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DNA-binding protein
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PDB id
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1bgw
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.5.99.1.3
- Dna topoisomerase (ATP-hydrolyzing).
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Reaction:
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ATP-dependent breakage, passage and rejoining of double-stranded DNA.
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Gene Ontology (GO) functional annotation
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Cellular component
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chromosome
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1 term
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Biological process
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DNA metabolic process
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3 terms
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Biochemical function
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DNA binding
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4 terms
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DOI no:
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Nature
379:225-232
(1996)
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PubMed id:
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| |
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Structure and mechanism of DNA topoisomerase II.
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J.M.Berger,
S.J.Gamblin,
S.C.Harrison,
J.C.Wang.
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ABSTRACT
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The crystal structure of a large fragment of yeast type II DNA topoisomerase
reveals a heart-shaped dimeric protein with a large central hole. It provides a
molecular model of the enzyme as an ATP-modulated clamp with two sets of jaws at
opposite ends, connected by multiple joints. An enzyme with bound DNA can admit
a second DNA duplex through one set of jaws, transport it through the cleaved
first duplex, and expel it through the other set of jaws.
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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
|
|
|
|
|
|
J.Liu,
C.H.Leung,
A.L.Chow,
R.W.Sun,
S.C.Yan,
and
C.M.Che
(2011).
Cyclometalated platinum(II) complexes as topoisomerase IIα poisons.
|
| |
Chem Commun (Camb), 47,
719-721.
|
|
|
|
|
|
|
K.L.Gilroy,
and
C.A.Austin
(2011).
The Impact of the C-Terminal Domain on the Interaction of Human DNA Topoisomerase II α and β with DNA.
|
| |
PLoS One, 6,
e14693.
|
|
|
|
|
|
|
M.Chmielewska,
M.Dubińska-Magiera,
M.Sopel,
D.Rzepecka,
C.J.Hutchison,
M.W.Goldberg,
and
R.Rzepecki
(2011).
Embryonic and adult isoforms of XLAP2 form microdomains associated with chromatin and the nuclear envelope.
|
| |
Cell Tissue Res, 344,
97.
|
|
|
|
|
|
|
N.M.Baker,
S.Weigand,
S.Maar-Mathias,
and
A.Mondragón
(2011).
Solution structures of DNA-bound gyrase.
|
| |
Nucleic Acids Res, 39,
755-766.
|
|
|
|
|
|
|
A.J.Schoeffler,
A.P.May,
and
J.M.Berger
(2010).
A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function.
|
| |
Nucleic Acids Res, 38,
7830-7844.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
B.D.Bax,
P.F.Chan,
D.S.Eggleston,
A.Fosberry,
D.R.Gentry,
F.Gorrec,
I.Giordano,
M.M.Hann,
A.Hennessy,
M.Hibbs,
J.Huang,
E.Jones,
J.Jones,
K.K.Brown,
C.J.Lewis,
E.W.May,
M.R.Saunders,
O.Singh,
C.E.Spitzfaden,
C.Shen,
A.Shillings,
A.J.Theobald,
A.Wohlkonig,
N.D.Pearson,
and
M.N.Gwynn
(2010).
Type IIA topoisomerase inhibition by a new class of antibacterial agents.
|
| |
Nature, 466,
935-940.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
B.H.Schmidt,
A.B.Burgin,
J.E.Deweese,
N.Osheroff,
and
J.M.Berger
(2010).
A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases.
|
| |
Nature, 465,
641-644.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
C.B.Moelans,
R.A.de Weger,
M.T.van Blokland,
E.van der Wall,
and
P.J.van Diest
(2010).
Simultaneous detection of TOP2A and HER2 gene amplification by multiplex ligation-dependent probe amplification in breast cancer.
|
| |
Mod Pathol, 23,
62-70.
|
|
|
|
|
|
|
C.García-Estrada,
C.F.Prada,
C.Fernández-Rubio,
F.Rojo-Vázquez,
and
R.Balaña-Fouce
(2010).
DNA topoisomerases in apicomplexan parasites: promising targets for drug discovery.
|
| |
Proc Biol Sci, 277,
1777-1787.
|
|
|
|
|
|
|
C.Hu,
D.Xu,
W.Du,
S.Qian,
L.Wang,
J.Lou,
Q.He,
B.Yang,
and
Y.Hu
(2010).
Novel 4 beta-anilino-podophyllotoxin derivatives: design synthesis and biological evaluation as potent DNA-topoisomerase II poisons and anti-MDR agents.
|
| |
Mol Biosyst, 6,
410-420.
|
|
|
|
|
|
|
G.L.Chee,
J.C.Yalowich,
A.Bodner,
X.Wu,
and
B.B.Hasinoff
(2010).
A diazirine-based photoaffinity etoposide probe for labeling topoisomerase II.
|
| |
Bioorg Med Chem, 18,
830-838.
|
|
|
|
|
|
|
H.Ryu,
M.Furuta,
D.Kirkpatrick,
S.P.Gygi,
and
Y.Azuma
(2010).
PIASy-dependent SUMOylation regulates DNA topoisomerase IIalpha activity.
|
| |
J Cell Biol, 191,
783-794.
|
|
|
|
|
|
|
J.E.Deweese,
and
N.Osheroff
(2010).
The Use of Divalent Metal Ions by Type II Topoisomerases.
|
| |
Metallomics, 2,
450-459.
|
|
|
|
|
|
|
J.Piton,
S.Petrella,
M.Delarue,
G.André-Leroux,
V.Jarlier,
A.Aubry,
and
C.Mayer
(2010).
Structural insights into the quinolone resistance mechanism of Mycobacterium tuberculosis DNA gyrase.
|
| |
PLoS One, 5,
e12245.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.Anupama,
J.P.Seiler,
and
P.B.Murthy
(2010).
A comparative analysis of chromosomal aberrations in cultured human lymphocytes due to fluoroquinolone drugs at different expression periods.
|
| |
Arch Toxicol, 84,
411-420.
|
|
|
|
|
|
|
M.Maiti,
and
G.S.Kumar
(2010).
Polymorphic nucleic Acid binding of bioactive isoquinoline alkaloids and their role in cancer.
|
| |
J Nucleic Acids, 2010,
0.
|
|
|
|
|
|
|
P.Xie
(2010).
Dynamics of strand passage catalyzed by topoisomerase II.
|
| |
Eur Biophys J, 39,
1251-1259.
|
|
|
|
|
|
|
R.Napieralski,
N.Brünner,
K.Mengele,
and
M.Schmitt
(2010).
Emerging biomarkers in breast cancer care.
|
| |
Biomark Med, 4,
505-522.
|
|
|
|
|
|
|
W.Yang
(2010).
Topoisomerases and site-specific recombinases: similarities in structure and mechanism.
|
| |
Crit Rev Biochem Mol Biol, 45,
520-534.
|
|
|
|
|
|
|
Y.B.Zhang,
L.S.Feng,
X.F.You,
Q.Guo,
H.Y.Guo,
and
M.L.Liu
(2010).
Synthesis and in vitro antibacterial activity of 7-(3-alkoxyimino-4-methyl-4-methylaminopiperidin-1-yl)-fluoroquinolone derivatives.
|
| |
Arch Pharm (Weinheim), 343,
143-151.
|
|
|
|
|
|
|
A.Gubaev,
M.Hilbert,
and
D.Klostermeier
(2009).
The DNA-gate of Bacillus subtilis gyrase is predominantly in the closed conformation during the DNA supercoiling reaction.
|
| |
Proc Natl Acad Sci U S A, 106,
13278-13283.
|
|
|
|
|
|
|
A.Muslimović,
S.Nyström,
Y.Gao,
and
O.Hammarsten
(2009).
Numerical analysis of etoposide induced DNA breaks.
|
| |
PLoS One, 4,
e5859.
|
|
|
|
|
|
|
E.A.Outwin,
A.Irmisch,
J.M.Murray,
and
M.J.O'Connell
(2009).
Smc5-Smc6-dependent removal of cohesin from mitotic chromosomes.
|
| |
Mol Cell Biol, 29,
4363-4375.
|
|
|
|
|
|
|
G.Fu,
J.Wu,
D.Zhu,
Y.Hu,
L.Bi,
X.E.Zhang,
and
d.a. .C.Wang
(2009).
Crystallization and preliminary crystallographic studies of Mycobacterium tuberculosis DNA gyrase B C-terminal domain, part of the enzyme reaction core.
|
| |
Acta Crystallogr Sect F Struct Biol Cryst Commun, 65,
350-352.
|
|
|
|
|
|
|
G.Fu,
J.Wu,
W.Liu,
D.Zhu,
Y.Hu,
J.Deng,
X.E.Zhang,
L.Bi,
and
D.C.Wang
(2009).
Crystal structure of DNA gyrase B' domain sheds lights on the mechanism for T-segment navigation.
|
| |
Nucleic Acids Res, 37,
5908-5916.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
I.Laponogov,
M.K.Sohi,
D.A.Veselkov,
X.S.Pan,
R.Sawhney,
A.W.Thompson,
K.E.McAuley,
L.M.Fisher,
and
M.R.Sanderson
(2009).
Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases.
|
| |
Nat Struct Mol Biol, 16,
667-669.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.C.Wang,
and
J.C.Wang
(2009).
A journey in the world of DNA rings and beyond.
|
| |
Annu Rev Biochem, 78,
31-54.
|
|
|
|
|
|
|
J.E.Deweese,
A.M.Burch,
A.B.Burgin,
and
N.Osheroff
(2009).
Use of divalent metal ions in the dna cleavage reaction of human type II topoisomerases.
|
| |
Biochemistry, 48,
1862-1869.
|
|
|
|
|
|
|
J.E.Deweese,
and
N.Osheroff
(2009).
The DNA cleavage reaction of topoisomerase II: wolf in sheep's clothing.
|
| |
Nucleic Acids Res, 37,
738-748.
|
|
|
|
|
|
|
J.L.Nitiss
(2009).
DNA topoisomerase II and its growing repertoire of biological functions.
|
| |
Nat Rev Cancer, 9,
327-337.
|
|
|
|
|
|
|
J.L.Nitiss
(2009).
Targeting DNA topoisomerase II in cancer chemotherapy.
|
| |
Nat Rev Cancer, 9,
338-350.
|
|
|
|
|
|
|
J.S.Koo,
W.Jung,
E.Shin,
H.D.Lee,
J.Jeong,
K.H.Kim,
H.Jeong,
and
S.W.Hong
(2009).
Impact of grade, hormone receptor, and HER-2 status in women with breast cancer on response to specific chemotherapeutic agents by in vitro adenosine triphosphate-based chemotherapy response assay.
|
| |
J Korean Med Sci, 24,
1150-1157.
|
|
|
|
|
|
|
M.Yanagida
(2009).
Clearing the way for mitosis: is cohesin a target?
|
| |
Nat Rev Mol Cell Biol, 10,
489-496.
|
|
|
|
|
|
|
T.R.Collins,
G.G.Hammes,
and
T.S.Hsieh
(2009).
Analysis of the eukaryotic topoisomerase II DNA gate: a single-molecule FRET and structural perspective.
|
| |
Nucleic Acids Res, 37,
712-720.
|
|
|
|
|
|
|
X.S.Pan,
K.A.Gould,
and
L.M.Fisher
(2009).
Probing the differential interactions of quinazolinedione PD 0305970 and quinolones with gyrase and topoisomerase IV.
|
| |
Antimicrob Agents Chemother, 53,
3822-3831.
|
|
|
|
|
|
|
A.J.Schoeffler,
and
J.M.Berger
(2008).
DNA topoisomerases: harnessing and constraining energy to govern chromosome topology.
|
| |
Q Rev Biophys, 41,
41.
|
|
|
|
|
|
|
D.Passarella,
F.Belinghieri,
M.Scarpellini,
G.Pratesi,
F.Zunino,
O.M.Gia,
L.D.Via,
G.Santoro,
and
B.Danieli
(2008).
Synthesis and biological evaluation of pyrroloiminoquinone derivatives.
|
| |
Bioorg Med Chem, 16,
2431-2438.
|
|
|
|
|
|
|
F.Gao,
H.Chao,
and
L.N.Ji
(2008).
DNA binding, photocleavage, and topoisomerase inhibition of functionalized ruthenium(II)-polypyridine complexes.
|
| |
Chem Biodivers, 5,
1962-1979.
|
|
|
|
|
|
|
F.Mueller-Planitz,
and
D.Herschlag
(2008).
Coupling between ATP binding and DNA cleavage by DNA topoisomerase II: A unifying kinetic and structural mechanism.
|
| |
J Biol Chem, 283,
17463-17476.
|
|
|
|
|
|
|
G.R.Ruan,
H.S.Zhao,
Y.Chang,
J.L.Li,
Y.Z.Qin,
Y.R.Liu,
S.S.Chen,
and
X.J.Huang
(2008).
Adenovirus-mediated PDCD5 gene transfer sensitizes K562 cells to apoptosis induced by idarubicin in vitro and in vivo.
|
| |
Apoptosis, 13,
641-648.
|
|
|
|
|
|
|
J.E.Deweese,
A.B.Burgin,
and
N.Osheroff
(2008).
Human topoisomerase IIalpha uses a two-metal-ion mechanism for DNA cleavage.
|
| |
Nucleic Acids Res, 36,
4883-4893.
|
|
|
|
|
|
|
J.E.Deweese,
A.B.Burgin,
and
N.Osheroff
(2008).
Using 3'-bridging phosphorothiolates to isolate the forward DNA cleavage reaction of human topoisomerase IIalpha.
|
| |
Biochemistry, 47,
4129-4140.
|
|
|
|
|
|
|
L.P.Swift,
S.M.Cutts,
A.Nudelman,
I.Levovich,
A.Rephaeli,
and
D.R.Phillips
(2008).
The cardio-protecting agent and topoisomerase II catalytic inhibitor sobuzoxane enhances doxorubicin-DNA adduct mediated cytotoxicity.
|
| |
Cancer Chemother Pharmacol, 61,
739-749.
|
|
|
|
|
|
|
O.J.Bandele,
and
N.Osheroff
(2008).
The efficacy of topoisomerase II-targeted anticancer agents reflects the persistence of drug-induced cleavage complexes in cells.
|
| |
Biochemistry, 47,
11900-11908.
|
|
|
|
|
|
|
S.W.Park,
A.M.Parrott,
D.T.Fritz,
Y.Park,
M.B.Mathews,
and
C.G.Lee
(2008).
Regulation of the catalytic function of topoisomerase II alpha through association with RNA.
|
| |
Nucleic Acids Res, 36,
6080-6090.
|
|
|
|
|
|
|
Y.H.Kao,
H.P.Hsieh,
S.K.Chitlimalla,
W.Y.Pan,
C.C.Kuo,
Y.C.Tsai,
W.H.Lin,
S.E.Chuang,
and
J.Y.Chang
(2008).
A novel peroxisome proliferator-activated receptor alpha/gamma agonist, BPR1H0101, inhibits topoisomerase II catalytic activity in human cancer cells.
|
| |
Anticancer Drugs, 19,
151-158.
|
|
|
|
|
|
|
Y.Hirano,
H.Takahashi,
M.Kumeta,
K.Hizume,
Y.Hirai,
S.Otsuka,
S.H.Yoshimura,
and
K.Takeyasu
(2008).
Nuclear architecture and chromatin dynamics revealed by atomic force microscopy in combination with biochemistry and cell biology.
|
| |
Pflugers Arch, 456,
139-153.
|
|
|
|
|
|
|
A.K.McClendon,
and
N.Osheroff
(2007).
DNA topoisomerase II, genotoxicity, and cancer.
|
| |
Mutat Res, 623,
83-97.
|
|
|
|
|
|
|
B.Letafat,
S.Emami,
N.Mohammadhosseini,
M.A.Faramarzi,
N.Samadi,
A.Shafiee,
and
A.Foroumadi
(2007).
Synthesis and antibacterial activity of new N-[2-(thiophen-3-yl)ethyl] piperazinyl quinolones.
|
| |
Chem Pharm Bull (Tokyo), 55,
894-898.
|
|
|
|
|
|
|
F.Gao,
H.Chao,
J.Q.Wang,
Y.X.Yuan,
B.Sun,
Y.F.Wei,
B.Peng,
and
L.N.Ji
(2007).
Targeting topoisomerase II with the chiral DNA-intercalating ruthenium(II) polypyridyl complexes.
|
| |
J Biol Inorg Chem, 12,
1015-1027.
|
|
|
|
|
|
|
F.Mueller-Planitz,
and
D.Herschlag
(2007).
DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity.
|
| |
Nucleic Acids Res, 35,
3764-3773.
|
|
|
|
|
|
|
G.Ren,
K.Gao,
F.D.Bushman,
and
M.Yeager
(2007).
Single-particle image reconstruction of a tetramer of HIV integrase bound to DNA.
|
| |
J Mol Biol, 366,
286-294.
|
|
|
|
|
|
|
I.Laponogov,
D.A.Veselkov,
M.K.Sohi,
X.S.Pan,
A.Achari,
C.Yang,
J.D.Ferrara,
L.M.Fisher,
and
M.R.Sanderson
(2007).
Breakage-reunion domain of Streptococcus pneumoniae topoisomerase IV: crystal structure of a gram-positive quinolone target.
|
| |
PLoS ONE, 2,
e301.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.C.Wang
(2007).
Unlocking and opening a DNA gate.
|
| |
Proc Natl Acad Sci U S A, 104,
4773-4774.
|
|
|
|
|
|
|
K.C.Dong,
and
J.M.Berger
(2007).
Structural basis for gate-DNA recognition and bending by type IIA topoisomerases.
|
| |
Nature, 450,
1201-1205.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
K.D.Corbett,
P.Benedetti,
and
J.M.Berger
(2007).
Holoenzyme assembly and ATP-mediated conformational dynamics of topoisomerase VI.
|
| |
Nat Struct Mol Biol, 14,
611-619.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
K.Hizume,
S.Araki,
K.Yoshikawa,
and
K.Takeyasu
(2007).
Topoisomerase II, scaffold component, promotes chromatin compaction in vitro in a linker-histone H1-dependent manner.
|
| |
Nucleic Acids Res, 35,
2787-2799.
|
|
|
|
|
|
|
L.Costenaro,
J.G.Grossmann,
C.Ebel,
and
A.Maxwell
(2007).
Modular structure of the full-length DNA gyrase B subunit revealed by small-angle X-ray scattering.
|
| |
Structure, 15,
329-339.
|
|
|
|
|
|
|
L.H.Meng,
and
J.Ding
(2007).
Salvicine, a novel topoisomerase II inhibitor, exerts its potent anticancer activity by ROS generation.
|
| |
Acta Pharmacol Sin, 28,
1460-1465.
|
|
|
|
|
|
|
O.J.Bandele,
and
N.Osheroff
(2007).
Bioflavonoids as poisons of human topoisomerase II alpha and II beta.
|
| |
Biochemistry, 46,
6097-6108.
|
|
|
|
|
|
|
R.M.Linka,
A.C.Porter,
A.Volkov,
C.Mielke,
F.Boege,
and
M.O.Christensen
(2007).
C-terminal regions of topoisomerase IIalpha and IIbeta determine isoform-specific functioning of the enzymes in vivo.
|
| |
Nucleic Acids Res, 35,
3810-3822.
|
|
|
|
|
|
|
R.Mattila,
K.Alanen,
and
S.Syrjänen
(2007).
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PDB code:
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Proc Natl Acad Sci U S A, 101,
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PDB code:
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N.Suda,
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Structure, 12,
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PDB code:
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S.M.Nelson,
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J Biol Chem, 279,
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A human topoisomerase II alpha heterodimer with only one ATP binding site can go through successive catalytic cycles.
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J Biol Chem, 278,
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PDB codes:
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M.D.Stone,
Z.Bryant,
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Proc Natl Acad Sci U S A, 100,
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Mol Cell, 11,
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PDB code:
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|
|
|
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|
Q.A.Khan,
G.Kohlhagen,
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Proc Natl Acad Sci U S A, 100,
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Proc Natl Acad Sci U S A, 100,
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PDB codes:
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|
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S.Kang,
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Functional dissection of the C-terminal domain of type II DNA topoisomerase from the kinetoplastid hemoflagellate Leishmania donovani.
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Nucleic Acids Res, 31,
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Mol Cell, 10,
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PDB code:
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|
|
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D.Strumberg,
J.L.Nitiss,
J.Dong,
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Antimicrob Agents Chemother, 46,
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J.C.Wang
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Nat Rev Mol Cell Biol, 3,
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J.Heddle,
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Quinolone-binding pocket of DNA gyrase: role of GyrB.
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Antimicrob Agents Chemother, 46,
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S.Trigueros,
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A GyrB-GyrA fusion protein expressed in yeast cells is able to remove DNA supercoils but cannot substitute eukaryotic topoisomerase II.
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Genes Cells, 7,
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T.Hu,
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ATPase domain of eukaryotic DNA topoisomerase II. Inhibition of ATPase activity by the anti-cancer drug bisdioxopiperazine and ATP/ADP-induced dimerization.
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J Biol Chem, 277,
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U.Kellner,
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Lancet Oncol, 3,
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A.Fedier,
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Resistance to topoisomerase poisons due to loss of DNA mismatch repair.
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Int J Cancer, 93,
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B.D.Lovett,
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Proc Natl Acad Sci U S A, 98,
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D.C.Hooper
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D.C.Hooper
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Antimicrob Agents Chemother, 45,
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D.Leroy,
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Analysis of etoposide binding to subdomains of human DNA topoisomerase II alpha in the absence of DNA.
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Biochemistry, 40,
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F.J.del Castillo,
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