Ku (protein)

Ku complex family
Identifiers
AliasesKu70:Ku80 heterodimerKu70:Ku80Ku Autoantigen
External IDsGeneCards: [1]; OMA:- orthologs
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

n/a

n/a

RefSeq (protein)

n/a

n/a

Location (UCSC)n/an/a
PubMed searchn/an/a
Wikidata
View/Edit Human
X-ray repair
cross-complementing 5
Crystal structure of human Ku bound to DNA. Ku70 is shown in purple, Ku80 in blue, and the DNA strand in green.[1]
Identifiers
SymbolXRCC5
Alt. symbolsKu80
NCBI gene7520
HGNC12833
OMIM194364
PDB1JEY
RefSeqNM_021141
UniProtP13010
Other data
LocusChr. 2 q35
Search for
StructuresSwiss-model
DomainsInterPro
X-ray repair
cross-complementing 6
Identifiers
SymbolXRCC6
Alt. symbolsKu70, G22P1
NCBI gene2547
HGNC4055
OMIM152690
PDB1JEY
RefSeqNM_001469
UniProtP12956
Other data
LocusChr. 22 q11-q13
Search for
StructuresSwiss-model
DomainsInterPro
Ku70/Ku80 N-terminal alpha/beta domain
crystal structure of the ku heterodimer
Identifiers
SymbolKu_N
PfamPF03731
Pfam clanCL0128
InterProIPR005161
SCOP21jey / SCOPe / SUPFAM
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary
Ku70/Ku80 beta-barrel domain
crystal structure of the ku heterodimer bound to dna
Identifiers
SymbolKu
PfamPF02735
InterProIPR006164
PROSITEPDOC00252
SCOP21jey / SCOPe / SUPFAM
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary
Ku70/Ku80 C-terminal arm
crystal structure of the ku heterodimer bound to dna
Identifiers
SymbolKu_C
PfamPF03730
InterProIPR005160
SCOP21jey / SCOPe / SUPFAM
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary
Ku C terminal domain like
the 3d solution structure of the c-terminal region of ku86
Identifiers
SymbolKu_PK_bind
PfamPF08785
InterProIPR014893
SCOP21q2z / SCOPe / SUPFAM
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary

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 Rossmann 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]

  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. Bibcode:2001Natur.412..607W. doi:10.1038/35088000. PMID 11493912. S2CID 4371575.
  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. S2CID 43588474.
  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. Bibcode:2000Natur.404..510D. 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. Bibcode:2000PNAS...97.6630F. 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.