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PDBsum entry 1rxv
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Hydrolase/DNA
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PDB id
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1rxv
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* Residue conservation analysis
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PDB id:
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Hydrolase/DNA
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Title:
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Crystal structure of a. Fulgidus fen-1 bound to DNA
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Structure:
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5'-d( T Pa Pg Pc Pa Pt Pc Pg Pg). Chain: c, d. Engineered: yes. Flap structure-specific endonuclease. Chain: a, b. Engineered: yes
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Source:
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Synthetic: yes. Other_details: synthetic upstream primer DNA. Archaeoglobus fulgidus. Organism_taxid: 2234. Gene: fen, af0264. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
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Resolution:
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2.50Å
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R-factor:
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0.274
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R-free:
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0.309
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Authors:
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B.R.Chapados,D.J.Hosfield,S.Han,J.Qiu,B.Yelent,B.Shen,J.A.Tainer
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Key ref:
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B.R.Chapados
et al.
(2004).
Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair.
Cell,
116,
39-50.
PubMed id:
DOI:
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Date:
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18-Dec-03
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Release date:
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27-Jan-04
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PROCHECK
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Headers
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References
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O29975
(FEN_ARCFU) -
Flap endonuclease 1 from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)
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Seq:
Struc:
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336 a.a.
305 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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DOI no:
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Cell
116:39-50
(2004)
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PubMed id:
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Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair.
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B.R.Chapados,
D.J.Hosfield,
S.Han,
J.Qiu,
B.Yelent,
B.Shen,
J.A.Tainer.
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ABSTRACT
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Flap EndoNuclease-1 (FEN-1) and the processivity factor proliferating cell
nuclear antigen (PCNA) are central to DNA replication and repair. To clarify the
molecular basis of FEN-1 specificity and PCNA activation, we report here
structures of FEN-1:DNA and PCNA:FEN-1-peptide complexes, along with
fluorescence resonance energy transfer (FRET) and mutational results. FEN-1
binds the unpaired 3' DNA end (3' flap), opens and kinks the DNA, and promotes
conformational closing of a flexible helical clamp to facilitate 5' cleavage
specificity. Ordering of unstructured C-terminal regions in FEN-1 and PCNA
creates an intermolecular beta sheet interface that directly links adjacent PCNA
and DNA binding regions of FEN-1 and suggests how PCNA stimulates FEN-1
activity. The DNA and protein conformational changes, composite complex
structures, FRET, and mutational results support enzyme-PCNA alignments and a
kinked DNA pivot point that appear suitable to coordinate rotary handoffs of
kinked DNA intermediates among enzymes localized by the three PCNA binding sites.
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Selected figure(s)
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Figure 1.
Figure 1. FEN-1 3# Flap Recognition and Substrate Specificity
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Figure 5.
Figure 5. # Zipper Formation at the FEN-1:PCNA Binding Interface and PCNA Stimulation of FEN-1 Activity
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The above figures are
reprinted
by permission from Cell Press:
Cell
(2004,
116,
39-50)
copyright 2004.
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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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A.De Biasio,
R.Sánchez,
J.Prieto,
M.Villate,
R.Campos-Olivas,
and
F.J.Blanco
(2011).
Reduced Stability and Increased Dynamics in the Human Proliferating Cell Nuclear Antigen (PCNA) Relative to the Yeast Homolog.
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PLoS One,
6,
e16600.
|
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|
|
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C.Creze,
R.Lestini,
J.Kühn,
A.Ligabue,
H.F.Becker,
M.Czjzek,
D.Flament,
and
H.Myllykallio
(2011).
Structure and function of a novel endonuclease acting on branched DNA substrates.
|
| |
Biochem Soc Trans,
39,
145-149.
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|
|
|
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D.Bubeck,
M.A.Reijns,
S.C.Graham,
K.R.Astell,
E.Y.Jones,
and
A.P.Jackson
(2011).
PCNA directs type 2 RNase H activity on DNA replication and repair substrates.
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| |
Nucleic Acids Res,
39,
3652-3666.
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PDB codes:
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D.Dorjsuren,
D.Kim,
D.J.Maloney,
D.M.Wilson,
and
A.Simeonov
(2011).
Complementary non-radioactive assays for investigation of human flap endonuclease 1 activity.
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| |
Nucleic Acids Res,
39,
e11.
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|
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J.E.Ladner,
M.Pan,
J.Hurwitz,
and
Z.Kelman
(2011).
Crystal structures of two active proliferating cell nuclear antigens (PCNAs) encoded by Thermococcus kodakaraensis.
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Proc Natl Acad Sci U S A,
108,
2711-2716.
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PDB codes:
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J.G.Glanzer,
S.Liu,
and
G.G.Oakley
(2011).
Small molecule inhibitor of the RPA70 N-terminal protein interaction domain discovered using in silico and in vitro methods.
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| |
Bioorg Med Chem,
19,
2589-2595.
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J.Orans,
E.A.McSweeney,
R.R.Iyer,
M.A.Hast,
H.W.Hellinga,
P.Modrich,
and
L.S.Beese
(2011).
Structures of human exonuclease 1 DNA complexes suggest a unified mechanism for nuclease family.
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Cell,
145,
212-223.
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PDB codes:
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L.Zheng,
and
B.Shen
(2011).
Okazaki fragment maturation: nucleases take centre stage.
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J Mol Cell Biol,
3,
23-30.
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L.Zheng,
J.Jia,
L.D.Finger,
Z.Guo,
C.Zer,
and
B.Shen
(2011).
Functional regulation of FEN1 nuclease and its link to cancer.
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| |
Nucleic Acids Res,
39,
781-794.
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M.Pan,
L.M.Kelman,
and
Z.Kelman
(2011).
The archaeal PCNA proteins.
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Biochem Soc Trans,
39,
20-24.
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|
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R.S.Williams,
and
T.A.Kunkel
(2011).
FEN nucleases: bind, bend, fray, cut.
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Cell,
145,
171-172.
|
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|
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|
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S.A.MacNeill
(2011).
Protein-protein interactions in the archaeal core replisome.
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| |
Biochem Soc Trans,
39,
163-168.
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|
|
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|
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S.E.Tsutakawa,
S.Classen,
B.R.Chapados,
A.S.Arvai,
L.D.Finger,
G.Guenther,
C.G.Tomlinson,
P.Thompson,
A.H.Sarker,
B.Shen,
P.K.Cooper,
J.A.Grasby,
and
J.A.Tainer
(2011).
Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily.
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| |
Cell,
145,
198-211.
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PDB codes:
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T.R.Beattie,
and
S.D.Bell
(2011).
The role of the DNA sliding clamp in Okazaki fragment maturation in archaea and eukaryotes.
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| |
Biochem Soc Trans,
39,
70-76.
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|
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W.Yang
(2011).
Nucleases: diversity of structure, function and mechanism.
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| |
Q Rev Biophys,
44,
1.
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D.I.Pretto,
S.Tsutakawa,
C.A.Brosey,
A.Castillo,
M.E.Chagot,
J.A.Smith,
J.A.Tainer,
and
W.J.Chazin
(2010).
Structural dynamics and single-stranded DNA binding activity of the three N-terminal domains of the large subunit of replication protein A from small angle X-ray scattering.
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Biochemistry,
49,
2880-2889.
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H.Masai,
T.Tanaka,
and
D.Kohda
(2010).
Stalled replication forks: making ends meet for recognition and stabilization.
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Bioessays,
32,
687-697.
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J.A.Stewart,
J.L.Campbell,
and
R.A.Bambara
(2010).
Dna2 is a structure-specific nuclease, with affinity for 5'-flap intermediates.
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| |
Nucleic Acids Res,
38,
920-930.
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J.A.Tainer,
J.A.McCammon,
and
I.Ivanov
(2010).
Recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading.
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| |
J Am Chem Soc,
132,
7372-7378.
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J.L.Tubbs,
and
J.A.Tainer
(2010).
Alkyltransferase-like proteins: molecular switches between DNA repair pathways.
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| |
Cell Mol Life Sci,
67,
3749-3762.
|
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R.D.Hutton,
T.D.Craggs,
M.F.White,
and
J.C.Penedo
(2010).
PCNA and XPF cooperate to distort DNA substrates.
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| |
Nucleic Acids Res,
38,
1664-1675.
|
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|
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Y.Fridman,
N.Palgi,
D.Dovrat,
S.Ben-Aroya,
P.Hieter,
and
A.Aharoni
(2010).
Subtle alterations in PCNA-partner interactions severely impair DNA replication and repair.
|
| |
PLoS Biol,
8,
e1000507.
|
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|
|
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|
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A.López Castel,
A.E.Tomkinson,
and
C.E.Pearson
(2009).
CTG/CAG repeat instability is modulated by the levels of human DNA ligase I and its interaction with proliferating cell nuclear antigen: a distinction between replication and slipped-DNA repair.
|
| |
J Biol Chem,
284,
26631-26645.
|
|
|
|
|
|
|
A.S.Doré,
M.L.Kilkenny,
N.J.Rzechorzek,
and
L.H.Pearl
(2009).
Crystal structure of the rad9-rad1-hus1 DNA damage checkpoint complex--implications for clamp loading and regulation.
|
| |
Mol Cell,
34,
735-745.
|
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PDB code:
|
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|
|
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|
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B.Ren,
J.Kühn,
L.Meslet-Cladiere,
J.Briffotaux,
C.Norais,
R.Lavigne,
D.Flament,
R.Ladenstein,
and
H.Myllykallio
(2009).
Structure and function of a novel endonuclease acting on branched DNA substrates.
|
| |
EMBO J,
28,
2479-2489.
|
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PDB code:
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|
|
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|
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D.S.Shin,
M.Didonato,
D.P.Barondeau,
G.L.Hura,
C.Hitomi,
J.A.Berglund,
E.D.Getzoff,
S.C.Cary,
and
J.A.Tainer
(2009).
Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis.
|
| |
J Mol Biol,
385,
1534-1555.
|
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PDB codes:
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E.Morgunova,
F.C.Gray,
S.A.Macneill,
and
R.Ladenstein
(2009).
Structural insights into the adaptation of proliferating cell nuclear antigen (PCNA) from Haloferax volcanii to a high-salt environment.
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Acta Crystallogr D Biol Crystallogr,
65,
1081-1088.
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PDB code:
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F.J.López de Saro
(2009).
Regulation of interactions with sliding clamps during DNA replication and repair.
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Curr Genomics,
10,
206-215.
|
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H.M.Roth,
I.Tessmer,
B.Van Houten,
and
C.Kisker
(2009).
Bax1 is a novel endonuclease: implications for archaeal nucleotide excision repair.
|
| |
J Biol Chem,
284,
32272-32278.
|
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|
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|
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J.A.Winter,
P.Christofi,
S.Morroll,
and
K.A.Bunting
(2009).
The crystal structure of Haloferax volcanii proliferating cell nuclear antigen reveals unique surface charge characteristics due to halophilic adaptation.
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BMC Struct Biol,
9,
55.
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PDB code:
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J.J.Perry,
R.M.Harris,
D.Moiani,
A.J.Olson,
and
J.A.Tainer
(2009).
p38alpha MAP kinase C-terminal domain binding pocket characterized by crystallographic and computational analyses.
|
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J Mol Biol,
391,
1.
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PDB code:
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J.L.Tubbs,
V.Latypov,
S.Kanugula,
A.Butt,
M.Melikishvili,
R.Kraehenbuehl,
O.Fleck,
A.Marriott,
A.J.Watson,
B.Verbeek,
G.McGown,
M.Thorncroft,
M.F.Santibanez-Koref,
C.Millington,
A.S.Arvai,
M.D.Kroeger,
L.A.Peterson,
D.M.Williams,
M.G.Fried,
G.P.Margison,
A.E.Pegg,
and
J.A.Tainer
(2009).
Flipping of alkylated DNA damage bridges base and nucleotide excision repair.
|
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Nature,
459,
808-813.
|
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PDB codes:
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K.K.Karanja,
and
D.M.Livingston
(2009).
C-terminal flap endonuclease (rad27) mutations: lethal interactions with a DNA ligase I mutation (cdc9-p) and suppression by proliferating cell nuclear antigen (POL30) in Saccharomyces cerevisiae.
|
| |
Genetics,
183,
63-78.
|
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|
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K.Murayama,
S.Nakayama,
M.Kato-Murayama,
R.Akasaka,
N.Ohbayashi,
Y.Kamewari-Hayami,
T.Terada,
M.Shirouzu,
T.Tsurumi,
and
S.Yokoyama
(2009).
Crystal structure of epstein-barr virus DNA polymerase processivity factor BMRF1.
|
| |
J Biol Chem,
284,
35896-35905.
|
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PDB code:
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K.T.Ehmsen,
and
W.D.Heyer
(2009).
A junction branch point adjacent to a DNA backbone nick directs substrate cleavage by Saccharomyces cerevisiae Mus81-Mms4.
|
| |
Nucleic Acids Res,
37,
2026-2036.
|
|
|
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|
|
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L.D.Finger,
M.S.Blanchard,
C.A.Theimer,
B.Sengerová,
P.Singh,
V.Chavez,
F.Liu,
J.A.Grasby,
and
B.Shen
(2009).
The 3'-flap pocket of human flap endonuclease 1 is critical for substrate binding and catalysis.
|
| |
J Biol Chem,
284,
22184-22194.
|
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|
|
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|
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L.Schomacher,
J.P.Chong,
P.McDermott,
W.Kramer,
and
H.J.Fritz
(2009).
DNA uracil repair initiated by the archaeal ExoIII homologue Mth212 via direct strand incision.
|
| |
Nucleic Acids Res,
37,
2283-2293.
|
|
|
|
|
|
|
M.Yang,
H.Guo,
C.Wu,
Y.He,
D.Yu,
L.Zhou,
F.Wang,
J.Xu,
W.Tan,
G.Wang,
B.Shen,
J.Yuan,
T.Wu,
and
D.Lin
(2009).
Functional FEN1 polymorphisms are associated with DNA damage levels and lung cancer risk.
|
| |
Hum Mutat,
30,
1320-1328.
|
|
|
|
|
|
|
N.K.Bernstein,
M.Hammel,
R.S.Mani,
M.Weinfeld,
M.Pelikan,
J.A.Tainer,
and
J.N.Glover
(2009).
Mechanism of DNA substrate recognition by the mammalian DNA repair enzyme, Polynucleotide Kinase.
|
| |
Nucleic Acids Res,
37,
6161-6173.
|
|
|
|
|
|
|
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.
|
| |
Cell,
139,
87-99.
|
|
|
PDB codes:
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T.Rolef Ben-Shahar,
A.G.Castillo,
M.J.Osborne,
K.L.Borden,
J.Kornblatt,
and
A.Verreault
(2009).
Two fundamentally distinct PCNA interaction peptides contribute to chromatin assembly factor 1 function.
|
| |
Mol Cell Biol,
29,
6353-6365.
|
|
|
|
|
|
|
A.Rottach,
E.Kremmer,
D.Nowak,
P.Boisguerin,
R.Volkmer,
M.C.Cardoso,
H.Leonhardt,
and
U.Rothbauer
(2008).
Generation and characterization of a rat monoclonal antibody specific for PCNA.
|
| |
Hybridoma (Larchmt),
27,
91-98.
|
|
|
|
|
|
|
A.S.Jaiswal,
and
S.Narayan
(2008).
A novel function of adenomatous polyposis coli (APC) in regulating DNA repair.
|
| |
Cancer Lett,
271,
272-280.
|
|
|
|
|
|
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D.E.Kainov,
M.Vitorino,
J.Cavarelli,
A.Poterszman,
and
J.M.Egly
(2008).
Structural basis for group A trichothiodystrophy.
|
| |
Nat Struct Mol Biol,
15,
980-984.
|
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PDB codes:
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E.D.Garcin,
D.J.Hosfield,
S.A.Desai,
B.J.Haas,
M.Björas,
R.P.Cunningham,
and
J.A.Tainer
(2008).
DNA apurinic-apyrimidinic site binding and excision by endonuclease IV.
|
| |
Nat Struct Mol Biol,
15,
515-522.
|
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|
PDB codes:
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|
|
|
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K.Syson,
C.Tomlinson,
B.R.Chapados,
J.R.Sayers,
J.A.Tainer,
N.H.Williams,
and
J.A.Grasby
(2008).
Three metal ions participate in the reaction catalyzed by t5 flap endonuclease.
|
| |
J Biol Chem,
283,
28741-28746.
|
|
|
|
|
|
|
L.Fan,
J.O.Fuss,
Q.J.Cheng,
A.S.Arvai,
M.Hammel,
V.A.Roberts,
P.K.Cooper,
and
J.A.Tainer
(2008).
XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations.
|
| |
Cell,
133,
789-800.
|
|
|
PDB codes:
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|
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|
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L.J.Casta,
J.S.Buguliskis,
Y.Matsumoto,
and
T.F.Taraschi
(2008).
Expression and biochemical characterization of the Plasmodium falciparum DNA repair enzyme, flap endonuclease-1 (PfFEN-1).
|
| |
Mol Biochem Parasitol,
157,
1.
|
|
|
|
|
|
|
M.L.Hegde,
C.A.Theriot,
A.Das,
P.M.Hegde,
Z.Guo,
R.K.Gary,
T.K.Hazra,
B.Shen,
and
S.Mitra
(2008).
Physical and Functional Interaction between Human Oxidized Base-specific DNA Glycosylase NEIL1 and Flap Endonuclease 1.
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J Biol Chem,
283,
27028-27037.
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R.E.Georgescu,
S.S.Kim,
O.Yurieva,
J.Kuriyan,
X.P.Kong,
and
M.O'Donnell
(2008).
Structure of a sliding clamp on DNA.
|
| |
Cell,
132,
43-54.
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|
|
PDB code:
|
|
|
|
|
|
|
|
R.S.Williams,
G.Moncalian,
J.S.Williams,
Y.Yamada,
O.Limbo,
D.S.Shin,
L.M.Groocock,
D.Cahill,
C.Hitomi,
G.Guenther,
D.Moiani,
J.P.Carney,
P.Russell,
and
J.A.Tainer
(2008).
Mre11 dimers coordinate DNA end bridging and nuclease processing in double-strand-break repair.
|
| |
Cell,
135,
97.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
S.Sakurai,
K.Kitano,
H.Morioka,
and
T.Hakoshima
(2008).
Crystallization and preliminary crystallographic analysis of the catalytic domain of human flap endonuclease 1 in complex with a nicked DNA product: use of a DPCS kit for efficient protein-DNA complex crystallization.
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| |
Acta Crystallogr Sect F Struct Biol Cryst Commun,
64,
39-43.
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V.Hlinkova,
G.Xing,
J.Bauer,
Y.J.Shin,
I.Dionne,
K.R.Rajashankar,
S.D.Bell,
and
H.Ling
(2008).
Structures of monomeric, dimeric and trimeric PCNA: PCNA-ring assembly and opening.
|
| |
Acta Crystallogr D Biol Crystallogr,
64,
941-949.
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|
|
PDB codes:
|
|
|
|
|
|
|
|
Z.Guo,
V.Chavez,
P.Singh,
L.D.Finger,
H.Hang,
M.L.Hegde,
and
B.Shen
(2008).
Comprehensive mapping of the C-terminus of flap endonuclease-1 reveals distinct interaction sites for five proteins that represent different DNA replication and repair pathways.
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J Mol Biol,
377,
679-690.
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C.D.Putnam,
M.Hammel,
G.L.Hura,
and
J.A.Tainer
(2007).
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.
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Q Rev Biophys,
40,
191-285.
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G.L.Moldovan,
B.Pfander,
and
S.Jentsch
(2007).
PCNA, the maestro of the replication fork.
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| |
Cell,
129,
665-679.
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J.J.Perry,
L.Fan,
and
J.A.Tainer
(2007).
Developing master keys to brain pathology, cancer and aging from the structural biology of proteins controlling reactive oxygen species and DNA repair.
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Neuroscience,
145,
1280-1299.
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J.M.Devos,
S.J.Tomanicek,
C.E.Jones,
N.G.Nossal,
and
T.C.Mueser
(2007).
Crystal structure of bacteriophage T4 5' nuclease in complex with a branched DNA reveals how flap endonuclease-1 family nucleases bind their substrates.
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| |
J Biol Chem,
282,
31713-31724.
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PDB code:
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|
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|
|
K.Sasaki,
T.Ose,
N.Okamoto,
K.Maenaka,
T.Tanaka,
H.Masai,
M.Saito,
T.Shirai,
and
D.Kohda
(2007).
Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA.
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EMBO J,
26,
2584-2593.
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L.Schermelleh,
A.Haemmer,
F.Spada,
N.Rösing,
D.Meilinger,
U.Rothbauer,
M.C.Cardoso,
and
H.Leonhardt
(2007).
Dynamics of Dnmt1 interaction with the replication machinery and its role in postreplicative maintenance of DNA methylation.
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Nucleic Acids Res,
35,
4301-4312.
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L.Zheng,
H.Dai,
J.Qiu,
Q.Huang,
and
B.Shen
(2007).
Disruption of the FEN-1/PCNA interaction results in DNA replication defects, pulmonary hypoplasia, pancytopenia, and newborn lethality in mice.
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Mol Cell Biol,
27,
3176-3186.
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M.Hohl,
I.Dunand-Sauthier,
L.Staresincic,
P.Jaquier-Gubler,
F.Thorel,
M.Modesti,
S.G.Clarkson,
and
O.D.Schärer
(2007).
Domain swapping between FEN-1 and XPG defines regions in XPG that mediate nucleotide excision repair activity and substrate specificity.
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Nucleic Acids Res,
35,
3053-3063.
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M.R.Hodskinson,
L.M.Allen,
D.P.Thomson,
and
J.R.Sayers
(2007).
Molecular interactions of Escherichia coli ExoIX and identification of its associated 3'-5' exonuclease activity.
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| |
Nucleic Acids Res,
35,
4094-4102.
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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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R.Williams,
B.Sengerová,
S.Osborne,
K.Syson,
S.Ault,
A.Kilgour,
B.R.Chapados,
J.A.Tainer,
J.R.Sayers,
and
J.A.Grasby
(2007).
Comparison of the catalytic parameters and reaction specificities of a phage and an archaeal flap endonuclease.
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| |
J Mol Biol,
371,
34-48.
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|
S.S.Shell,
C.D.Putnam,
and
R.D.Kolodner
(2007).
The N terminus of Saccharomyces cerevisiae Msh6 is an unstructured tether to PCNA.
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| |
Mol Cell,
26,
565-578.
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|
S.Vijayakumar,
B.R.Chapados,
K.H.Schmidt,
R.D.Kolodner,
J.A.Tainer,
and
A.E.Tomkinson
(2007).
The C-terminal domain of yeast PCNA is required for physical and functional interactions with Cdc9 DNA ligase.
|
| |
Nucleic Acids Res,
35,
1624-1637.
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|
PDB code:
|
|
|
|
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|
|
V.Vacic,
C.J.Oldfield,
A.Mohan,
P.Radivojac,
M.S.Cortese,
V.N.Uversky,
and
A.K.Dunker
(2007).
Characterization of molecular recognition features, MoRFs, and their binding partners.
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J Proteome Res,
6,
2351-2366.
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A.S.Doré,
M.L.Kilkenny,
S.A.Jones,
A.W.Oliver,
S.M.Roe,
S.D.Bell,
and
L.H.Pearl
(2006).
Structure of an archaeal PCNA1-PCNA2-FEN1 complex: elucidating PCNA subunit and client enzyme specificity.
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| |
Nucleic Acids Res,
34,
4515-4526.
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|
|
PDB code:
|
|
|
|
|
|
|
|
B.A.Appleton,
J.Brooks,
A.Loregian,
D.J.Filman,
D.M.Coen,
and
J.M.Hogle
(2006).
Crystal structure of the cytomegalovirus DNA polymerase subunit UL44 in complex with the C terminus from the catalytic subunit. Differences in structure and function relative to unliganded UL44.
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| |
J Biol Chem,
281,
5224-5232.
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PDB code:
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|
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|
|
|
|
|
C.Indiani,
and
M.O'Donnell
(2006).
The replication clamp-loading machine at work in the three domains of life.
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Nat Rev Mol Cell Biol,
7,
751-761.
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E.R.Barry,
and
S.D.Bell
(2006).
DNA replication in the archaea.
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| |
Microbiol Mol Biol Rev,
70,
876-887.
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F.J.López de Saro,
M.G.Marinus,
P.Modrich,
and
M.O'Donnell
(2006).
The beta sliding clamp binds to multiple sites within MutL and MutS.
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| |
J Biol Chem,
281,
14340-14349.
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H.Remaut,
and
G.Waksman
(2006).
Protein-protein interaction through beta-strand addition.
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Trends Biochem Sci,
31,
436-444.
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I.Ivanov,
B.R.Chapados,
J.A.McCammon,
and
J.A.Tainer
(2006).
Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications.
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Nucleic Acids Res,
34,
6023-6033.
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J.M.Pascal,
O.V.Tsodikov,
G.L.Hura,
W.Song,
E.A.Cotner,
S.Classen,
A.E.Tomkinson,
J.A.Tainer,
and
T.Ellenberger
(2006).
A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA.
|
| |
Mol Cell,
24,
279-291.
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|
|
PDB codes:
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|
|
M.Da Silva,
L.Shen,
V.Tcherepanov,
C.Watson,
and
C.Upton
(2006).
Predicted function of the vaccinia virus G5R protein.
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Bioinformatics,
22,
2846-2850.
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R.Liu,
J.Qiu,
L.D.Finger,
L.Zheng,
and
B.Shen
(2006).
The DNA-protein interaction modes of FEN-1 with gap substrates and their implication in preventing duplication mutations.
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Nucleic Acids Res,
34,
1772-1784.
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B.Shen,
P.Singh,
R.Liu,
J.Qiu,
L.Zheng,
L.D.Finger,
and
S.Alas
(2005).
Multiple but dissectible functions of FEN-1 nucleases in nucleic acid processing, genome stability and diseases.
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| |
Bioessays,
27,
717-729.
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E.W.Refsland,
and
D.M.Livingston
(2005).
Interactions among DNA ligase I, the flap endonuclease and proliferating cell nuclear antigen in the expansion and contraction of CAG repeat tracts in yeast.
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| |
Genetics,
171,
923-934.
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G.Kontopidis,
S.Y.Wu,
D.I.Zheleva,
P.Taylor,
C.McInnes,
D.P.Lane,
P.M.Fischer,
and
M.D.Walkinshaw
(2005).
Structural and biochemical studies of human proliferating cell nuclear antigen complexes provide a rationale for cyclin association and inhibitor design.
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| |
Proc Natl Acad Sci U S A,
102,
1871-1876.
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|
PDB codes:
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|
|
M.Newman,
J.Murray-Rust,
J.Lally,
J.Rudolf,
A.Fadden,
P.P.Knowles,
M.F.White,
and
N.Q.McDonald
(2005).
Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition.
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| |
EMBO J,
24,
895-905.
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PDB codes:
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|
O.Gangisetty,
C.E.Jones,
M.Bhagwat,
and
N.G.Nossal
(2005).
Maturation of bacteriophage T4 lagging strand fragments depends on interaction of T4 RNase H with T4 32 protein rather than the T4 gene 45 clamp.
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| |
J Biol Chem,
280,
12876-12887.
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R.Ko,
and
S.E.Bennett
(2005).
Physical and functional interaction of human nuclear uracil-DNA glycosylase with proliferating cell nuclear antigen.
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DNA Repair (Amst),
4,
1421-1431.
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S.N.Naryzhny,
H.Zhao,
and
H.Lee
(2005).
Proliferating cell nuclear antigen (PCNA) may function as a double homotrimer complex in the mammalian cell.
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J Biol Chem,
280,
13888-13894.
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S.Sakurai,
K.Kitano,
H.Yamaguchi,
K.Hamada,
K.Okada,
K.Fukuda,
M.Uchida,
E.Ohtsuka,
H.Morioka,
and
T.Hakoshima
(2005).
Structural basis for recruitment of human flap endonuclease 1 to PCNA.
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| |
EMBO J,
24,
683-693.
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PDB code:
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|
T.A.Kunkel,
and
D.A.Erie
(2005).
DNA mismatch repair.
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| |
Annu Rev Biochem,
74,
681-710.
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D.L.Ho,
W.M.Byrnes,
W.P.Ma,
Y.Shi,
D.J.Callaway,
and
Z.Bu
(2004).
Structure-specific DNA-induced conformational changes in Taq polymerase revealed by small angle neutron scattering.
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J Biol Chem,
279,
39146-39154.
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E.Friedrich-Heineken,
and
U.Hübscher
(2004).
The Fen1 extrahelical 3'-flap pocket is conserved from archaea to human and regulates DNA substrate specificity.
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Nucleic Acids Res,
32,
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H.M.Tseng,
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Processing and joining of DNA ends coordinated by interactions among Dnl4/Lif1, Pol4, and FEN-1.
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J Biol Chem,
279,
47580-47588.
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J.A.Surtees,
and
E.Alani
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Replication factors license exonuclease I in mismatch repair.
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Mol Cell,
15,
164-166.
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J.B.Bruning,
and
Y.Shamoo
(2004).
Structural and thermodynamic analysis of human PCNA with peptides derived from DNA polymerase-delta p66 subunit and flap endonuclease-1.
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| |
Structure,
12,
2209-2219.
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|
PDB codes:
|
|
|
|
|
|
|
|
J.Qiu,
R.Liu,
B.R.Chapados,
M.Sherman,
J.A.Tainer,
and
B.Shen
(2004).
Interaction interface of human flap endonuclease-1 with its DNA substrates.
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J Biol Chem,
279,
24394-24402.
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M.E.Stauffer,
and
W.J.Chazin
(2004).
Structural mechanisms of DNA replication, repair, and recombination.
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J Biol Chem,
279,
30915-30918.
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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.
|
|
Links
