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]
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.)
Plantsedit
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]
Bacteria and archaeaedit
Bacteria usually have only one Ku gene (if they have one at all). Unusually, Mesorhizobium loti has two, mlr9624 and mlr9623.[17]
Archaea usually also only have one Ku gene (for the ~4% of species that have one at all). The evolutionary history is blurred by extensive horizontal gene transfer with bacteria.[18]
Bacterial and archaeal Ku proteins are unlike their eukaryotic counterparts in that they only have the central beta-barrel domain.
Nameedit
The name 'Ku' is derived from the surname of the Japanese patient in which it was discovered.[19]
Referencesedit
^ abcPDB: 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.
^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.
^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. PMC362923. PMID 2247066.
^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.
^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. PMC311082. PMID 11483577.
^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.
^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. PMC4721590. PMID 10761921.
^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. PMC18682. PMID 10823907.
^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. PMC1170529. PMID 9501103.
^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. PMC2799038. PMID 19896964.
^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. PMC2169178. PMID 17875923.
^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. PMC3532656. PMID 23050791.
^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. PMC3589543. PMID 23282329.
^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. PMC3418588. PMID 22810623.
^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. PMC5502450. PMID 28584163.
^Pitcher RS, Brissett NC, Doherty AJ (2007). "Nonhomologous end-joining in bacteria: a microbial perspective". Annual Review of Microbiology. 61 (1). Annual Reviews: 259–82. doi:10.1146/annurev.micro.61.080706.093354. PMID 17506672.
^Sharda M, Badrinarayanan A, Seshasayee AS (December 2020). "Evolutionary and Comparative Analysis of Bacterial Nonhomologous End Joining Repair". Genome Biology and Evolution. 12 (12): 2450–2466. doi:10.1093/gbe/evaa223. PMC7719229. PMID 33078828.
^Dynan WS, Yoo S (April 1998). "Interaction of Ku protein and DNA-dependent protein kinase catalytic subunit with nucleic acids". Nucleic Acids Research. 26 (7): 1551–9. doi:10.1093/nar/26.7.1551. PMC147477. PMID 9512523.
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
External linksedit
April 11, 2024
protein, dimeric, protein, complex, that, binds, double, strand, break, ends, required, homologous, joining, nhej, pathway, repair, evolutionarily, conserved, from, bacteria, humans, ancestral, bacterial, homodimer, copies, same, protein, bound, each, other, e. 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 Ku complex familyIdentifiersAliasesKu70 Ku80 heterodimerKu70 Ku80Ku AutoantigenExternal IDsGeneCards 1 OrthologsSpeciesHumanMouseEntrezn an aEnsembln an aUniProtnan aRefSeq mRNA n an aRefSeq protein n an aLocation UCSC n an aPubMed searchn an aWikidataView Edit HumanX ray repaircross complementing 5Crystal structure of human Ku bound to DNA Ku70 is shown in purple Ku80 in blue and the DNA strand in green 1 IdentifiersSymbolXRCC5Alt symbolsKu80NCBI gene7520HGNC12833OMIM194364PDB1JEYRefSeqNM 021141UniProtP13010Other dataLocusChr 2 q35Search forStructuresSwiss modelDomainsInterProX ray repaircross complementing 6IdentifiersSymbolXRCC6Alt symbolsKu70 G22P1NCBI gene2547HGNC4055OMIM152690PDB1JEYRefSeqNM 001469UniProtP12956Other dataLocusChr 22 q11 q13Search forStructuresSwiss modelDomainsInterProKu70 Ku80 N terminal alpha beta domaincrystal structure of the ku heterodimerIdentifiersSymbolKu NPfamPF03731Pfam clanCL0128InterProIPR005161SCOP21jey SCOPe SUPFAMAvailable protein structures Pfam structures ECOD PDBRCSB PDB PDBe PDBjPDBsumstructure summaryKu70 Ku80 beta barrel domaincrystal structure of the ku heterodimer bound to dnaIdentifiersSymbolKuPfamPF02735InterProIPR006164PROSITEPDOC00252SCOP21jey SCOPe SUPFAMAvailable protein structures Pfam structures ECOD PDBRCSB PDB PDBe PDBjPDBsumstructure summaryKu70 Ku80 C terminal armcrystal structure of the ku heterodimer bound to dnaIdentifiersSymbolKu CPfamPF03730InterProIPR005160SCOP21jey SCOPe SUPFAMAvailable protein structures Pfam structures ECOD PDBRCSB PDB PDBe PDBjPDBsumstructure summaryKu C terminal domain likethe 3d solution structure of the c terminal region of ku86IdentifiersSymbolKu PK bindPfamPF08785InterProIPR014893SCOP21q2z SCOPe SUPFAMAvailable protein structures Pfam structures ECOD PDBRCSB PDB PDBe PDBjPDBsumstructure summaryThe 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 Contents 1 Aging 2 Plants 3 Bacteria and archaea 4 Name 5 References 6 External linksAging editMutant 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 Plants editKu70 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 Bacteria and archaea editBacteria usually have only one Ku gene if they have one at all Unusually Mesorhizobium loti has two mlr9624 and mlr9623 17 Archaea usually also only have one Ku gene for the 4 of species that have one at all The evolutionary history is blurred by extensive horizontal gene transfer with bacteria 18 Bacterial and archaeal Ku proteins are unlike their eukaryotic counterparts in that they only have the central beta barrel domain Name editThe name Ku is derived from the surname of the Japanese patient in which it was discovered 19 References edit 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 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 Carter T Vancurova 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 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 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 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 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 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 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 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 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 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 New York Chapter 1 pp 1 47 open access but read only https www novapublishers com catalog product info php products id 43247 Archived 2014 10 25 at the Wayback Machine ISBN 978 1604565812 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 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 Kazda A Zellinger B Rossler M Derboven E Kusenda B Riha K August 2012 Chromosome end protection by blunt ended telomeres Genes amp Development 26 15 1703 13 doi 10 1101 gad 194944 112 PMC 3418588 PMID 22810623 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 Pitcher RS Brissett NC Doherty AJ 2007 Nonhomologous end joining in bacteria a microbial perspective Annual Review of Microbiology 61 1 Annual Reviews 259 82 doi 10 1146 annurev micro 61 080706 093354 PMID 17506672 Sharda M Badrinarayanan A Seshasayee AS December 2020 Evolutionary and Comparative Analysis of Bacterial Nonhomologous End Joining Repair Genome Biology and Evolution 12 12 2450 2466 doi 10 1093 gbe evaa223 PMC 7719229 PMID 33078828 Dynan WS Yoo S April 1998 Interaction of Ku protein and DNA dependent protein kinase catalytic subunit with nucleic acids Nucleic Acids Research 26 7 1551 9 doi 10 1093 nar 26 7 1551 PMC 147477 PMID 9512523 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 IPR014893External links edit Retrieved from https en wikipedia org w index php title Ku protein amp oldid 1134211861, wikipedia, wiki, book, books, library,
