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* Residue conservation analysis
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Enzyme class 2:
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Chains A, B:
E.C.3.6.4.-
- ?????
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Enzyme class 3:
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Chain A:
E.C.4.2.99.-
- ?????
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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DOI no:
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Nature
412:607-614
(2001)
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PubMed id:
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Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair.
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J.R.Walker,
R.A.Corpina,
J.Goldberg.
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ABSTRACT
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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.
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Selected figure(s)
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Figure 2.
Figure 2: Structure of the Ku-DNA complex. a, View down the
DNA helix. Ku70 is coloured red and Ku80 orange. Only the 14-bp
duplex portion of DNA is shown; the sugar-phosphate backbone is
coloured light grey and the bases dark grey. b, Side view. Black
line indicates the molecular dyad axis. Terminal base pairs are
numbered +8 (broken DNA end) and -6. c, Abbreviated topology
diagram showing the fold of Ku70 and Ku80. Green rods indicate
 -helices;
blue arrows indicate  -strands.
d, Stereo difference electron density map viewed down the
molecular dyad axis (white symbol). Blue contour lines show
electron density at the 2.4  -level
in a |F[o]| - |F[c]| (2.5 Å resolution) map calculated after
simulated-annealing refinement of a model lacking nucleotides
from levels -2 to +6 of the 34-residue oligonucleotide.
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Figure 4.
Figure 4: Surface depictions of Ku. a, Space-filling model
showing Ku bound to DNA. The model was prepared by fitting a
32-bp B DNA to the crystallographically observed duplex. DNA
extends towards the viewer to the +11 level. Ku70 is coloured
red and Ku80 orange. DNA is shown with one light grey and one
dark grey strand. b, Molecular surface representation of Ku is
coloured according to electrostatic potential, calculated using
the program GRASP44. Negative potential is coloured red and
positive potential blue.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2001,
412,
607-614)
copyright 2001.
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Figures were
selected
by the author.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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L.Feng,
and
J.Chen
(2012).
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A.G.Milbradt,
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R.E.Luna,
P.Selenko,
A.M.Näär,
and
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(2011).
Structure of the VP16 transactivator target in the Mediator.
|
| |
Nat Struct Mol Biol,
18,
410-415.
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PDB code:
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A.Shahi,
J.H.Lee,
Y.Kang,
S.H.Lee,
J.W.Hyun,
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and
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Mismatch-repair protein MSH6 is associated with Ku70 and regulates DNA double-strand break repair.
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Nucleic Acids Res,
39,
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and
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Structure and VP16 binding of the Mediator Med25 activator interaction domain.
|
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Nat Struct Mol Biol,
18,
404-409.
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PDB code:
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F.Bontems,
A.Verger,
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Z.Lens,
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and
D.Monté
(2011).
NMR structure of the human Mediator MED25 ACID domain.
|
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J Struct Biol,
174,
245-251.
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PDB code:
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K.Lammens,
D.J.Bemeleit,
C.Möckel,
E.Clausing,
A.Schele,
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and
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The Mre11:Rad50 structure shows an ATP-dependent molecular clamp in DNA double-strand break repair.
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Cell,
145,
54-66.
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PDB codes:
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K.Yano,
K.Morotomi-Yano,
K.J.Lee,
and
D.J.Chen
(2011).
Functional significance of the interaction with Ku in DNA double-strand break recognition of XLF.
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FEBS Lett,
585,
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L.Li,
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F.V.Rassool,
and
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Defective nonhomologous end joining blocks B-cell development in FLT3/ITD mice.
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Blood,
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3131-3139.
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S.Hu,
and
F.A.Cucinotta
(2011).
Modelling the way Ku binds DNA.
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Radiat Prot Dosimetry,
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C.C.Dvorak,
and
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Radiosensitive severe combined immunodeficiency disease.
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Immunol Allergy Clin North Am,
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C.Oberle,
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Regulation of the DNA Damage Response to DSBs by Post-Translational Modifications.
|
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Curr Genomics,
11,
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C.S.Cierniewski,
I.Papiewska-Pajak,
M.Malinowski,
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J.Kryczka,
T.Wysocki,
J.Niewiarowska,
and
R.Bednarek
(2010).
Thymosin beta4 regulates migration of colon cancer cells by a pathway involving interaction with Ku80.
|
| |
Ann N Y Acad Sci,
1194,
60-71.
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E.Y.Shim,
W.H.Chung,
M.L.Nicolette,
Y.Zhang,
M.Davis,
Z.Zhu,
T.T.Paull,
G.Ira,
and
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Saccharomyces cerevisiae Mre11/Rad50/Xrs2 and Ku proteins regulate association of Exo1 and Dna2 with DNA breaks.
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EMBO J,
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F.V.Rassool,
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Targeting abnormal DNA double strand break repair in cancer.
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Cell Mol Life Sci,
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F.Zafar,
S.B.Seidler,
A.Kronenberg,
D.Schild,
and
C.Wiese
(2010).
Homologous recombination contributes to the repair of DNA double-strand breaks induced by high-energy iron ions.
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Radiat Res,
173,
27-39.
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H.Wang,
X.Zhang,
P.Wang,
X.Yu,
J.Essers,
D.Chen,
R.Kanaar,
S.Takeda,
and
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(2010).
Characteristics of DNA-binding proteins determine the biological sensitivity to high-linear energy transfer radiation.
|
| |
Nucleic Acids Res,
38,
3245-3251.
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L.Tian,
G.Peng,
J.M.Parant,
V.Leventaki,
E.Drakos,
Q.Zhang,
J.Parker-Thornburg,
T.J.Shackleford,
H.Dai,
S.Y.Lin,
G.Lozano,
G.Z.Rassidakis,
and
F.X.Claret
(2010).
Essential roles of Jab1 in cell survival, spontaneous DNA damage and DNA repair.
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Oncogene,
29,
6125-6137.
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M.D.Vodenicharov,
N.Laterreur,
and
R.J.Wellinger
(2010).
Telomere capping in non-dividing yeast cells requires Yku and Rap1.
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EMBO J,
29,
3007-3019.
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M.Hammel,
Y.Yu,
B.L.Mahaney,
B.Cai,
R.Ye,
B.M.Phipps,
R.P.Rambo,
G.L.Hura,
M.Pelikan,
S.So,
R.M.Abolfath,
D.J.Chen,
S.P.Lees-Miller,
and
J.A.Tainer
(2010).
Ku and DNA-dependent protein kinase dynamic conformations and assembly regulate DNA binding and the initial non-homologous end joining complex.
|
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J Biol Chem,
285,
1414-1423.
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M.R.Lieber
(2010).
The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway.
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Annu Rev Biochem,
79,
181-211.
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M.R.Lieber,
J.Gu,
H.Lu,
N.Shimazaki,
and
A.G.Tsai
(2010).
Nonhomologous DNA end joining (NHEJ) and chromosomal translocations in humans.
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| |
Subcell Biochem,
50,
279-296.
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M.Tomita
(2010).
Involvement of DNA-PK and ATM in radiation- and heat-induced DNA damage recognition and apoptotic cell death.
|
| |
J Radiat Res (Tokyo),
51,
493-501.
|
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P.J.O'Donovan,
and
D.M.Livingston
(2010).
BRCA1 and BRCA2: breast/ovarian cancer susceptibility gene products and participants in DNA double-strand break repair.
|
| |
Carcinogenesis,
31,
961-967.
|
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|
S.A.Roberts,
N.Strande,
M.D.Burkhalter,
C.Strom,
J.M.Havener,
P.Hasty,
and
D.A.Ramsden
(2010).
Ku is a 5'-dRP/AP lyase that excises nucleotide damage near broken ends.
|
| |
Nature,
464,
1214-1217.
|
|
|
|
|
|
|
S.J.Orlando,
Y.Santiago,
R.C.DeKelver,
Y.Freyvert,
E.A.Boydston,
E.A.Moehle,
V.M.Choi,
S.M.Gopalan,
J.F.Lou,
J.Li,
J.C.Miller,
M.C.Holmes,
P.D.Gregory,
F.D.Urnov,
and
G.J.Cost
(2010).
Zinc-finger nuclease-driven targeted integration into mammalian genomes using donors with limited chromosomal homology.
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Nucleic Acids Res,
38,
e152.
|
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T.Ochi,
B.L.Sibanda,
Q.Wu,
D.Y.Chirgadze,
V.M.Bolanos-Garcia,
and
T.L.Blundell
(2010).
Structural biology of DNA repair: spatial organisation of the multicomponent complexes of nonhomologous end joining.
|
| |
J Nucleic Acids,
2010,
0.
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W.Y.Mansour,
T.Rhein,
and
J.Dahm-Daphi
(2010).
The alternative end-joining pathway for repair of DNA double-strand breaks requires PARP1 but is not dependent upon microhomologies.
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Nucleic Acids Res,
38,
6065-6077.
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Y.K.Choi,
K.Nash,
B.J.Byrne,
N.Muzyczka,
and
S.Song
(2010).
The effect of DNA-dependent protein kinase on adeno-associated virus replication.
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| |
PLoS One,
5,
e15073.
|
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Y.Zhang,
M.Gostissa,
D.G.Hildebrand,
M.S.Becker,
C.Boboila,
R.Chiarle,
S.Lewis,
and
F.W.Alt
(2010).
The role of mechanistic factors in promoting chromosomal translocations found in lymphoid and other cancers.
|
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Adv Immunol,
106,
93.
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A.J.Hartlerode,
and
R.Scully
(2009).
Mechanisms of double-strand break repair in somatic mammalian cells.
|
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Biochem J,
423,
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A.V.Mikelsaar,
A.Sünter,
P.Toomik,
K.Karpson,
and
E.Juronen
(2009).
New anti-Ku80 monoclonal antibody F10H2.B3 as a useful marker for dividing cells in culture.
|
| |
Hybridoma (Larchmt),
28,
107-111.
|
|
|
|
|
|
|
B.A.Fox,
J.G.Ristuccia,
J.P.Gigley,
and
D.J.Bzik
(2009).
Efficient gene replacements in Toxoplasma gondii strains deficient for nonhomologous end joining.
|
| |
Eukaryot Cell,
8,
520-529.
|
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B.L.Mahaney,
K.Meek,
and
S.P.Lees-Miller
(2009).
Repair of ionizing radiation-induced DNA double-strand breaks by non-homologous end-joining.
|
| |
Biochem J,
417,
639-650.
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C.A.Lovejoy,
and
D.Cortez
(2009).
Common mechanisms of PIKK regulation.
|
| |
DNA Repair (Amst),
8,
1004-1008.
|
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E.R.Guggenheim,
D.Xu,
C.X.Zhang,
P.V.Chang,
and
S.J.Lippard
(2009).
Photoaffinity isolation and identification of proteins in cancer cell extracts that bind to platinum-modified DNA.
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Chembiochem,
10,
141-157.
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E.Rampakakis,
and
M.Zannis-Hadjopoulos
(2009).
Transient dsDNA breaks during pre-replication complex assembly.
|
| |
Nucleic Acids Res,
37,
5714-5724.
|
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E.Riballo,
L.Woodbine,
T.Stiff,
S.A.Walker,
A.A.Goodarzi,
and
P.A.Jeggo
(2009).
XLF-Cernunnos promotes DNA ligase IV-XRCC4 re-adenylation following ligation.
|
| |
Nucleic Acids Res,
37,
482-492.
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E.Weterings,
N.S.Verkaik,
G.Keijzers,
B.I.Florea,
S.Y.Wang,
L.G.Ortega,
N.Uematsu,
D.J.Chen,
and
D.C.van Gent
(2009).
The Ku80 carboxy terminus stimulates joining and artemis-mediated processing of DNA ends.
|
| |
Mol Cell Biol,
29,
1134-1142.
|
|
|
|
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G.De Boeck,
R.G.Forsyth,
M.Praet,
and
P.C.Hogendoorn
(2009).
Telomere-associated proteins: cross-talk between telomere maintenance and telomere-lengthening mechanisms.
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J Pathol,
217,
327-344.
|
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G.Liti,
S.Haricharan,
F.A.Cubillos,
A.L.Tierney,
S.Sharp,
A.A.Bertuch,
L.Parts,
E.Bailes,
and
E.J.Louis
(2009).
Segregating YKU80 and TLC1 alleles underlying natural variation in telomere properties in wild yeast.
|
| |
PLoS Genet,
5,
e1000659.
|
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|
|
|
|
J.Zhuang,
G.Jiang,
H.Willers,
and
F.Xia
(2009).
Exonuclease function of human Mre11 promotes deletional nonhomologous end joining.
|
| |
J Biol Chem,
284,
30565-30573.
|
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|
|
K.M.Sinha,
M.S.Glickman,
and
S.Shuman
(2009).
Mutational analysis of Mycobacterium UvrD1 identifies functional groups required for ATP hydrolysis, DNA unwinding, and chemomechanical coupling.
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| |
Biochemistry,
48,
4019-4030.
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K.Yano,
K.Morotomi-Yano,
N.Adachi,
and
H.Akiyama
(2009).
Molecular mechanism of protein assembly on DNA double-strand breaks in the non-homologous end-joining pathway.
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| |
J Radiat Res (Tokyo),
50,
97.
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|
M.H.Huynh,
and
V.B.Carruthers
(2009).
Tagging of endogenous genes in a Toxoplasma gondii strain lacking Ku80.
|
| |
Eukaryot Cell,
8,
530-539.
|
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|
P.Jeggo,
and
M.F.Lavin
(2009).
Cellular radiosensitivity: how much better do we understand it?
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| |
Int J Radiat Biol,
85,
1061-1081.
|
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|
P.Soto,
and
L.C.Smith
(2009).
BH4 peptide derived from Bcl-xL and Bax-inhibitor peptide suppresses apoptotic mitochondrial changes in heat stressed bovine oocytes.
|
| |
Mol Reprod Dev,
76,
637-646.
|
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|
R.Suzuki,
H.Shindo,
A.Tase,
Y.Kikuchi,
M.Shimizu,
and
T.Yamazaki
(2009).
Solution structures and DNA binding properties of the N-terminal SAP domains of SUMO E3 ligases from Saccharomyces cerevisiae and Oryza sativa.
|
| |
Proteins,
75,
336-347.
|
|
|
PDB codes:
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|
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|
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S.M.Bennett,
T.M.Neher,
A.Shatilla,
and
J.J.Turchi
(2009).
Molecular analysis of Ku redox regulation.
|
| |
BMC Mol Biol,
10,
86.
|
|
|
|
|
|
|
T.J.Wu,
Y.H.Chiang,
Y.C.Lin,
C.R.Tsai,
T.Y.Yu,
M.T.Sung,
Y.H.Lee,
and
J.J.Lin
(2009).
Sequential Loading of Saccharomyces cerevisiae Ku and Cdc13p to Telomeres.
|
| |
J Biol Chem,
284,
12801-12808.
|
|
|
|
|
|
|
T.Miyoshi,
J.Kanoh,
and
F.Ishikawa
(2009).
Fission yeast Ku protein is required for recovery from DNA replication stress.
|
| |
Genes Cells,
14,
1091-1103.
|
|
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|
|
|
|
T.Yamada,
K.Makimura,
K.Satoh,
Y.Umeda,
Y.Ishihara,
and
S.Abe
(2009).
Agrobacterium tumefaciens-mediated transformation of the dermatophyte, Trichophyton mentagrophytes: an efficient tool for gene transfer.
|
| |
Med Mycol,
47,
485-494.
|
|
|
|
|
|
|
V.Gama,
J.A.Gomez,
L.D.Mayo,
M.W.Jackson,
D.Danielpour,
K.Song,
A.L.Haas,
M.J.Laughlin,
and
S.Matsuyama
(2009).
Hdm2 is a ubiquitin ligase of Ku70-Akt promotes cell survival by inhibiting Hdm2-dependent Ku70 destabilization.
|
| |
Cell Death Differ,
16,
758-769.
|
|
|
|
|
|
|
Y.Zhang,
E.Y.Shim,
M.Davis,
and
S.E.Lee
(2009).
Regulation of repair choice: Cdk1 suppresses recruitment of end joining factors at DNA breaks.
|
| |
DNA Repair (Amst),
8,
1235-1241.
|
|
|
|
|
|
|
A.Kulkarni,
and
D.M.Wilson
(2008).
The involvement of DNA-damage and -repair defects in neurological dysfunction.
|
| |
Am J Hum Genet,
82,
539-566.
|
|
|
|
|
|
|
B.Baños,
J.M.Lázaro,
L.Villar,
M.Salas,
and
M.de Vega
(2008).
Editing of misaligned 3'-termini by an intrinsic 3'-5' exonuclease activity residing in the PHP domain of a family X DNA polymerase.
|
| |
Nucleic Acids Res,
36,
5736-5749.
|
|
|
|
|
|
|
C.L.Vandre,
R.T.Kamakaka,
and
D.H.Rivier
(2008).
The DNA end-binding protein Ku regulates silencing at the internal HML and HMR loci in Saccharomyces cerevisiae.
|
| |
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Disruption of the Arabidopsis AtKu80 gene demonstrates an essential role for AtKu80 protein in efficient repair of DNA double-strand breaks in vivo.
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Plant J,
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The mechanism and regulation of chromosomal V(D)J recombination.
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Cell,
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Studies on the mode of Ku interaction with DNA.
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J Biol Chem,
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Regulation of osteocalcin gene expression by a novel Ku antigen transcription factor complex.
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J Biol Chem,
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G.Li,
C.Nelsen,
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Ku86 is essential in human somatic cells.
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Proc Natl Acad Sci U S A,
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Identification of a DNA nonhomologous end-joining complex in bacteria.
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Science,
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Mol Cell,
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Int J Biochem Cell Biol,
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J.M.Watson,
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Telomere length deregulation and enhanced sensitivity to genotoxic stress in Arabidopsis mutants deficient in Ku70.
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EMBO J,
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Conversion of phosphoglycolate to phosphate termini on 3' overhangs of DNA double strand breaks by the human tyrosyl-DNA phosphodiesterase hTdp1.
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Resistance of 3'-phosphoglycolate DNA ends to digestion by mammalian DNase III.
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Radiat Res,
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Specific interaction of IP6 with human Ku70/80, the DNA-binding subunit of DNA-PK.
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Synapsis of DNA ends by DNA-dependent protein kinase.
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DNA end-binding specificity of human Rad50/Mre11 is influenced by ATP.
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Ku heterodimer binds to both ends of the Werner protein and functional interaction occurs at the Werner N-terminus.
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BRCA1 facilitates microhomology-mediated end joining of DNA double strand breaks.
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J Biol Chem,
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Curr Biol,
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Ku DNA end-binding protein modulates homologous repair of double-strand breaks in mammalian cells.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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