Molecule of the Month: Non-Homologous End Joining Supercomplexes
Lethal double-strand breaks in the DNA genome are repaired by NHEJ
Essential DNA Repair
NHEJ In Action
Exploring the Structure
Ku Protein and DNA
Ku protein solves a tricky molecular challenge: how do you recognize a broken DNA strand? It does this using shape. DNA is a long strand and usually proteins need to wrap around it. Ku, on the other hand, is shaped like a closed ring, so DNA needs to thread through the hole in the middle. This is only possible at an end of the strand. The structure shown here (PDB ID 1jey) shows the heterodimer of Ku70 and Ku80 with a short piece of DNA threaded through the cavity inside. Several positively-charged lysine and arginine amino acids (white) line the cavity and interact with the DNA backbone. The blunt end of the DNA is in magenta. A short hairpin (yellow) was added to the DNA by the researchers to assist with the structure determination, forming a knuckle that locks the DNA in one place.
Topics for Further Discussion
- Search for “Artemis” or “polymerase mu” at the main RCSB site to explore some of the enzymes involved in NHEJ. For example, look at PDB ID 7sgl to see Artemis acting on a broken DNA end.
- Inhibitors that block NHEJ are being developed for use in cancer treatment. For example, look at PDB ID 7otw.
Related PDB-101 Resources
- Browse Cancer
- Browse Central Dogma
- 7nfc: Chaplin, A.K., Hardwick, S.W., Stavridi, A.K., Buehl, C.J., Goff, N.J., Ropars, V., Liang, S., De Oliveira, T.M., Chirgadze, D.Y., Meek, K., Charbonnier, J.B., Blundell, T.L. (2021) Cryo-EM of NHEJ supercomplexes provides insights into DNA repair. Mol Cell 81: 3400
- 7lsy: Chen, S., Lee, L., Naila, T., Fishbain, S., Wang, A., Tomkinson, A.E., Lees-Miller, S.P., He, Y. (2021) Structural basis of long-range to short-range synaptic transition in NHEJ. Nature 593: 294-298
- Zhao, B., Rothenberg, E., Ramsden, D.A., Lieber, M.R. (2020) The molecular basis and disease relevance of non-homologous DNA end joining. Nat Rev Mol Cell Biol 21, 765–781.
- Chang, H.Y.H., Pannunzio, N.R., Adachi, N., Lieber, M.R. (2017) Non-homologous DNA end joining and alternative pathways to double-strand break repair. Nat Rev Mol Cell Biol 18, 495-506.
- 3w1b: Ochi, T., Gu, X., Blundell, T.L. (2013) Structure of the catalytic region of DNA ligase IV in complex with an artemis fragment sheds light on double-strand break repair. Structure 21: 672-679
- 1jey: Walker, J.R., Corpina, R.A., Goldberg, J. (2001) Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. Nature 412: 607-614
July 2022, Gabriela Diaz-Figueroa, Michael Egozi, Syeda Jannath, Jasmine Maddy, David Goodselldoi:10.2210/rcsb_pdb/mom_2022_7