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37  structures 1220  species 0  interactions 2244  sequences 72  architectures

Family: Ku_C (PF03730)

Summary: Ku70/Ku80 C-terminal arm

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This is the Wikipedia entry entitled "Ku (protein)". More...

Ku (protein) Edit Wikipedia article

X-ray repair
cross-complementing 5
Ku bound to DNA.png
Crystal structure of human Ku bound to DNA. Ku70 is shown in purple, Ku80 in blue, and the DNA strand in green.[1]
Alt. symbolsKu80
NCBI gene7520
Other data
LocusChr. 2 q35
X-ray repair
cross-complementing 6
Alt. symbolsKu70, G22P1
NCBI gene2547
Other data
LocusChr. 22 q11-q13
Ku70/Ku80 N-terminal alpha/beta domain
PDB 1jeq EBI.jpg
crystal structure of the ku heterodimer
Pfam clanCL0128
Ku70/Ku80 beta-barrel domain
PDB 1jey EBI.jpg
crystal structure of the ku heterodimer bound to dna
Ku70/Ku80 C-terminal arm
PDB 1jey EBI.jpg
crystal structure of the ku heterodimer bound to dna
Ku C terminal domain like
PDB 1q2z EBI.jpg
the 3d solution structure of the c-terminal region of ku86

Ku is a dimeric protein complex 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 humans. The ancestral bacterial Ku is a homodimer (two copies of the same protein bound to each other).[2] Eukaryotic Ku is a heterodimer of two polypeptides, Ku70 (XRCC6) and Ku80 (XRCC5), 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.[1] 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.[3] Ku is thought to function as a molecular scaffold to which other proteins involved in NHEJ can bind, orienting the double-strand break for ligation.

The Ku70 and Ku80 proteins consist of three structural domains. The N-terminal domain is an alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold.[4] The central domain of Ku70 and Ku80 is a DNA-binding beta-barrel domain. Ku makes only a few contacts with the sugar-phosphate backbone, and none with the DNA bases, but it fits sterically to major and minor groove contours forming a ring that encircles duplex DNA, cradling two full turns of the DNA molecule. By forming a bridge between the broken DNA ends, Ku acts to structurally support and align the DNA ends, to protect them from degradation, and to prevent promiscuous binding to unbroken DNA. Ku effectively aligns the DNA, while still allowing access of polymerases, nucleases and ligases to the broken DNA ends to promote end joining.[5] The C-terminal arm is an alpha helical region which embraces the central beta-barrel domain of the opposite subunit.[1] In some cases a fourth domain is present at the C-terminus, which binds to DNA-dependent protein kinase catalytic subunit.[6]

Both subunits of Ku have been experimentally knocked out in mice. These mice exhibit chromosomal instability, indicating that NHEJ is important for genome maintenance.[7][8]

In many organisms, Ku has additional functions at telomeres in addition to its role in DNA repair.[9]

Abundance of Ku80 seems to be related to species longevity.[10]


Mutant mice defective in Ku70, or Ku80, or double mutant mice deficient in both Ku70 and Ku80 exhibit early aging.[11] The mean lifespans of the three mutant mouse strains were similar to each other, at about 37 weeks, compared to 108 weeks for the wild-type control. Six specific signs of aging were examined, and the three mutant mice were found to display the same aging signs as the control mice, but at a much earlier age. Cancer incidence was not increased in the mutant mice. These results suggest that Ku function is important for longevity assurance and that the NHEJ pathway of DNA repair (mediated by Ku) has a key role in repairing DNA double-strand breaks that would otherwise cause early aging.[12] (Also see DNA damage theory of aging.)


Ku70 and Ku80 have also been experimentally characterized in plants, where they appear to play a similar role to that in other eukaryotes. In rice, suppression of either protein has been shown to promote homologous recombination (HR)[13] This effect was exploited to improve gene targeting (GT) efficiency in Arabidopsis thaliana. In the study, the frequency of HR-based GT using a zinc-finger nuclease (ZFN) was increased up to sixteen times in ku70 mutants[14] This result has promising implications for genome editing across eukaryotes as DSB repair mechanisms are highly conserved. A substantial difference is that in plants, Ku is also involved in maintaining an alternate telomere morphology characterized by blunt-ends or short (≤ 3-nt) 3’ overhangs.[15] This function is independent of the role of Ku in DSB repair, as removing the ability of the Ku complex to translocate along DNA has been shown to preserve blunt-ended telomeres while impeding DNA repair.[16]


The name 'Ku' is derived from the surname of the Japanese patient in which it was discovered.[17]


  1. ^ a b c PDB: 1JEY​; Walker JR, Corpina RA, Goldberg J (August 2001). "Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair". Nature. 412 (6847): 607–14. doi:10.1038/35088000. PMID 11493912.
  2. ^ Doherty AJ, Jackson SP, Weller GR (July 2001). "Identification of bacterial homologues of the Ku DNA repair proteins". FEBS Lett. 500 (3): 186–8. doi:10.1016/S0014-5793(01)02589-3. PMID 11445083.
  3. ^ Carter T, Vancurová I, Sun I, Lou W, DeLeon S (December 1990). "A DNA-activated protein kinase from HeLa cell nuclei". Mol. Cell. Biol. 10 (12): 6460–71. doi:10.1128/MCB.10.12.6460. PMC 362923. PMID 2247066.
  4. ^ Sugihara T, Wadhwa R, Kaul SC, Mitsui Y (April 1999). "A novel testis-specific metallothionein-like protein, tesmin, is an early marker of male germ cell differentiation". Genomics. 57 (1): 130–6. doi:10.1006/geno.1999.5756. PMID 10191092.
  5. ^ Aravind L, Koonin EV (August 2001). "Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system". Genome Res. 11 (8): 1365–74. doi:10.1101/gr.181001. PMC 311082. PMID 11483577.
  6. ^ Harris R, Esposito D, Sankar A, Maman JD, Hinks JA, Pearl LH, Driscoll PC (January 2004). "The 3D solution structure of the C-terminal region of Ku86 (Ku86CTR)". J. Mol. Biol. 335 (2): 573–82. doi:10.1016/j.jmb.2003.10.047. PMID 14672664.
  7. ^ Difilippantonio MJ, Zhu J, Chen HT, Meffre E, Nussenzweig MC, Max EE, Ried T, Nussenzweig A (March 2000). "DNA repair protein Ku80 suppresses chromosomal aberrations and malignant transformation". Nature. 404 (6777): 510–4. doi:10.1038/35006670. PMC 4721590. PMID 10761921.
  8. ^ Ferguson DO, Sekiguchi JM, Chang S, Frank KM, Gao Y, DePinho RA, Alt FW (June 2000). "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. 97 (12): 6630–3. doi:10.1073/pnas.110152897. PMC 18682. PMID 10823907.
  9. ^ Boulton SJ, Jackson SP (March 1998). "Components of the Ku-dependent non-homologous end-joining pathway are involved in telomeric length maintenance and telomeric silencing". EMBO J. 17 (6): 1819–28. doi:10.1093/emboj/17.6.1819. PMC 1170529. PMID 9501103.
  10. ^ Lorenzini A, Johnson FB, Oliver A, Tresini M, Smith JS, Hdeib M, Sell C, Cristofalo VJ, Stamato TD (Nov–Dec 2009). "Significant Correlation of Species Longevity with DNA Double Strand Break-Recognition but not with Telomere Length". Mech Ageing Dev. 130 (11–12): 784–92. doi:10.1016/j.mad.2009.10.004. PMC 2799038. PMID 19896964.
  11. ^ Li H, Vogel H, Holcomb VB, Gu Y, Hasty P (2007). "Deletion of Ku70, Ku80, or both causes early aging without substantially increased cancer". Mol. Cell. Biol. 27 (23): 8205–14. doi:10.1128/MCB.00785-07. PMC 2169178. PMID 17875923.
  12. ^ Bernstein H, Payne CM, Bernstein C, Garewal H, Dvorak K (2008). Cancer and aging as consequences of un-repaired DNA damage. In: New Research on DNA Damages (Editors: Honoka Kimura and Aoi Suzuki) Nova Science Publishers, Inc., New York, Chapter 1, pp. 1-47. open access, but read only ISBN 978-1604565812
  13. ^ Nishizawa-Yokoi A, Nonaka S, Saika H, Kwon YI, Osakabe K, Toki S (December 2012). "Suppression of Ku70/80 or Lig4 leads to decreased stable transformation and enhanced homologous recombination in rice". The New Phytologist. 196 (4): 1048–59. doi:10.1111/j.1469-8137.2012.04350.x. PMC 3532656. PMID 23050791.
  14. ^ Qi Y, Zhang Y, Zhang F, Baller JA, Cleland SC, Ryu Y, Starker CG, Voytas DF (March 2013). "Increasing frequencies of site-specific mutagenesis and gene targeting in Arabidopsis by manipulating DNA repair pathways". Genome Research. 23 (3): 547–54. doi:10.1101/gr.145557.112. PMC 3589543. PMID 23282329.
  15. ^ Kazda A, Zellinger B, Rössler M, Derboven E, Kusenda B, Riha K (August 2012). "Chromosome end protection by blunt-ended telomeres". Genes & Development. 26 (15): 1703–13. doi:10.1101/gad.194944.112. PMC 3418588. PMID 22810623.
  16. ^ Valuchova S, Fulnecek J, Prokop Z, Stolt-Bergner P, Janouskova E, Hofr C, Riha K (June 2017). "Protection of Arabidopsis Blunt-Ended Telomeres Is Mediated by a Physical Association with the Ku Heterodimer". The Plant Cell. 29 (6): 1533–1545. doi:10.1105/tpc.17.00064. PMC 5502450. PMID 28584163.
  17. ^ Dynan, W.S. & Yoo, S. (1998) Nucleic Acids Research, 26 (7): 1551-1559. doi: 10.1093/nar/26.7.1551
This article incorporates text from the public domain Pfam and InterPro: IPR005161
This article incorporates text from the public domain Pfam and InterPro: IPR006164
This article incorporates text from the public domain Pfam and InterPro: IPR005160
This article incorporates text from the public domain Pfam and InterPro: IPR014893

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Ku70/Ku80 C-terminal arm Provide feedback

The Ku heterodimer (composed of Ku70 P12956 and Ku80 P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the C terminal arm. This alpha helical region embraces the beta-barrel domain PF02735 of the opposite subunit [1].

Literature references

  1. Walker JR, Corpina RA, Goldberg J; , Nature 2001;412:607-614.: Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. PUBMED:11493912 EPMC:11493912

  2. Aravind L, Koonin EV; , Genome Res 2001;11:1365-1374.: Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system. PUBMED:11483577 EPMC:11483577

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005160

The Ku heterodimer (composed of Ku70 SWISSPROT and Ku80 SWISSPROT ) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the C-terminal arm. This alpha helical region embraces the beta-barrel domain INTERPRO of the opposite subunit [ PUBMED:11493912 ].

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Seed source: Bateman A
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 76
Number in full: 2244
Average length of the domain: 90.00 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 13.84 %

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HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.2 21.2
Trusted cut-off 21.2 21.2
Noise cut-off 21.1 21.1
Model length: 91
Family (HMM) version: 16
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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Ku_C domain has been found. There are 37 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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