MRN) which detects DSB, and activates the ATM checkpoint kinase. Recently it was shown that maintaining Mre11 endonuclease activity is important cell survival but does not impair MRN's ability to recruit the necessary downstream factors to complete repair [7] .

References

Reference 7:Cell, Vol 135, 97-109, 03 October 2008Mre11 Dimers Coordinate DNA End Bridging and Nuclease Processing in Double-Strand-Break RepairR. Scott Williams,1,3,6 Gabriel Moncalian,1,3,6,8 Jessica S. Williams,1 Yoshiki Yamada,1 Oliver Limbo,1 David S. Shin,1,3 Lynda M. Groocock,1 Dana Cahill,4 Chiharu Hitomi,1,3 Grant Guenther,1 Davide Moiani,1,3 James P. Carney,4,7 Paul Russell,1,2,∗ and John A. Tainer1,3,5,∗∗

Here is the abstract of the crystal structure of Ku heterodimer bound to DNA (ref. 2 link).

Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair.Walker JR, Corpina RA, Goldberg J.Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.The Ku heterodimer (Ku70 and Ku80 subunits) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. The crystal structure of the human Ku heterodimer was determined both alone and bound to a 55-nucleotide DNA element at 2.7 and 2.5 A resolution, respectively. Ku70 and Ku80 share a common topology and form a dyad-symmetrical molecule with a preformed ring that encircles duplex DNA. The binding site can cradle two full turns of DNA while encircling only the central 3-4 base pairs (bp). Ku makes no contacts with DNA bases and few with the sugar-phosphate backbone, but it fits sterically to major and minor groove contours so as to position the DNA helix in a defined path through the protein ring. These features seem well designed to structurally support broken DNA ends and to bring the DNA helix into phase across the junction during end processing and ligation.