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DNA binding protein
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PDB id
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1cdz
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Contents |
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* Residue conservation analysis
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PDB id:
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| Name: |
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DNA binding protein
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Title:
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Brct domain from DNA-repair protein xrcc1
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Structure:
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Protein (DNA-repair protein xrcc1). Chain: a. Fragment: c-terminal brct domain. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Biol. unit:
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Dimer (from
)
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Resolution:
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3.20Å
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R-factor:
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0.224
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R-free:
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0.266
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Authors:
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X.Zhang,S.Morera,P.Bates,P.Whitehead,A.Coffer,K.Hainbucher, R.Nash,M.Sternberg,T.Lindahl,P.Freemont
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Key ref:
|
 |
X.Zhang
et al.
(1998).
Structure of an XRCC1 BRCT domain: a new protein-protein interaction module.
Embo J,
17,
6404-6411.
PubMed id:
DOI:
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Date:
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04-Mar-99
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Release date:
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28-Feb-00
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PROCHECK
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Headers
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References
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P18887
(XRCC1_HUMAN) -
DNA repair protein XRCC1
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Seq: Struc:
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633 a.a.
96 a.a.*
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Key: |
 |
PfamA domain |
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Secondary structure |
 |
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CATH domain |
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*
PDB and UniProt seqs differ
at 1 residue position (black
cross)
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Gene Ontology (GO) functional annotation
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Cellular component
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intracellular
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1 term
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DOI no:
|
Embo J
17:6404-6411
(1998)
|
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PubMed id:
|
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|
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| |
|
Structure of an XRCC1 BRCT domain: a new protein-protein interaction module.
|
|
X.Zhang,
S.Moréra,
P.A.Bates,
P.C.Whitehead,
A.I.Coffer,
K.Hainbucher,
R.A.Nash,
M.J.Sternberg,
T.Lindahl,
P.S.Freemont.
|
|
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|
| |
ABSTRACT
|
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| |
|
The BRCT domain (BRCA1 C-terminus), first identified in the breast cancer
suppressor protein BRCA1, is an evolutionarily conserved protein-protein
interaction region of approximately 95 amino acids found in a large number of
proteins involved in DNA repair, recombination and cell cycle control. Here we
describe the first three-dimensional structure and fold of a BRCT domain
determined by X-ray crystallography at 3.2 A resolution. The structure has been
obtained from the C-terminal region of the human DNA repair protein XRCC1, and
comprises a four-stranded parallel beta-sheet surrounded by three alpha-helices,
which form an autonomously folded domain. The compact XRCC1 structure explains
the observed sequence homology between different BRCT motifs and provides a
framework for modelling other BRCT domains. Furthermore, the established
structure of an XRCC1 BRCT homodimer suggests potential protein-protein
interaction sites for the complementary BRCT domain in DNA ligase III, since
these two domains form a stable heterodimeric complex. Based on the XRCC1 BRCT
structure, we have constructed a model for the C-terminal BRCT domain of BRCA1,
which frequently is mutated in familial breast and ovarian cancer. The model
allows insights into the effects of such mutations on the fold of the BRCT
domain.
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Literature references that cite this PDB file's key reference
|
|
 |
| |
PubMed id
|
 |
Reference
|
 |
|
|
|
 |
M.Rappas,
A.W.Oliver,
and
L.H.Pearl
(2011).
Structure and function of the Rad9-binding region of the DNA-damage checkpoint adaptor TopBP1.
|
| |
Nucleic Acids Res, 39,
313-324.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
M.Kobayashi,
E.Ab,
A.M.Bonvin,
and
G.Siegal
(2010).
Structure of the DNA-bound BRCA1 C-terminal region from human replication factor C p140 and model of the protein-DNA complex.
|
| |
J Biol Chem, 285,
10087-10097.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
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.
|
| |
J Mol Biol, 395,
908-915.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
S.Sterpone,
and
R.Cozzi
(2010).
Influence of XRCC1 Genetic Polymorphisms on Ionizing Radiation-Induced DNA Damage and Repair.
|
| |
J Nucleic Acids, 2010,
0.
|
 |
|
|
|
|
 |
S.Sterpone,
V.Mastellone,
L.Padua,
F.Novelli,
C.Patrono,
T.Cornetta,
D.Giammarino,
V.Donato,
A.Testa,
and
R.Cozzi
(2010).
Single-nucleotide polymorphisms in BER and HRR genes, XRCC1 haplotypes and breast cancer risk in Caucasian women.
|
| |
J Cancer Res Clin Oncol, 136,
631-636.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
K.M.Applebaum,
M.D.McClean,
H.H.Nelson,
C.J.Marsit,
B.C.Christensen,
and
K.T.Kelsey
(2009).
Smoking modifies the relationship between XRCC1 haplotypes and HPV16-negative head and neck squamous cell carcinoma.
|
| |
Int J Cancer, 124,
2690-2696.
|
 |
|
|
|
|
 |
P.Kotoglou,
A.Kalaitzakis,
P.Vezyraki,
T.Tzavaras,
L.K.Michalis,
F.Dantzer,
J.U.Jung,
and
C.Angelidis
(2009).
Hsp70 translocates to the nuclei and nucleoli, binds to XRCC1 and PARP-1, and protects HeLa cells from single-strand DNA breaks.
|
| |
Cell Stress Chaperones, 14,
391-406.
|
 |
|
|
|
|
 |
X.Yang,
L.M.Figueiredo,
A.Espinal,
E.Okubo,
and
B.Li
(2009).
RAP1 is essential for silencing telomeric variant surface glycoprotein genes in Trypanosoma brucei.
|
| |
Cell, 137,
99.
|
 |
|
|
|
|
 |
A.Ghosh,
S.Shuman,
and
C.D.Lima
(2008).
The structure of Fcp1, an essential RNA polymerase II CTD phosphatase.
|
| |
Mol Cell, 32,
478-490.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
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.
|
| |
J Virol, 82,
8849-8862.
|
 |
|
|
|
|
 |
E.Weterings,
and
D.J.Chen
(2008).
The endless tale of non-homologous end-joining.
|
| |
Cell Res, 18,
114-124.
|
 |
|
|
|
|
 |
T.Ellenberger,
and
A.E.Tomkinson
(2008).
Eukaryotic DNA ligases: structural and functional insights.
|
| |
Annu Rev Biochem, 77,
313-338.
|
 |
|
|
|
|
 |
A.F.Moon,
M.Garcia-Diaz,
V.K.Batra,
W.A.Beard,
K.Bebenek,
T.A.Kunkel,
S.H.Wilson,
and
L.C.Pedersen
(2007).
The X family portrait: structural insights into biological functions of X family polymerases.
|
| |
DNA Repair (Amst), 6,
1709-1725.
|
 |
|
|
|
|
 |
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.
|
| |
Biochemistry, 46,
12100-12110.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
R.Monaco,
R.Rosal,
M.A.Dolan,
M.R.Pincus,
and
P.W.Brandt-Rauf
(2007).
Conformational effects of a common codon 399 polymorphism on the BRCT1 domain of the XRCC1 protein.
|
| |
Protein J, 26,
541-546.
|
 |
|
|
|
|
 |
S.Y.Kang,
K.G.Lee,
W.Lee,
J.Y.Shim,
S.I.Ji,
K.W.Chung,
Y.K.Chung,
and
N.K.Kim
(2007).
Polymorphisms in the DNA repair gene XRCC1 associated with basal cell carcinoma and squamous cell carcinoma of the skin in a Korean population.
|
| |
Cancer Sci, 98,
716-720.
|
 |
|
|
|
|
 |
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.
|
| |
Genetics, 173,
541-555.
|
 |
|
|
|
|
 |
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.
|
| |
BMC Mol Biol, 7,
40.
|
 |
|
|
|
|
 |
E.Becker,
V.Meyer,
H.Madaoui,
and
R.Guerois
(2006).
Detection of a tandem BRCT in Nbs1 and Xrs2 with functional implications in the DNA damage response.
|
| |
Bioinformatics, 22,
1289-1292.
|
 |
|
|
|
|
 |
H.Cartagena-Lirola,
A.Durán,
and
M.H.Valdivieso
(2006).
The Schizosaccharomyces pombe cfr1+ gene participates in mating through a new pathway that is independent of fus1+.
|
| |
Yeast, 23,
375-388.
|
 |
|
|
|
|
 |
J.K.Chin,
V.I.Bashkirov,
W.D.Heyer,
and
F.E.Romesberg
(2006).
Esc4/Rtt107 and the control of recombination during replication.
|
| |
DNA Repair (Amst), 5,
618-628.
|
 |
|
|
|
|
 |
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.
|
| |
J Biol Chem, 281,
4308-4317.
|
 |
|
|
|
|
 |
N.Puebla-Osorio,
D.B.Lacey,
F.W.Alt,
and
C.Zhu
(2006).
Early embryonic lethality due to targeted inactivation of DNA ligase III.
|
| |
Mol Cell Biol, 26,
3935-3941.
|
 |
|
|
|
|
 |
T.Takeuchi,
T.Ishidoh,
H.Iijima,
I.Kuriyama,
N.Shimazaki,
O.Koiwai,
K.Kuramochi,
S.Kobayashi,
F.Sugawara,
K.Sakaguchi,
H.Yoshida,
and
Y.Mizushina
(2006).
Structural relationship of curcumin derivatives binding to the BRCT domain of human DNA polymerase lambda.
|
| |
Genes Cells, 11,
223-235.
|
 |
|
|
|
|
 |
W.C.Ladiges
(2006).
Mouse models of XRCC1 DNA repair polymorphisms and cancer.
|
| |
Oncogene, 25,
1612-1619.
|
 |
|
|
|
|
 |
J.E.Kim,
D.D.Billadeau,
and
J.Chen
(2005).
The tandem BRCT domains of Ect2 are required for both negative and positive regulation of Ect2 in cytokinesis.
|
| |
J Biol Chem, 280,
5733-5739.
|
 |
|
|
|
|
 |
J.M.Daley,
P.L.Palmbos,
D.Wu,
and
T.E.Wilson
(2005).
Nonhomologous end joining in yeast.
|
| |
Annu Rev Genet, 39,
431-451.
|
 |
|
|
|
|
 |
P.Chacko,
B.Rajan,
T.Joseph,
B.S.Mathew,
and
M.R.Pillai
(2005).
Polymorphisms in DNA repair gene XRCC1 and increased genetic susceptibility to breast cancer.
|
| |
Breast Cancer Res Treat, 89,
15-21.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
J.Han,
S.E.Hankinson,
G.A.Colditz,
and
D.J.Hunter
(2004).
Genetic variation in XRCC1, sun exposure, and risk of skin cancer.
|
| |
Br J Cancer, 91,
1604-1609.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
Y.G.Wang,
C.Nnakwe,
W.S.Lane,
M.Modesti,
and
K.M.Frank
(2004).
Phosphorylation and regulation of DNA ligase IV stability by DNA-dependent protein kinase.
|
| |
J Biol Chem, 279,
37282-37290.
|
 |
|
|
|
|
 |
B.T.Ang,
E.Yap,
J.Lim,
W.L.Tan,
P.Y.Ng,
I.Ng,
and
T.T.Yeo
(2003).
Poly(adenosine diphosphate-ribose) polymerase expression in human traumatic brain injury.
|
| |
J Neurosurg, 99,
125-130.
|
 |
|
|
|
|
 |
K.Fujita,
N.Shimazaki,
Y.Ohta,
T.Kubota,
S.Ibe,
S.Toji,
K.Tamai,
S.Fujisaki,
T.Hayano,
and
O.Koiwai
(2003).
Terminal deoxynucleotidyltransferase forms a ternary complex with a novel chromatin remodeling protein with 82 kDa and core histone.
|
| |
Genes Cells, 8,
559-571.
|
 |
|
|
|
|
 |
K.W.Caldecott
(2003).
Cell signaling. The BRCT domain: signaling with friends?
|
| |
Science, 302,
579-580.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
M.Ueno,
T.Nakazaki,
Y.Akamatsu,
K.Watanabe,
K.Tomita,
H.D.Lindsay,
H.Shinagawa,
and
H.Iwasaki
(2003).
Molecular characterization of the Schizosaccharomyces pombe nbs1+ gene involved in DNA repair and telomere maintenance.
|
| |
Mol Cell Biol, 23,
6553-6563.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
R.S.Williams,
and
J.N.Glover
(2003).
Structural consequences of a cancer-causing BRCA1-BRCT missense mutation.
|
| |
J Biol Chem, 278,
2630-2635.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
S.Okano,
L.Lan,
K.W.Caldecott,
T.Mori,
and
A.Yasui
(2003).
Spatial and temporal cellular responses to single-strand breaks in human cells.
|
| |
Mol Cell Biol, 23,
3974-3981.
|
 |
|
|
|
|
 |
T.Haliloglu,
A.Kolinski,
and
J.Skolnick
(2003).
Use of residual dipolar couplings as restraints in ab initio protein structure prediction.
|
| |
Biopolymers, 70,
548-562.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
Y.Takayama,
Y.Kamimura,
M.Okawa,
S.Muramatsu,
A.Sugino,
and
H.Araki
(2003).
GINS, a novel multiprotein complex required for chromosomal DNA replication in budding yeast.
|
| |
Genes Dev, 17,
1153-1165.
|
 |
|
|
|
|
 |
Z.Deng,
C.Atanasiu,
J.S.Burg,
D.Broccoli,
and
P.M.Lieberman
(2003).
Telomere repeat binding factors TRF1, TRF2, and hRAP1 modulate replication of Epstein-Barr virus OriP.
|
| |
J Virol, 77,
11992-12001.
|
 |
|
|
|
|
 |
A.V.Veselovsky,
Y.D.Ivanov,
A.S.Ivanov,
A.I.Archakov,
P.Lewi,
and
P.Janssen
(2002).
Protein-protein interactions: mechanisms and modification by drugs.
|
| |
J Mol Recognit, 15,
405-422.
|
 |
|
|
|
|
 |
B.Wang,
S.Matsuoka,
P.B.Carpenter,
and
S.J.Elledge
(2002).
53BP1, a mediator of the DNA damage checkpoint.
|
| |
Science, 298,
1435-1438.
|
 |
|
|
|
|
 |
C.C.Adams,
J.Jakovljevic,
J.Roman,
P.Harnpicharnchai,
and
J.L.Woolford
(2002).
Saccharomyces cerevisiae nucleolar protein Nop7p is necessary for biogenesis of 60S ribosomal subunits.
|
| |
RNA, 8,
150-165.
|
 |
|
|
|
|
 |
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:
|
 |
|
|
|
|
|
 |
D.J.Derbyshire,
B.P.Basu,
T.Date,
K.Iwabuchi,
and
A.J.Doherty
(2002).
Purification, crystallization and preliminary X-ray analysis of the BRCT domains of human 53BP1 bound to the p53 tumour suppressor.
|
| |
Acta Crystallogr D Biol Crystallogr, 58,
1826-1829.
|
 |
|
|
|
|
 |
H.Wang,
and
S.J.Elledge
(2002).
Genetic and physical interactions between DPB11 and DDC1 in the yeast DNA damage response pathway.
|
| |
Genetics, 160,
1295-1304.
|
 |
|
|
|
|
 |
I.V.Martin,
and
S.A.MacNeill
(2002).
ATP-dependent DNA ligases.
|
| |
Genome Biol, 3,
REVIEWS3005.
|
 |
|
|
|
|
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PDB codes:
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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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