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PDBsum entry 1qzh
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DNA binding protein/DNA
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PDB id
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1qzh
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Contents |
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* Residue conservation analysis
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PDB id:
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DNA binding protein/DNA
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Title:
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Crystal structure of pot1 (protection of telomere)- ssdna complex
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Structure:
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Telomeric single-stranded DNA. Chain: g, h, i, j, k, l. Engineered: yes. Protection of telomeres protein 1. Chain: a, b, c, d, e, f. Engineered: yes
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Source:
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Synthetic: yes. Schizosaccharomyces pombe. Fission yeast. Organism_taxid: 4896. Gene: pot1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
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Biol. unit:
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Dimer (from
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Resolution:
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2.40Å
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R-factor:
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0.249
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R-free:
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0.283
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Authors:
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M.Lei,E.R.Podell,P.Baumann,T.R.Cech
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Key ref:
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M.Lei
et al.
(2003).
DNA self-recognition in the structure of Pot1 bound to telomeric single-stranded DNA.
Nature,
426,
198-203.
PubMed id:
DOI:
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Date:
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16-Sep-03
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Release date:
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25-Nov-03
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PROCHECK
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Headers
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References
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O13988
(POT1_SCHPO) -
Protection of telomeres protein 1 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)
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Seq:
Struc:
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555 a.a.
170 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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G-G-T-T-A-C
6 bases
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G-G-T-T-A-C
6 bases
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G-G-T-T-A-C
6 bases
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G-G-T-T-A-C
6 bases
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G-G-T-T-A-C
6 bases
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G-G-T-T-A-C
6 bases
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DOI no:
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Nature
426:198-203
(2003)
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PubMed id:
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DNA self-recognition in the structure of Pot1 bound to telomeric single-stranded DNA.
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M.Lei,
E.R.Podell,
P.Baumann,
T.R.Cech.
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ABSTRACT
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Telomeres, specialized protein-DNA complexes that cap the ends of linear
chromosomes, are essential for protecting chromosomes from degradation and
end-to-end fusions. The Pot1 (protection of telomeres 1) protein is a widely
distributed eukaryotic end-capping protein, having been identified in fission
yeast, microsporidia, plants and animals. Schizosaccharomyces pombe Pot1p is
essential for telomere maintenance, and human POT1 has been implicated in
telomerase regulation. Pot1 binds telomeric single-stranded DNA (ssDNA) with
exceptionally high sequence specificity, the molecular basis of which has been
unknown. Here we describe the 1.9-A-resolution crystal structure of the
amino-terminal DNA-binding domain of S. pombe Pot1p complexed with ssDNA. The
protein adopts an oligonucleotide/oligosaccharide-binding (OB) fold with two
loops that protrude to form a clamp for ssDNA binding. The structure explains
the sequence specificity of binding: in the context of the Pot1 protein, DNA
self-recognition involving base-stacking and unusual G-T base pairs compacts the
DNA. Any sequence change disrupts the ability of the DNA to form this structure,
preventing it from contacting the array of protein hydrogen-bonding groups. The
structure also explains how Pot1p avoids binding the vast excess of RNA in the
nucleus.
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Selected figure(s)
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Figure 2.
Figure 2: Protein -ssDNA and ssDNA -ssDNA interactions in the
Pot1pN -GGTTAC complex. Potp1N is shown in blue, and the
ssDNA is coloured as in Fig. 1a. Protein -DNA intermolecular
hydrogen bonds are shown as dotted green lines, and ssDNA
intramolecular hydrogen bonds as dotted yellow lines. All panels
except e were generated using Molscript and Raster 3D (refs 28,
29). a, Stereoimage of the protein -ssDNA interactions. The
ssDNA is bound in a compact and folded conformation. b, c, ssDNA
self-recognition by G -T base-pairing interactions. The base
pairs are oriented such that all Watson -Crick donor/acceptor
groups of the bases face the inner side of the binding groove
and make extensive hydrogen-bonding interactions with the
protein. d, Interactions of the 3' end of the ssDNA. The
hydrogen bonds between A5 and the backbone phosphodiester groups
of T3 and T4 represent the second form of self-recognition. e,
Schematic representation of the Pot1pN -ssDNA interactions.
Bases of the DNA are shown as purple bars; phosphodiester groups
as yellow circles; sugar rings as cyan pentamers; and protein
residues as green boxes. Stacking and van der Waals interactions
between bases and protein are shown as blue arrows, and stacking
between bases as red arrows. Base-paring interactions of the
ssDNA are shown as red dashed lines.
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Figure 3.
Figure 3: Mutational analysis of residues important for Pot1pN
-ssDNA interaction. The protein is shown in blue and the DNA
in yellow. The mutated residues are shown in a ball-and-stick
model. Red, non-functional mutations T62V (0/84) and F88A
(0/156); green, functional mutations E13A (15/24), G47A
(88/160), I48T (62/148), T111V (24/48) and K153A (17/36). The
numbers in parentheses indicate the results of the
complementation analysis (number of isolates that lack wild-type
pot1^+ versus total number of isolates tested).
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2003,
426,
198-203)
copyright 2003.
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Figures were
selected
by an automated process.
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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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J.Nandakumar,
and
T.R.Cech
(2013).
Finding the end: recruitment of telomerase to telomeres.
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Nat Rev Mol Cell Biol,
14,
69-82.
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C.Cifuentes-Rojas,
K.Kannan,
L.Tseng,
and
D.E.Shippen
(2011).
Two RNA subunits and POT1a are components of Arabidopsis telomerase.
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Proc Natl Acad Sci U S A,
108,
73-78.
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J.Sun,
Y.Yang,
K.Wan,
N.Mao,
T.Y.Yu,
Y.C.Lin,
D.C.Dezwaan,
B.C.Freeman,
J.J.Lin,
N.F.Lue,
and
M.Lei
(2011).
Structural bases of dimerization of yeast telomere protein Cdc13 and its interaction with the catalytic subunit of DNA polymerase α.
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Cell Res,
21,
258-274.
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PDB codes:
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Y.Chen,
R.Rai,
Z.R.Zhou,
J.Kanoh,
C.Ribeyre,
Y.Yang,
H.Zheng,
P.Damay,
F.Wang,
H.Tsujii,
Y.Hiraoka,
D.Shore,
H.Y.Hu,
S.Chang,
and
M.Lei
(2011).
A conserved motif within RAP1 has diversified roles in telomere protection and regulation in different organisms.
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Nat Struct Mol Biol,
18,
213-221.
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PDB codes:
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D.Yang,
and
K.Okamoto
(2010).
Structural insights into G-quadruplexes: towards new anticancer drugs.
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Future Med Chem,
2,
619-646.
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F.Wang,
Y.Yang,
T.R.Singh,
V.Busygina,
R.Guo,
K.Wan,
W.Wang,
P.Sung,
A.R.Meetei,
and
M.Lei
(2010).
Crystal structures of RMI1 and RMI2, two OB-fold regulatory subunits of the BLM complex.
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Structure,
18,
1159-1170.
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PDB codes:
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J.Nandakumar,
E.R.Podell,
and
T.R.Cech
(2010).
How telomeric protein POT1 avoids RNA to achieve specificity for single-stranded DNA.
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Proc Natl Acad Sci U S A,
107,
651-656.
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PDB codes:
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R.L.Flynn,
and
L.Zou
(2010).
Oligonucleotide/oligosaccharide-binding fold proteins: a growing family of genome guardians.
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Crit Rev Biochem Mol Biol,
45,
266-275.
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X.Dai,
C.Huang,
A.Bhusari,
S.Sampathi,
K.Schubert,
and
W.Chai
(2010).
Molecular steps of G-overhang generation at human telomeres and its function in chromosome end protection.
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EMBO J,
29,
2788-2801.
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A.Ghosh,
M.L.Rossi,
J.Aulds,
D.Croteau,
and
V.A.Bohr
(2009).
Telomeric D-loops containing 8-oxo-2'-deoxyguanosine are preferred substrates for Werner and Bloom syndrome helicases and are bound by POT1.
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J Biol Chem,
284,
31074-31084.
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B.Meier,
L.J.Barber,
Y.Liu,
L.Shtessel,
S.J.Boulton,
A.Gartner,
and
S.Ahmed
(2009).
The MRT-1 nuclease is required for DNA crosslink repair and telomerase activity in vivo in Caenorhabditis elegans.
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EMBO J,
28,
3549-3563.
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B.R.Linger,
and
C.M.Price
(2009).
Conservation of telomere protein complexes: shuffling through evolution.
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Crit Rev Biochem Mol Biol,
44,
434-446.
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D.Lydall
(2009).
Taming the tiger by the tail: modulation of DNA damage responses by telomeres.
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EMBO J,
28,
2174-2187.
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E.V.Shakirov,
T.D.McKnight,
and
D.E.Shippen
(2009).
POT1-independent single-strand telomeric DNA binding activities in Brassicaceae.
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Plant J,
58,
1004-1015.
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E.V.Shakirov,
X.Song,
J.A.Joseph,
and
D.E.Shippen
(2009).
POT1 proteins in green algae and land plants: DNA-binding properties and evidence of co-evolution with telomeric DNA.
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Nucleic Acids Res,
37,
7455-7467.
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F.L.Meng,
Y.Hu,
N.Shen,
X.J.Tong,
J.Wang,
J.Ding,
and
J.Q.Zhou
(2009).
Sua5p a single-stranded telomeric DNA-binding protein facilitates telomere replication.
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EMBO J,
28,
1466-1478.
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H.He,
Y.Wang,
X.Guo,
S.Ramchandani,
J.Ma,
M.F.Shen,
D.A.Garcia,
Y.Deng,
A.S.Multani,
M.J.You,
and
S.Chang
(2009).
Pot1b deletion and telomerase haploinsufficiency in mice initiate an ATR-dependent DNA damage response and elicit phenotypes resembling dyskeratosis congenita.
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Mol Cell Biol,
29,
229-240.
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J.E.Croy,
S.E.Altschuler,
N.E.Grimm,
and
D.S.Wuttke
(2009).
Nonadditivity in the recognition of single-stranded DNA by the schizosaccharomyces pombe protection of telomeres 1 DNA-binding domain, Pot1-DBD.
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Biochemistry,
48,
6864-6875.
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J.Sun,
E.Y.Yu,
Y.Yang,
L.A.Confer,
S.H.Sun,
K.Wan,
N.F.Lue,
and
M.Lei
(2009).
Stn1-Ten1 is an Rpa2-Rpa3-like complex at telomeres.
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Genes Dev,
23,
2900-2914.
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PDB codes:
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R.E.Georgescu,
I.Kurth,
N.Y.Yao,
J.Stewart,
O.Yurieva,
and
M.O'Donnell
(2009).
Mechanism of polymerase collision release from sliding clamps on the lagging strand.
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EMBO J,
28,
2981-2991.
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Y.Li,
E.Bolderson,
R.Kumar,
P.A.Muniandy,
Y.Xue,
D.J.Richard,
M.Seidman,
T.K.Pandita,
K.K.Khanna,
and
W.Wang
(2009).
HSSB1 and hSSB2 form similar multiprotein complexes that participate in DNA damage response.
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J Biol Chem,
284,
23525-23531.
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A.M.Eldridge,
and
D.S.Wuttke
(2008).
Probing the mechanism of recognition of ssDNA by the Cdc13-DBD.
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Nucleic Acids Res,
36,
1624-1633.
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C.W.Pitt,
L.P.Valente,
D.Rhodes,
and
T.Simonsson
(2008).
Identification and characterization of an essential telomeric repeat binding factor in fission yeast.
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J Biol Chem,
283,
2693-2701.
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H.Xin,
D.Liu,
and
Z.Songyang
(2008).
The telosome/shelterin complex and its functions.
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Genome Biol,
9,
232.
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J.Dai,
M.Carver,
and
D.Yang
(2008).
Polymorphism of human telomeric quadruplex structures.
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Biochimie,
90,
1172-1183.
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J.Leonardi,
J.A.Box,
J.T.Bunch,
and
P.Baumann
(2008).
TER1, the RNA subunit of fission yeast telomerase.
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Nat Struct Mol Biol,
15,
26-33.
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K.Hekman,
K.Guja,
C.Larkin,
and
J.F.Schildbach
(2008).
An intrastrand three-DNA-base interaction is a key specificity determinant of F transfer initiation and of F TraI relaxase DNA recognition and cleavage.
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Nucleic Acids Res,
36,
4565-4572.
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K.Paeschke,
S.Juranek,
T.Simonsson,
A.Hempel,
D.Rhodes,
and
H.J.Lipps
(2008).
Telomerase recruitment by the telomere end binding protein-beta facilitates G-quadruplex DNA unfolding in ciliates.
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Nat Struct Mol Biol,
15,
598-604.
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T.Miyoshi,
J.Kanoh,
M.Saito,
and
F.Ishikawa
(2008).
Fission yeast Pot1-Tpp1 protects telomeres and regulates telomere length.
|
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Science,
320,
1341-1344.
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X.Song,
K.Leehy,
R.T.Warrington,
J.C.Lamb,
Y.V.Surovtseva,
and
D.E.Shippen
(2008).
STN1 protects chromosome ends in Arabidopsis thaliana.
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Proc Natl Acad Sci U S A,
105,
19815-19820.
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C.F.Chen,
and
S.J.Brill
(2007).
Binding and activation of DNA topoisomerase III by the Rmi1 subunit.
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J Biol Chem,
282,
28971-28979.
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D.J.Patel,
A.T.Phan,
and
V.Kuryavyi
(2007).
Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics.
|
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Nucleic Acids Res,
35,
7429-7455.
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H.Torigoe,
N.Dohmae,
F.Hanaoka,
and
A.Furukawa
(2007).
Mutational analyses of a single-stranded telomeric DNA binding domain of fission yeast pot1: conflict with X-ray crystallographic structure.
|
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Biosci Biotechnol Biochem,
71,
481-490.
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L.Oganesian,
and
T.M.Bryan
(2007).
Physiological relevance of telomeric G-quadruplex formation: a potential drug target.
|
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Bioessays,
29,
155-165.
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M.Matulić,
M.Sopta,
and
I.Rubelj
(2007).
Telomere dynamics: the means to an end.
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Cell Prolif,
40,
462-474.
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V.Martín,
L.L.Du,
S.Rozenzhak,
and
P.Russell
(2007).
Protection of telomeres by a conserved Stn1-Ten1 complex.
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Proc Natl Acad Sci U S A,
104,
14038-14043.
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Y.Xu,
R.Tashiro,
and
H.Sugiyama
(2007).
Photochemical determination of different DNA structures.
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Nat Protoc,
2,
78-87.
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A.Banerjee,
and
G.L.Verdine
(2006).
A nucleobase lesion remodels the interaction of its normal neighbor in a DNA glycosylase complex.
|
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Proc Natl Acad Sci U S A,
103,
15020-15025.
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PDB code:
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D.Churikov,
C.Wei,
and
C.M.Price
(2006).
Vertebrate POT1 restricts G-overhang length and prevents activation of a telomeric DNA damage checkpoint but is dispensable for overhang protection.
|
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Mol Cell Biol,
26,
6971-6982.
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H.He,
A.S.Multani,
W.Cosme-Blanco,
H.Tahara,
J.Ma,
S.Pathak,
Y.Deng,
and
S.Chang
(2006).
POT1b protects telomeres from end-to-end chromosomal fusions and aberrant homologous recombination.
|
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EMBO J,
25,
5180-5190.
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J.E.Croy,
and
D.S.Wuttke
(2006).
Themes in ssDNA recognition by telomere-end protection proteins.
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Trends Biochem Sci,
31,
516-525.
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L.Wu,
A.S.Multani,
H.He,
W.Cosme-Blanco,
Y.Deng,
J.M.Deng,
O.Bachilo,
S.Pathak,
H.Tahara,
S.M.Bailey,
Y.Deng,
R.R.Behringer,
and
S.Chang
(2006).
Pot1 deficiency initiates DNA damage checkpoint activation and aberrant homologous recombination at telomeres.
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Cell,
126,
49-62.
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N.Maizels
(2006).
Dynamic roles for G4 DNA in the biology of eukaryotic cells.
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Nat Struct Mol Biol,
13,
1055-1059.
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P.Buczek,
and
M.P.Horvath
(2006).
Thermodynamic characterization of binding Oxytricha nova single strand telomere DNA with the alpha protein N-terminal domain.
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J Mol Biol,
359,
1217-1234.
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T.Suzuki,
M.McKenzie,
E.Ott,
O.Ilkun,
and
M.P.Horvath
(2006).
DNA binding affinity and sequence permutation preference of the telomere protein from Euplotes crassus.
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Biochemistry,
45,
8628-8638.
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Y.Xu,
and
H.Sugiyama
(2006).
Photochemical approach to probing different DNA structures.
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| |
Angew Chem Int Ed Engl,
45,
1354-1362.
|
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C.Larkin,
S.Datta,
M.J.Harley,
B.J.Anderson,
A.Ebie,
V.Hargreaves,
and
J.F.Schildbach
(2005).
Inter- and intramolecular determinants of the specificity of single-stranded DNA binding and cleavage by the F factor relaxase.
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Structure,
13,
1533-1544.
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PDB code:
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D.L.Theobald,
and
D.S.Wuttke
(2005).
Divergent evolution within protein superfolds inferred from profile-based phylogenetics.
|
| |
J Mol Biol,
354,
722-737.
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E.V.Shakirov,
Y.V.Surovtseva,
N.Osbun,
and
D.E.Shippen
(2005).
The Arabidopsis Pot1 and Pot2 proteins function in telomere length homeostasis and chromosome end protection.
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Mol Cell Biol,
25,
7725-7733.
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J.Kao,
B.S.Rosenstein,
S.Peters,
M.T.Milano,
and
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Cellular response to DNA damage.
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Ann N Y Acad Sci,
1066,
243-258.
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J.T.Bunch,
N.S.Bae,
J.Leonardi,
and
P.Baumann
(2005).
Distinct requirements for Pot1 in limiting telomere length and maintaining chromosome stability.
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Mol Cell Biol,
25,
5567-5578.
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K.M.Trujillo,
J.T.Bunch,
and
P.Baumann
(2005).
Extended DNA binding site in Pot1 broadens sequence specificity to allow recognition of heterogeneous fission yeast telomeres.
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J Biol Chem,
280,
9119-9128.
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M.Brunori,
P.Luciano,
E.Gilson,
and
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The telomerase cycle: normal and pathological aspects.
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J Mol Med,
83,
244-257.
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M.Lei,
A.J.Zaug,
E.R.Podell,
and
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(2005).
Switching human telomerase on and off with hPOT1 protein in vitro.
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J Biol Chem,
280,
20449-20456.
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M.Nakamura,
A.Nabetani,
T.Mizuno,
F.Hanaoka,
and
F.Ishikawa
(2005).
Alterations of DNA and chromatin structures at telomeres and genetic instability in mouse cells defective in DNA polymerase alpha.
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Mol Cell Biol,
25,
11073-11088.
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P.Buczek,
R.S.Orr,
S.R.Pyper,
M.Shum,
E.Kimmel,
I.Ota,
S.E.Gerum,
and
M.P.Horvath
(2005).
Binding linkage in a telomere DNA-protein complex at the ends of Oxytricha nova chromosomes.
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| |
J Mol Biol,
350,
938-952.
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P.L.Opresko,
P.A.Mason,
E.R.Podell,
M.Lei,
I.D.Hickson,
T.R.Cech,
and
V.A.Bohr
(2005).
POT1 stimulates RecQ helicases WRN and BLM to unwind telomeric DNA substrates.
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| |
J Biol Chem,
280,
32069-32080.
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Q.Yang,
Y.L.Zheng,
and
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(2005).
POT1 and TRF2 cooperate to maintain telomeric integrity.
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Mol Cell Biol,
25,
1070-1080.
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T.Spreter,
M.Pech,
and
B.Beatrix
(2005).
The crystal structure of archaeal nascent polypeptide-associated complex (NAC) reveals a unique fold and the presence of a ubiquitin-associated domain.
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| |
J Biol Chem,
280,
15849-15854.
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PDB code:
|
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|
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|
|
T.T.Lee,
S.Agarwalla,
and
R.M.Stroud
(2005).
A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function.
|
| |
Cell,
120,
599-611.
|
|
|
PDB code:
|
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|
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|
|
Y.Enokizono,
Y.Konishi,
K.Nagata,
K.Ouhashi,
S.Uesugi,
F.Ishikawa,
and
M.Katahira
(2005).
Structure of hnRNP D complexed with single-stranded telomere DNA and unfolding of the quadruplex by heterogeneous nuclear ribonucleoprotein D.
|
| |
J Biol Chem,
280,
18862-18870.
|
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PDB codes:
|
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|
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|
|
A.Bochkarev,
and
E.Bochkareva
(2004).
From RPA to BRCA2: lessons from single-stranded DNA binding by the OB-fold.
|
| |
Curr Opin Struct Biol,
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36-42.
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C.Wei,
and
C.M.Price
(2004).
Cell cycle localization, dimerization, and binding domain architecture of the telomere protein cPot1.
|
| |
Mol Cell Biol,
24,
2091-2102.
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D.Liu,
A.Safari,
M.S.O'Connor,
D.W.Chan,
A.Laegeler,
J.Qin,
and
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(2004).
PTOP interacts with POT1 and regulates its localization to telomeres.
|
| |
Nat Cell Biol,
6,
673-680.
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J.C.Stern,
B.J.Anderson,
T.J.Owens,
and
J.F.Schildbach
(2004).
Energetics of the sequence-specific binding of single-stranded DNA by the F factor relaxase domain.
|
| |
J Biol Chem,
279,
29155-29159.
|
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|
|
|
J.H.Eastberg,
J.Pelletier,
and
B.L.Stoddard
(2004).
Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase.
|
| |
Nucleic Acids Res,
32,
653-660.
|
|
|
PDB codes:
|
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|
|
|
|
|
M.Lei,
E.R.Podell,
and
T.R.Cech
(2004).
Structure of human POT1 bound to telomeric single-stranded DNA provides a model for chromosome end-protection.
|
| |
Nat Struct Mol Biol,
11,
1223-1229.
|
|
|
PDB code:
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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
codes are
shown on the right.
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|
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