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PDBsum entry 1jnx
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Gene regulation
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PDB id
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1jnx
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.2.3.2.27
- RING-type E3 ubiquitin transferase.
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Reaction:
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S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N6- ubiquitinyl-[acceptor protein]-L-lysine
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DOI no:
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Nat Struct Biol
8:838-842
(2001)
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PubMed id:
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Crystal structure of the BRCT repeat region from the breast cancer-associated protein BRCA1.
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R.S.Williams,
R.Green,
J.N.Glover.
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ABSTRACT
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The C-terminal BRCT region of BRCA1 is essential for its DNA repair,
transcriptional regulation and tumor suppressor functions. Here we determine the
crystal structure of the BRCT domain of human BRCA1 at 2.5 A resolution. The
domain contains two BRCT repeats that adopt similar structures and are packed
together in a head-to-tail arrangement. Cancer-causing missense mutations occur
at the interface between the two repeats and destabilize the structure. The
manner by which the two BRCT repeats interact in BRCA1 may represent a general
mode of interaction between homologous domains within proteins that interact to
regulate the cellular response to DNA damage. The structure provides a basis to
predict the structural consequences of uncharacterized BRCA1 mutations.
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Selected figure(s)
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Figure 2.
Figure 2. The structure of the dual repeat BRCT domain of BRCA1.
a, A ribbons representation of the BRCT domain. The secondary
structure elements in the C-terminal BRCT repeat are labeled
'prime' to distinguish them from the corresponding secondary
structure elements in the N-terminal repeat. b, C  backbone
trace of the BRCA1 BRCT domain. The N-terminal BRCT repeat is
colored turquoise; the C-terminal repeat, gold; and the
inter-repeat linker, gray. The view is rotated 90° clockwise
from the view shown in (a). c, MAD-phased electron density at
2.9 Å resolution and contoured at 1.0  is
displayed for the inter-BRCT repeat interface. d, A stereo view
of a structural alignment of the N- and C-terminal BRCA1 BRCT
repeats and the C-terminal BRCT repeat from XRCC1 (ref. 10).
Least squares alignments were produced using O23.
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Figure 3.
Figure 3. The packing of BRCT repeats. a, Stereo view of the
interaction of three helices to form the core of the BRCT repeat
interface. b, An electrostatic surface representation of the
C-terminal BRCT repeat is displayed with a worm representation
of 2
from the N-terminal repeat. c, An electrostatic surface
representation of the N-terminal repeat is shown with a worm
representation of 1'
and 3'
from the C-terminal repeat. In (a -c), the N-terminal repeat is
colored turquoise; the C-terminal repeat, gold; and residues
that cause cancer when mutated, red. d, An amino acid sequence
alignment of the regions of BRCA1, 53BP1 and RAD9 that are
predicted to form BRCT -BRCT interfaces. Residues that
constitute this interface in BRCA1, as well as conserved
residues in h53BP1 and S. cerevisiae RAD9, are colored green.
Residues where cancer-causing missense mutations have been
identified are boxed in red.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(2001,
8,
838-842)
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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A.Aly,
and
S.Ganesan
(2011).
BRCA1, PARP, and 53BP1: conditional synthetic lethality and synthetic viability.
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J Mol Cell Biol,
3,
66-74.
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R.Naidu,
Y.C.Har,
and
N.A.Taib
(2011).
Genetic polymorphisms of TP53-binding protein 1 (TP53BP1) gene and association with breast cancer risk.
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APMIS,
119,
460-467.
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C.G.Murphy,
and
M.E.Moynahan
(2010).
BRCA gene structure and function in tumor suppression: a repair-centric perspective.
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Cancer J,
16,
39-47.
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J.S.Williams,
R.S.Williams,
C.L.Dovey,
G.Guenther,
J.A.Tainer,
and
P.Russell
(2010).
gammaH2A binds Brc1 to maintain genome integrity during S-phase.
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EMBO J,
29,
1136-1148.
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PDB codes:
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M.E.Moynahan,
and
M.Jasin
(2010).
Mitotic homologous recombination maintains genomic stability and suppresses tumorigenesis.
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Nat Rev Mol Cell Biol,
11,
196-207.
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M.W.Richards,
J.W.Leung,
S.M.Roe,
K.Li,
J.Chen,
and
R.Bayliss
(2010).
A pocket on the surface of the N-terminal BRCT domain of Mcph1 is required to prevent abnormal chromosome condensation.
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J Mol Biol,
395,
908-915.
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PDB code:
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P.J.Rowling,
R.Cook,
and
L.S.Itzhaki
(2010).
Toward classification of BRCA1 missense variants using a biophysical approach.
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J Biol Chem,
285,
20080-20087.
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S.J.Campbell,
R.A.Edwards,
and
J.N.Glover
(2010).
Comparison of the structures and peptide binding specificities of the BRCT domains of MDC1 and BRCA1.
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Structure,
18,
167-176.
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PDB codes:
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S.Millevoi,
S.Bernat,
D.Telly,
F.Fouque,
L.Gladieff,
G.Favre,
S.Vagner,
and
C.Toulas
(2010).
The c.5242C>A BRCA1 missense variant induces exon skipping by increasing splicing repressors binding.
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Breast Cancer Res Treat,
120,
391-399.
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A.De Nicolo,
E.Parisini,
Q.Zhong,
M.Dalla Palma,
K.A.Stoeckert,
S.M.Domchek,
K.L.Nathanson,
M.A.Caligo,
M.Vidal,
M.E.Cusick,
and
J.E.Garber
(2009).
Multimodal assessment of protein functional deficiency supports pathogenicity of BRCA1 p.V1688del.
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Cancer Res,
69,
7030-7037.
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H.Li,
M.Sekine,
S.Seng,
S.Avraham,
and
H.K.Avraham
(2009).
BRCA1 interacts with Smad3 and regulates Smad3-mediated TGF-beta signaling during oxidative stress responses.
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PLoS One,
4,
e7091.
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I.Drikos,
G.Nounesis,
and
C.E.Vorgias
(2009).
Characterization of cancer-linked BRCA1-BRCT missense variants and their interaction with phosphoprotein targets.
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Proteins,
77,
464-476.
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M.Carvalho,
M.A.Pino,
R.Karchin,
J.Beddor,
M.Godinho-Netto,
R.D.Mesquita,
R.S.Rodarte,
D.C.Vaz,
V.A.Monteiro,
S.Manoukian,
M.Colombo,
C.B.Ripamonti,
R.Rosenquist,
G.Suthers,
A.Borg,
P.Radice,
S.A.Grist,
A.N.Monteiro,
and
B.Billack
(2009).
Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1.
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Mutat Res,
660,
1.
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R.S.Williams,
G.E.Dodson,
O.Limbo,
Y.Yamada,
J.S.Williams,
G.Guenther,
S.Classen,
J.N.Glover,
H.Iwasaki,
P.Russell,
and
J.A.Tainer
(2009).
Nbs1 flexibly tethers Ctp1 and Mre11-Rad50 to coordinate DNA double-strand break processing and repair.
|
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Cell,
139,
87-99.
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PDB codes:
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A.Kumar,
W.S.Joo,
G.Meinke,
S.Moine,
E.N.Naumova,
and
P.A.Bullock
(2008).
Evidence for a structural relationship between BRCT domains and the helicase domains of the replication initiators encoded by the Polyomaviridae and Papillomaviridae families of DNA tumor viruses.
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J Virol,
82,
8849-8862.
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C.J.Oldfield,
J.Meng,
J.Y.Yang,
M.Q.Yang,
V.N.Uversky,
and
A.K.Dunker
(2008).
Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners.
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BMC Genomics,
9,
S1.
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L.Chen,
C.J.Nievera,
A.Y.Lee,
and
X.Wu
(2008).
Cell cycle-dependent complex formation of BRCA1.CtIP.MRN is important for DNA double-strand break repair.
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J Biol Chem,
283,
7713-7720.
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R.A.Edwards,
M.S.Lee,
S.E.Tsutakawa,
R.S.Williams,
J.A.Tainer,
and
J.N.Glover
(2008).
The BARD1 C-terminal domain structure and interactions with polyadenylation factor CstF-50.
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Biochemistry,
47,
11446-11456.
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R.A.Greenberg
(2008).
Recognition of DNA double strand breaks by the BRCA1 tumor suppressor network.
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Chromosoma,
117,
305-317.
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R.Naseem,
and
M.Webb
(2008).
Analysis of the DNA binding activity of BRCA1 and its modulation by the tumour suppressor p53.
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PLoS ONE,
3,
e2336.
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Y.Nominé,
M.V.Botuyan,
Z.Bajzer,
W.G.Owen,
A.J.Caride,
E.Wasielewski,
and
G.Mer
(2008).
Kinetic analysis of interaction of BRCA1 tandem breast cancer c-terminal domains with phosphorylated peptides reveals two binding conformations.
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Biochemistry,
47,
9866-9879.
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Y.Shen,
and
L.Tong
(2008).
Structural evidence for direct interactions between the BRCT domains of human BRCA1 and a phospho-peptide from human ACC1.
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Biochemistry,
47,
5767-5773.
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PDB code:
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C.A.Gough,
T.Gojobori,
and
T.Imanishi
(2007).
Cancer-related mutations in BRCA1-BRCT cause long-range structural changes in protein-protein binding sites: a molecular dynamics study.
|
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Proteins,
66,
69-86.
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E.F.DeRose,
M.W.Clarkson,
S.A.Gilmore,
C.J.Galban,
A.Tripathy,
J.M.Havener,
G.A.Mueller,
D.A.Ramsden,
R.E.London,
and
A.L.Lee
(2007).
Solution structure of polymerase mu's BRCT Domain reveals an element essential for its role in nonhomologous end joining.
|
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Biochemistry,
46,
12100-12110.
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PDB code:
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E.Kumaraswamy,
and
R.Shiekhattar
(2007).
Activation of BRCA1/BRCA2-associated helicase BACH1 is required for timely progression through S phase.
|
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Mol Cell Biol,
27,
6733-6741.
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M.Hölzel,
T.Grimm,
M.Rohrmoser,
A.Malamoussi,
T.Harasim,
A.Gruber-Eber,
E.Kremmer,
and
D.Eick
(2007).
The BRCT domain of mammalian Pes1 is crucial for nucleolar localization and rRNA processing.
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Nucleic Acids Res,
35,
789-800.
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P.Vasickova,
E.Machackova,
M.Lukesova,
J.Damborsky,
O.Horky,
H.Pavlu,
J.Kuklova,
V.Kosinova,
M.Navratilova,
and
L.Foretova
(2007).
High occurrence of BRCA1 intragenic rearrangements in hereditary breast and ovarian cancer syndrome in the Czech Republic.
|
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BMC Med Genet,
8,
32.
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R.S.Williams,
J.S.Williams,
and
J.A.Tainer
(2007).
Mre11-Rad50-Nbs1 is a keystone complex connecting DNA repair machinery, double-strand break signaling, and the chromatin template.
|
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Biochem Cell Biol,
85,
509-520.
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C.Gabrielse,
C.T.Miller,
K.H.McConnell,
A.DeWard,
C.A.Fox,
and
M.Weinreich
(2006).
A Dbf4p BRCA1 C-terminal-like domain required for the response to replication fork arrest in budding yeast.
|
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Genetics,
173,
541-555.
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D.C.Zappulla,
A.S.Maharaj,
J.J.Connelly,
R.A.Jockusch,
and
R.Sternglanz
(2006).
Rtt107/Esc4 binds silent chromatin and DNA repair proteins using different BRCT motifs.
|
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BMC Mol Biol,
7,
40.
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J.Liu,
Y.Pan,
B.Ma,
and
R.Nussinov
(2006).
"Similarity trap" in protein-protein interactions could be carcinogenic: simulations of p53 core domain complexed with 53BP1 and BRCA1 BRCT domains.
|
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Structure,
14,
1811-1821.
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J.N.Glover
(2006).
Insights into the molecular basis of human hereditary breast cancer from studies of the BRCA1 BRCT domain.
|
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Fam Cancer,
5,
89-93.
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M.Kobayashi,
F.Figaroa,
N.Meeuwenoord,
L.E.Jansen,
and
G.Siegal
(2006).
Characterization of the DNA binding and structural properties of the BRCT region of human replication factor C p140 subunit.
|
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J Biol Chem,
281,
4308-4317.
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P.K.Lovelock,
S.Healey,
W.Au,
E.Y.Sum,
A.Tesoriero,
E.M.Wong,
S.Hinson,
R.Brinkworth,
A.Bekessy,
O.Diez,
L.Izatt,
E.Solomon,
M.Jenkins,
H.Renard,
J.Hopper,
P.Waring,
S.V.Tavtigian,
D.Goldgar,
G.J.Lindeman,
J.E.Visvader,
F.J.Couch,
B.R.Henderson,
M.Southey,
G.Chenevix-Trench,
A.B.Spurdle,
and
M.A.Brown
(2006).
Genetic, functional, and histopathological evaluation of two C-terminal BRCA1 missense variants.
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J Med Genet,
43,
74-83.
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S.V.Tavtigian,
A.M.Deffenbaugh,
L.Yin,
T.Judkins,
T.Scholl,
P.B.Samollow,
D.de Silva,
A.Zharkikh,
and
A.Thomas
(2006).
Comprehensive statistical study of 452 BRCA1 missense substitutions with classification of eight recurrent substitutions as neutral.
|
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J Med Genet,
43,
295-305.
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S.V.Tavtigian,
P.B.Samollow,
D.de Silva,
and
A.Thomas
(2006).
An analysis of unclassified missense substitutions in human BRCA1.
|
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Fam Cancer,
5,
77-88.
|
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A.Feki,
C.E.Jefford,
P.Berardi,
J.Y.Wu,
L.Cartier,
K.H.Krause,
and
I.Irminger-Finger
(2005).
BARD1 induces apoptosis by catalysing phosphorylation of p53 by DNA-damage response kinase.
|
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Oncogene,
24,
3726-3736.
|
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C.M.Phelan,
V.Dapic,
B.Tice,
R.Favis,
E.Kwan,
F.Barany,
S.Manoukian,
P.Radice,
R.B.van der Luijt,
B.P.van Nesselrooij,
G.Chenevix-Trench,
kConFab,
T.Caldes,
M.de la Hoya,
S.Lindquist,
S.V.Tavtigian,
D.Goldgar,
A.Borg,
S.A.Narod,
and
A.N.Monteiro
(2005).
Classification of BRCA1 missense variants of unknown clinical significance.
|
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J Med Genet,
42,
138-146.
|
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C.Pettigrew,
N.Wayte,
P.K.Lovelock,
S.V.Tavtigian,
G.Chenevix-Trench,
A.B.Spurdle,
and
M.A.Brown
(2005).
Evolutionary conservation analysis increases the colocalization of predicted exonic splicing enhancers in the BRCA1 gene with missense sequence changes and in-frame deletions, but not polymorphisms.
|
| |
Breast Cancer Res,
7,
R929-R939.
|
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|
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F.J.Stevens,
C.Kuemmel,
G.Babnigg,
and
F.R.Collart
(2005).
Efficient recognition of protein fold at low sequence identity by conservative application of Psi-BLAST: application.
|
| |
J Mol Recognit,
18,
150-157.
|
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M.S.Lee,
R.A.Edwards,
G.L.Thede,
and
J.N.Glover
(2005).
Structure of the BRCT repeat domain of MDC1 and its specificity for the free COOH-terminal end of the gamma-H2AX histone tail.
|
| |
J Biol Chem,
280,
32053-32056.
|
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PDB code:
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|
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M.Stucki,
J.A.Clapperton,
D.Mohammad,
M.B.Yaffe,
S.J.Smerdon,
and
S.P.Jackson
(2005).
MDC1 directly binds phosphorylated histone H2AX to regulate cellular responses to DNA double-strand breaks.
|
| |
Cell,
123,
1213-1226.
|
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PDB code:
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P.T.Beernink,
M.Hwang,
M.Ramirez,
M.B.Murphy,
S.A.Doyle,
and
M.P.Thelen
(2005).
Specificity of protein interactions mediated by BRCT domains of the XRCC1 DNA repair protein.
|
| |
J Biol Chem,
280,
30206-30213.
|
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|
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|
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R.S.Williams,
N.Bernstein,
M.S.Lee,
M.L.Rakovszky,
D.Cui,
R.Green,
M.Weinfeld,
and
J.N.Glover
(2005).
Structural basis for phosphorylation-dependent signaling in the DNA-damage response.
|
| |
Biochem Cell Biol,
83,
721-727.
|
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V.N.Uversky,
C.J.Oldfield,
and
A.K.Dunker
(2005).
Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling.
|
| |
J Mol Recognit,
18,
343-384.
|
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W.W.Au,
and
B.R.Henderson
(2005).
The BRCA1 RING and BRCT domains cooperate in targeting BRCA1 to ionizing radiation-induced nuclear foci.
|
| |
J Biol Chem,
280,
6993-7001.
|
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A.Moisan,
C.Larochelle,
B.Guillemette,
and
L.Gaudreau
(2004).
BRCA1 can modulate RNA polymerase II carboxy-terminal domain phosphorylation levels.
|
| |
Mol Cell Biol,
24,
6947-6956.
|
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C.M.Ekblad,
A.Friedler,
D.Veprintsev,
R.L.Weinberg,
and
L.S.Itzhaki
(2004).
Comparison of BRCT domains of BRCA1 and 53BP1: a biophysical analysis.
|
| |
Protein Sci,
13,
617-625.
|
|
|
|
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|
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G.Charier,
J.Couprie,
B.Alpha-Bazin,
V.Meyer,
E.Quéméneur,
R.Guérois,
I.Callebaut,
B.Gilquin,
and
S.Zinn-Justin
(2004).
The Tudor tandem of 53BP1: a new structural motif involved in DNA and RG-rich peptide binding.
|
| |
Structure,
12,
1551-1562.
|
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PDB code:
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J.A.Clapperton,
I.A.Manke,
D.M.Lowery,
T.Ho,
L.F.Haire,
M.B.Yaffe,
and
S.J.Smerdon
(2004).
Structure and mechanism of BRCA1 BRCT domain recognition of phosphorylated BACH1 with implications for cancer.
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| |
Nat Struct Mol Biol,
11,
512-518.
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|
PDB code:
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J.N.Glover,
R.S.Williams,
and
M.S.Lee
(2004).
Interactions between BRCT repeats and phosphoproteins: tangled up in two.
|
| |
Trends Biochem Sci,
29,
579-585.
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L.L.Du,
B.A.Moser,
and
P.Russell
(2004).
Homo-oligomerization is the essential function of the tandem BRCT domains in the checkpoint protein Crb2.
|
| |
J Biol Chem,
279,
38409-38414.
|
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R.S.Williams,
M.S.Lee,
D.D.Hau,
and
J.N.Glover
(2004).
Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1.
|
| |
Nat Struct Mol Biol,
11,
519-525.
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|
PDB codes:
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E.M.Rosen,
S.Fan,
R.G.Pestell,
and
I.D.Goldberg
(2003).
BRCA1 gene in breast cancer.
|
| |
J Cell Physiol,
196,
19-41.
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I.A.Manke,
D.M.Lowery,
A.Nguyen,
and
M.B.Yaffe
(2003).
BRCT repeats as phosphopeptide-binding modules involved in protein targeting.
|
| |
Science,
302,
636-639.
|
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M.Rodriguez,
X.Yu,
J.Chen,
and
Z.Songyang
(2003).
Phosphopeptide binding specificities of BRCA1 COOH-terminal (BRCT) domains.
|
| |
J Biol Chem,
278,
52914-52918.
|
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|
|
N.Foray,
D.Marot,
A.Gabriel,
V.Randrianarison,
A.M.Carr,
M.Perricaudet,
A.Ashworth,
and
P.Jeggo
(2003).
A subset of ATM- and ATR-dependent phosphorylation events requires the BRCA1 protein.
|
| |
EMBO J,
22,
2860-2871.
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R.S.Williams,
D.I.Chasman,
D.D.Hau,
B.Hui,
A.Y.Lau,
and
J.N.Glover
(2003).
Detection of protein folding defects caused by BRCA1-BRCT truncation and missense mutations.
|
| |
J Biol Chem,
278,
53007-53016.
|
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R.S.Williams,
and
J.N.Glover
(2003).
Structural consequences of a cancer-causing BRCA1-BRCT missense mutation.
|
| |
J Biol Chem,
278,
2630-2635.
|
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|
PDB code:
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|
S.A.Krum,
G.A.Miranda,
C.Lin,
and
T.F.Lane
(2003).
BRCA1 associates with processive RNA polymerase II.
|
| |
J Biol Chem,
278,
52012-52020.
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S.Lafarge,
and
M.H.Montané
(2003).
Characterization of Arabidopsis thaliana ortholog of the human breast cancer susceptibility gene 1: AtBRCA1, strongly induced by gamma rays.
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| |
Nucleic Acids Res,
31,
1148-1155.
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|
X.Yu,
C.C.Chini,
M.He,
G.Mer,
and
J.Chen
(2003).
The BRCT domain is a phospho-protein binding domain.
|
| |
Science,
302,
639-642.
|
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|
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|
|
Y.L.Shang,
A.J.Bodero,
and
P.L.Chen
(2003).
NFBD1, a novel nuclear protein with signature motifs of FHA and BRCT, and an internal 41-amino acid repeat sequence, is an early participant in DNA damage response.
|
| |
J Biol Chem,
278,
6323-6329.
|
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|
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|
|
B.Wang,
S.Matsuoka,
P.B.Carpenter,
and
S.J.Elledge
(2002).
53BP1, a mediator of the DNA damage checkpoint.
|
| |
Science,
298,
1435-1438.
|
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D.C.Daniel
(2002).
Highlight: BRCA1 and BRCA2 proteins in breast cancer.
|
| |
Microsc Res Tech,
59,
68-83.
|
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|
D.J.Derbyshire,
B.P.Basu,
L.C.Serpell,
W.S.Joo,
T.Date,
K.Iwabuchi,
and
A.J.Doherty
(2002).
Crystal structure of human 53BP1 BRCT domains bound to p53 tumour suppressor.
|
| |
EMBO J,
21,
3863-3872.
|
|
|
PDB code:
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|
N.Foray,
D.Marot,
V.Randrianarison,
N.D.Venezia,
D.Picard,
M.Perricaudet,
V.Favaudon,
and
P.Jeggo
(2002).
Constitutive association of BRCA1 and c-Abl and its ATM-dependent disruption after irradiation.
|
| |
Mol Cell Biol,
22,
4020-4032.
|
|
|
|
|
|
|
W.S.Joo,
P.D.Jeffrey,
S.B.Cantor,
M.S.Finnin,
D.M.Livingston,
and
N.P.Pavletich
(2002).
Structure of the 53BP1 BRCT region bound to p53 and its comparison to the Brca1 BRCT structure.
|
| |
Genes Dev,
16,
583-593.
|
|
|
PDB codes:
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|
R.Baer
(2001).
With the ends in sight: images from the BRCA1 tumor suppressor.
|
| |
Nat Struct Biol,
8,
822-824.
|
|
|
|
|
|
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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|
Links
