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PDBsum entry 1oyy
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.3.6.4.12
- Dna helicase.
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Reaction:
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ATP + H2O = ADP + phosphate + H+
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ATP
Bound ligand (Het Group name = )
matches with 93.75% similarity
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+
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H2O
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=
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ADP
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+
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phosphate
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+
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H(+)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Embo J
22:4910-4921
(2003)
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PubMed id:
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High-resolution structure of the E.coli RecQ helicase catalytic core.
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D.A.Bernstein,
M.C.Zittel,
J.L.Keck.
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ABSTRACT
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RecQ family helicases catalyze critical genome maintenance reactions in
bacterial and eukaryotic cells, playing key roles in several DNA metabolic
processes. Mutations in recQ genes are linked to genome instability and human
disease. To define the physical basis of RecQ enzyme function, we have
determined a 1.8 A resolution crystal structure of the catalytic core of
Escherichia coli RecQ in its unbound form and a 2.5 A resolution structure of
the core bound to the ATP analog ATPgammaS. The RecQ core comprises four
conserved subdomains; two of these combine to form its helicase region, while
the others form unexpected Zn(2+)-binding and winged-helix motifs. The
structures reveal the molecular basis of missense mutations that cause Bloom's
syndrome, a human RecQ-associated disease. Finally, based on findings from the
structures, we propose a mechanism for RecQ activity that could explain its
functional coordination with topoisomerase III.
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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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B.Lucic,
Y.Zhang,
O.King,
R.Mendoza-Maldonado,
M.Berti,
F.H.Niesen,
N.A.Burgess-Brown,
A.C.Pike,
C.D.Cooper,
O.Gileadi,
and
A.Vindigni
(2011).
A prominent beta-hairpin structure in the winged-helix domain of RECQ1 is required for DNA unwinding and oligomer formation.
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Nucleic Acids Res,
39,
1703-1717.
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C.F.Chen,
and
S.J.Brill
(2010).
An essential DNA strand-exchange activity is conserved in the divergent N-termini of BLM orthologs.
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EMBO J,
29,
1713-1725.
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K.A.Hoadley,
and
J.L.Keck
(2010).
Werner helicase wings DNA binding.
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Structure,
18,
149-151.
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K.Kitano,
S.Y.Kim,
and
T.Hakoshima
(2010).
Structural basis for DNA strand separation by the unconventional winged-helix domain of RecQ helicase WRN.
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Structure,
18,
177-187.
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PDB code:
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M.Gyimesi,
K.Sarlós,
and
M.Kovács
(2010).
Processive translocation mechanism of the human Bloom's syndrome helicase along single-stranded DNA.
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Nucleic Acids Res,
38,
4404-4414.
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N.Li,
E.Henry,
E.Guiot,
P.Rigolet,
J.C.Brochon,
X.G.Xi,
and
E.Deprez
(2010).
Multiple Escherichia coli RecQ helicase monomers cooperate to unwind long DNA substrates: a fluorescence cross-correlation spectroscopy study.
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J Biol Chem,
285,
6922-6936.
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P.Cejka,
and
S.C.Kowalczykowski
(2010).
The full-length Saccharomyces cerevisiae Sgs1 protein is a vigorous DNA helicase that preferentially unwinds holliday junctions.
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J Biol Chem,
285,
8290-8301.
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P.Umate,
R.Tuteja,
and
N.Tuteja
(2010).
Genome-wide analysis of helicase gene family from rice and Arabidopsis: a comparison with yeast and human.
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Plant Mol Biol,
73,
449-465.
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Y.M.Kim,
and
B.S.Choi
(2010).
Structure and function of the regulatory HRDC domain from human Bloom syndrome protein.
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Nucleic Acids Res,
38,
7764-7777.
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PDB code:
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Y.Wu,
and
R.M.Brosh
(2010).
Distinct roles of RECQ1 in the maintenance of genomic stability.
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DNA Repair (Amst),
9,
315-324.
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A.C.Pike,
B.Shrestha,
V.Popuri,
N.Burgess-Brown,
L.Muzzolini,
S.Costantini,
A.Vindigni,
and
O.Gileadi
(2009).
Structure of the human RECQ1 helicase reveals a putative strand-separation pin.
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Proc Natl Acad Sci U S A,
106,
1039-1044.
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PDB code:
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A.Vindigni,
and
I.D.Hickson
(2009).
RecQ helicases: multiple structures for multiple functions?
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HFSP J,
3,
153-164.
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J.G.Yodh,
B.C.Stevens,
R.Kanagaraj,
P.Janscak,
and
T.Ha
(2009).
BLM helicase measures DNA unwound before switching strands and hRPA promotes unwinding reinitiation.
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EMBO J,
28,
405-416.
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M.P.Killoran,
P.L.Kohler,
J.P.Dillard,
and
J.L.Keck
(2009).
RecQ DNA helicase HRDC domains are critical determinants in Neisseria gonorrhoeae pilin antigenic variation and DNA repair.
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Mol Microbiol,
71,
158-171.
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R.D.Shereda,
N.J.Reiter,
S.E.Butcher,
and
J.L.Keck
(2009).
Identification of the SSB binding site on E. coli RecQ reveals a conserved surface for binding SSB's C terminus.
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J Mol Biol,
386,
612-625.
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T.Oyama,
H.Oka,
K.Mayanagi,
T.Shirai,
K.Matoba,
R.Fujikane,
Y.Ishino,
and
K.Morikawa
(2009).
Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm.
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BMC Struct Biol,
9,
2.
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PDB codes:
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W.K.Chu,
and
I.D.Hickson
(2009).
RecQ helicases: multifunctional genome caretakers.
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Nat Rev Cancer,
9,
644-654.
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Y.Wu,
A.N.Suhasini,
and
R.M.Brosh
(2009).
Welcome the family of FANCJ-like helicases to the block of genome stability maintenance proteins.
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Cell Mol Life Sci,
66,
1209-1222.
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D.Lu,
and
J.L.Keck
(2008).
Structural basis of Escherichia coli single-stranded DNA-binding protein stimulation of exonuclease I.
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Proc Natl Acad Sci U S A,
105,
9169-9174.
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PDB codes:
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E.J.Enemark,
and
L.Joshua-Tor
(2008).
On helicases and other motor proteins.
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Curr Opin Struct Biol,
18,
243-257.
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K.M.Sinha,
N.C.Stephanou,
M.C.Unciuleac,
M.S.Glickman,
and
S.Shuman
(2008).
Domain requirements for DNA unwinding by mycobacterial UvrD2, an essential DNA helicase.
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Biochemistry,
47,
9355-9364.
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M.P.Killoran,
and
J.L.Keck
(2008).
Structure and function of the regulatory C-terminal HRDC domain from Deinococcus radiodurans RecQ.
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Nucleic Acids Res,
36,
3139-3149.
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PDB code:
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N.Cicmil,
and
R.H.Huang
(2008).
Crystal structure of QueC from Bacillus subtilis: an enzyme involved in preQ1 biosynthesis.
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Proteins,
72,
1084-1088.
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PDB code:
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R.Gupta,
and
R.M.Brosh
(2008).
Helicases as prospective targets for anti-cancer therapy.
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Anticancer Agents Med Chem,
8,
390-401.
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T.M.Lohman,
E.J.Tomko,
and
C.G.Wu
(2008).
Non-hexameric DNA helicases and translocases: mechanisms and regulation.
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Nat Rev Mol Cell Biol,
9,
391-401.
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V.Popuri,
C.Z.Bachrati,
L.Muzzolini,
G.Mosedale,
S.Costantini,
E.Giacomini,
I.D.Hickson,
and
A.Vindigni
(2008).
The Human RecQ helicases, BLM and RECQ1, display distinct DNA substrate specificities.
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J Biol Chem,
283,
17766-17776.
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X.Zhang,
T.Nakashima,
Y.Kakuta,
M.Yao,
I.Tanaka,
and
M.Kimura
(2008).
Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshii OT3.
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Protein Sci,
17,
136-145.
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PDB code:
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Y.Yang,
S.X.Dou,
H.Ren,
P.Y.Wang,
X.D.Zhang,
M.Qian,
B.Y.Pan,
and
X.G.Xi
(2008).
Evidence for a functional dimeric form of the PcrA helicase in DNA unwinding.
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Nucleic Acids Res,
36,
1976-1989.
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A.Niedziela-Majka,
M.A.Chesnik,
E.J.Tomko,
and
T.M.Lohman
(2007).
Bacillus stearothermophilus PcrA monomer is a single-stranded DNA translocase but not a processive helicase in vitro.
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J Biol Chem,
282,
27076-27085.
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D.N.Frick,
S.Banik,
and
R.S.Rypma
(2007).
Role of divalent metal cations in ATP hydrolysis catalyzed by the hepatitis C virus NS3 helicase: magnesium provides a bridge for ATP to fuel unwinding.
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J Mol Biol,
365,
1017-1032.
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H.Ren,
S.X.Dou,
P.Rigolet,
Y.Yang,
P.Y.Wang,
M.Amor-Gueret,
and
X.G.Xi
(2007).
The arginine finger of the Bloom syndrome protein: its structural organization and its role in energy coupling.
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Nucleic Acids Res,
35,
6029-6041.
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I.D.Kerr,
S.Sivakolundu,
Z.Li,
J.C.Buchsbaum,
L.A.Knox,
R.Kriwacki,
and
S.W.White
(2007).
Crystallographic and NMR analyses of UvsW and UvsW.1 from bacteriophage T4.
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J Biol Chem,
282,
34392-34400.
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PDB codes:
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J.A.Harrigan,
J.Piotrowski,
L.Di Noto,
R.L.Levine,
and
V.A.Bohr
(2007).
Metal-catalyzed oxidation of the Werner syndrome protein causes loss of catalytic activities and impaired protein-protein interactions.
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J Biol Chem,
282,
36403-36411.
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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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K.Kitano,
N.Yoshihara,
and
T.Hakoshima
(2007).
Crystal structure of the HRDC domain of human Werner syndrome protein, WRN.
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J Biol Chem,
282,
2717-2728.
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PDB codes:
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L.Muzzolini,
F.Beuron,
A.Patwardhan,
V.Popuri,
S.Cui,
B.Niccolini,
M.Rappas,
P.S.Freemont,
and
A.Vindigni
(2007).
Different quaternary structures of human RECQ1 are associated with its dual enzymatic activity.
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PLoS Biol,
5,
e20.
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M.R.Singleton,
M.S.Dillingham,
and
D.B.Wigley
(2007).
Structure and mechanism of helicases and nucleic acid translocases.
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Annu Rev Biochem,
76,
23-50.
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R.B.Guo,
P.Rigolet,
H.Ren,
B.Zhang,
X.D.Zhang,
S.X.Dou,
P.Y.Wang,
M.Amor-Gueret,
and
X.G.Xi
(2007).
Structural and functional analyses of disease-causing missense mutations in Bloom syndrome protein.
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Nucleic Acids Res,
35,
6297-6310.
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R.D.Shereda,
D.A.Bernstein,
and
J.L.Keck
(2007).
A central role for SSB in Escherichia coli RecQ DNA helicase function.
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J Biol Chem,
282,
19247-19258.
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C.Ralf,
I.D.Hickson,
and
L.Wu
(2006).
The Bloom's syndrome helicase can promote the regression of a model replication fork.
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J Biol Chem,
281,
22839-22846.
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D.Keramisanou,
N.Biris,
I.Gelis,
G.Sianidis,
S.Karamanou,
A.Economou,
and
C.G.Kalodimos
(2006).
Disorder-order folding transitions underlie catalysis in the helicase motor of SecA.
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Nat Struct Mol Biol,
13,
594-602.
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J.D.Bartos,
W.Wang,
J.E.Pike,
and
R.A.Bambara
(2006).
Mechanisms by which Bloom protein can disrupt recombination intermediates of Okazaki fragment maturation.
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J Biol Chem,
281,
32227-32239.
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J.J.Perry,
S.M.Yannone,
L.G.Holden,
C.Hitomi,
A.Asaithamby,
S.Han,
P.K.Cooper,
D.J.Chen,
and
J.A.Tainer
(2006).
WRN exonuclease structure and molecular mechanism imply an editing role in DNA end processing.
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Nat Struct Mol Biol,
13,
414-422.
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PDB codes:
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J.Y.Lee,
and
W.Yang
(2006).
UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke.
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Cell,
127,
1349-1360.
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PDB codes:
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L.Wu,
and
I.D.Hickson
(2006).
DNA helicases required for homologous recombination and repair of damaged replication forks.
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Annu Rev Genet,
40,
279-306.
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M.D.Allen,
C.G.Grummitt,
C.Hilcenko,
S.Y.Min,
L.M.Tonkin,
C.M.Johnson,
S.M.Freund,
M.Bycroft,
and
A.J.Warren
(2006).
Solution structure of the nonmethyl-CpG-binding CXXC domain of the leukaemia-associated MLL histone methyltransferase.
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EMBO J,
25,
4503-4512.
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PDB code:
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M.P.Killoran,
and
J.L.Keck
(2006).
Sit down, relax and unwind: structural insights into RecQ helicase mechanisms.
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Nucleic Acids Res,
34,
4098-4105.
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M.P.Killoran,
and
J.L.Keck
(2006).
Three HRDC domains differentially modulate Deinococcus radiodurans RecQ DNA helicase biochemical activity.
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J Biol Chem,
281,
12849-12857.
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X.D.Zhang,
S.X.Dou,
P.Xie,
J.S.Hu,
P.Y.Wang,
and
X.G.Xi
(2006).
Escherichia coli RecQ is a rapid, efficient, and monomeric helicase.
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J Biol Chem,
281,
12655-12663.
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A.Machwe,
L.Xiao,
J.Groden,
S.W.Matson,
and
D.K.Orren
(2005).
RecQ family members combine strand pairing and unwinding activities to catalyze strand exchange.
|
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J Biol Chem,
280,
23397-23407.
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C.F.Cheok,
L.Wu,
P.L.Garcia,
P.Janscak,
and
I.D.Hickson
(2005).
The Bloom's syndrome helicase promotes the annealing of complementary single-stranded DNA.
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Nucleic Acids Res,
33,
3932-3941.
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C.P.Guy,
and
E.L.Bolt
(2005).
Archaeal Hel308 helicase targets replication forks in vivo and in vitro and unwinds lagging strands.
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Nucleic Acids Res,
33,
3678-3690.
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D.A.Bernstein,
and
J.L.Keck
(2005).
Conferring substrate specificity to DNA helicases: role of the RecQ HRDC domain.
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Structure,
13,
1173-1182.
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PDB code:
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I.Leiros,
J.Timmins,
D.R.Hall,
and
S.McSweeney
(2005).
Crystal structure and DNA-binding analysis of RecO from Deinococcus radiodurans.
|
| |
EMBO J,
24,
906-918.
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PDB code:
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J.S.Hu,
H.Feng,
W.Zeng,
G.X.Lin,
and
X.G.Xi
(2005).
Solution structure of a multifunctional DNA- and protein-binding motif of human Werner syndrome protein.
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| |
Proc Natl Acad Sci U S A,
102,
18379-18384.
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PDB code:
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J.W.Lee,
R.Kusumoto,
K.M.Doherty,
G.X.Lin,
W.Zeng,
W.H.Cheng,
C.von Kobbe,
R.M.Brosh,
J.S.Hu,
and
V.A.Bohr
(2005).
Modulation of Werner syndrome protein function by a single mutation in the conserved RecQ domain.
|
| |
J Biol Chem,
280,
39627-39636.
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J.Wu,
A.K.Bera,
R.J.Kuhn,
and
J.L.Smith
(2005).
Structure of the Flavivirus helicase: implications for catalytic activity, protein interactions, and proteolytic processing.
|
| |
J Virol,
79,
10268-10277.
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PDB codes:
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L.Wu,
K.L.Chan,
C.Ralf,
D.A.Bernstein,
P.L.Garcia,
V.A.Bohr,
A.Vindigni,
P.Janscak,
J.L.Keck,
and
I.D.Hickson
(2005).
The HRDC domain of BLM is required for the dissolution of double Holliday junctions.
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| |
EMBO J,
24,
2679-2687.
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M.C.Zittel,
and
J.L.Keck
(2005).
Coupling DNA-binding and ATP hydrolysis in Escherichia coli RecQ: role of a highly conserved aromatic-rich sequence.
|
| |
Nucleic Acids Res,
33,
6982-6991.
|
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N.H.Thomä,
B.K.Czyzewski,
A.A.Alexeev,
A.V.Mazin,
S.C.Kowalczykowski,
and
N.P.Pavletich
(2005).
Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54.
|
| |
Nat Struct Mol Biol,
12,
350-356.
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PDB code:
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R.B.Guo,
P.Rigolet,
L.Zargarian,
S.Fermandjian,
and
X.G.Xi
(2005).
Structural and functional characterizations reveal the importance of a zinc binding domain in Bloom's syndrome helicase.
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| |
Nucleic Acids Res,
33,
3109-3124.
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PDB code:
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PDB codes:
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