-
1
-
-
50649101663
-
DNA topoisomerases: Harnessing and constraining energy to govern chromosome topology
-
Schoeffler, A. J. & Berger, J. M. DNA topoisomerases: harnessing and constraining energy to govern chromosome topology. Q. Rev. Biophys. 41, 41-101 (2008).
-
(2008)
Q. Rev. Biophys.
, vol.41
, pp. 41-101
-
-
Schoeffler, A.J.1
Berger, J.M.2
-
2
-
-
63349086953
-
The DNA cleavage reaction of topoisomerase II: Wolf in sheep's clothing
-
Deweese, J. E. & Osheroff, N. The DNA cleavage reaction of topoisomerase II: wolf in sheep's clothing. Nucleic Acids Res. 37, 738-748 (2009).
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 738-748
-
-
Deweese, J.E.1
Osheroff, N.2
-
3
-
-
0026448670
-
The capture of a DNA double helix by an ATP-dependent protein clamp: A key step in DNA transport by type II DNA topoisomerases
-
Roca, J. & Wang, J. C. The capture of a DNA double helix by an ATP-dependent protein clamp: a key step in DNA transport by type II DNA topoisomerases. Cell 71, 833-840 (1992).
-
(1992)
Cell
, vol.71
, pp. 833-840
-
-
Roca, J.1
Wang, J.C.2
-
4
-
-
0029961651
-
DNA transport by a type II topoisomerase: Direct evidence for a two-gate mechanism
-
Roca, J., Berger, J. M., Harrison, S. C. & Wang, J. C. DNA transport by a type II topoisomerase: direct evidence for a two-gate mechanism. Proc. Natl Acad. Sci. USA 93, 4057-4062 (1996).
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 4057-4062
-
-
Roca, J.1
Berger, J.M.2
Harrison, S.C.3
Wang, J.C.4
-
5
-
-
0024519424
-
Inducible overexpression, purification, and active site mapping of DNA topoisomerase II from the yeast Saccharomyces cerevisiae
-
Worland, S. T. & Wang, J. C. Inducible overexpression, purification, and active site mapping of DNA topoisomerase II from the yeast Saccharomyces cerevisiae. J. Biol. Chem. 264, 4412-4416 (1989).
-
(1989)
J. Biol. Chem.
, vol.264
, pp. 4412-4416
-
-
Worland, S.T.1
Wang, J.C.2
-
6
-
-
0020490617
-
Yeast DNA topoisomerase II. An ATP-dependent type II topoisomerase that catalyzes the catenation, decatenation, unknotting, and relaxation of double-stranded DNA rings
-
Goto, T. & Wang, J. C. Yeast DNA topoisomerase II. An ATP-dependent type II topoisomerase that catalyzes the catenation, decatenation, unknotting, and relaxation of double-stranded DNA rings. J. Biol. Chem. 257, 5866-5872 (1982).
-
(1982)
J. Biol. Chem.
, vol.257
, pp. 5866-5872
-
-
Goto, T.1
Wang, J.C.2
-
7
-
-
0021235437
-
The purification and characterization of DNA topoisomerases i and II of the yeast Saccharomyces cerevisiae
-
Goto, T., Laipis, P. & Wang, J. C. The purification and characterization of DNA topoisomerases I and II of the yeast Saccharomyces cerevisiae. J. Biol. Chem. 259, 10422-10429 (1984).
-
(1984)
J. Biol. Chem.
, vol.259
, pp. 10422-10429
-
-
Goto, T.1
Laipis, P.2
Wang, J.C.3
-
8
-
-
0034673121
-
Mutagenesis of E477 or K505 in the B9 domain of human topoisomerase IIb increases the requirement for magnesium ions during strand passage
-
West, K. L. et al. Mutagenesis of E477 or K505 in the B9 domain of human topoisomerase IIb increases the requirement for magnesium ions during strand passage. Biochemistry 39, 1223-1233 (2000).
-
(2000)
Biochemistry
, vol.39
, pp. 1223-1233
-
-
West, K.L.1
-
9
-
-
0036304446
-
The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: A proposed two metal-ion mechanism
-
Noble, C. G. & Maxwell, A. The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: a proposed two metal-ion mechanism. J. Mol. Biol. 318, 361-371 (2002).
-
(2002)
J. Mol. Biol.
, vol.318
, pp. 361-371
-
-
Noble, C.G.1
Maxwell, A.2
-
10
-
-
70349762697
-
Metal ion interactions in the DNA cleavage/ligation active site of human topoisomerase Iia
-
Deweese, J. E., Guengerich, F. P., Burgin, A. B. & Osheroff, N. Metal ion interactions in the DNA cleavage/ligation active site of human topoisomerase IIa.Biochemistry 48, 8940-8947 (2009).
-
(2009)
Biochemistry
, vol.48
, pp. 8940-8947
-
-
Deweese, J.E.1
Guengerich, F.P.2
Burgin, A.B.3
Osheroff, N.4
-
11
-
-
0027184481
-
A general two-metal-ion mechanism for catalytic RNA
-
Steitz, T. A. & Steitz, J. A. A general two-metal-ion mechanism for catalytic RNA. Proc. Natl Acad. Sci. USA 90, 6498-6502 (1993).
-
(1993)
Proc. Natl Acad. Sci. USA
, vol.90
, pp. 6498-6502
-
-
Steitz, T.A.1
Steitz, J.A.2
-
13
-
-
37549023863
-
Structural basis for gate-DNA recognition and bending by type IIA topoisomerases
-
Dong, K. C. & Berger, J. M. Structural basis for gate-DNA recognition and bending by type IIA topoisomerases. Nature 450, 1201-1205 (2007).
-
(2007)
Nature
, vol.450
, pp. 1201-1205
-
-
Dong, K.C.1
Berger, J.M.2
-
14
-
-
0029165078
-
A novel suicide substrate for DNA topoisomerases and site-specific recombinases
-
Burgin, A. B. Jr, Huizenga, B. N. & Nash, H. A. A novel suicide substrate for DNA topoisomerases and site-specific recombinases. Nucleic Acids Res. 23, 2973-2979 (1995).
-
(1995)
Nucleic Acids Res.
, vol.23
, pp. 2973-2979
-
-
Burgin Jr., A.B.1
Huizenga, B.N.2
Nash, H.A.3
-
15
-
-
0032489634
-
Crystal structures of human topoisomerase i in covalent and noncovalent complexes with DNA
-
Redinbo, M. R., Stewart, L., Kuhn, P., Champoux, J. J. & Hol, W. G. Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. Science 279, 1504-1513 (1998).
-
(1998)
Science
, vol.279
, pp. 1504-1513
-
-
Redinbo, M.R.1
Stewart, L.2
Kuhn, P.3
Champoux, J.J.4
Hol, W.G.5
-
16
-
-
0029666424
-
2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions
-
2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions. Biochemistry 35, 8110-8119 (1996).
-
(1996)
Biochemistry
, vol.35
, pp. 8110-8119
-
-
Wang, J.1
Yu, P.2
Lin, T.C.3
Konigsberg, W.H.4
Steitz, T.A.5
-
17
-
-
33646004109
-
Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release
-
Nowotny, M. & Yang, W. Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release. EMBO J. 25, 1924-1933 (2006).
-
(2006)
EMBO J.
, vol.25
, pp. 1924-1933
-
-
Nowotny, M.1
Yang, W.2
-
18
-
-
0032530488
-
Toprim - A conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins
-
Aravind, L., Leipe, D. D. & Koonin, E. V. Toprim-a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. Nucleic Acids Res. 26, 4205-4213 (1998).
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 4205-4213
-
-
Aravind, L.1
Leipe, D.D.2
Koonin, E.V.3
-
19
-
-
0032493748
-
Identification of active site residues in the "gyrA" half of yeast DNA topoisomerase II
-
Liu, Q. & Wang, J. C. Identification of active site residues in the "GyrA" half of yeast DNA topoisomerase II. J. Biol. Chem. 273, 20252-20260 (1998).
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 20252-20260
-
-
Liu, Q.1
Wang, J.C.2
-
20
-
-
0034637574
-
Assignment of functional amino acids around the active site of human DNA topoisomerase IIa
-
Okada, Y. et al. Assignment of functional amino acids around the active site of human DNA topoisomerase IIa. J. Biol. Chem. 275, 24630-24638 (2000).
-
(2000)
J. Biol. Chem.
, vol.275
, pp. 24630-24638
-
-
Okada, Y.1
-
21
-
-
0033229826
-
Structure and function of an archaeal topoisomerase VI subunit with homology to the meiotic recombination factor Spo11
-
Nichols, M. D., DeAngelis, K., Keck, J. L. & Berger, J. M. Structure and function of an archaeal topoisomerase VI subunit with homology to the meiotic recombination factor Spo11. EMBO J. 18, 6177-6188 (1999).
-
(1999)
EMBO J.
, vol.18
, pp. 6177-6188
-
-
Nichols, M.D.1
Deangelis, K.2
Keck, J.L.3
Berger, J.M.4
-
22
-
-
0032493293
-
Structural similarities between topoisomerases that cleave one or both DNA strands
-
Berger, J. M., Fass, D., Wang, J. C. & Harrison, S. C. Structural similarities between topoisomerases that cleave one or both DNA strands. Proc. Natl Acad. Sci. USA 95, 7876-7881 (1998).
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 7876-7881
-
-
Berger, J.M.1
Fass, D.2
Wang, J.C.3
Harrison, S.C.4
-
23
-
-
0025770051
-
Mechanistic studies on E. coli DNA topoisomerase I: Divalent ion effects
-
Domanico, P. L. & Tse-Dinh, Y. C. Mechanistic studies on E. coli DNA topoisomerase I: divalent ion effects. J. Inorg. Biochem. 42, 87-96 (1991).
-
(1991)
J. Inorg. Biochem.
, vol.42
, pp. 87-96
-
-
Domanico, P.L.1
Tse-Dinh, Y.C.2
-
24
-
-
0035963340
-
Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule
-
Changela, A., DiGate, R. J. & Mondragon, A. Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule. Nature 411, 1077-1081 (2001).
-
(2001)
Nature
, vol.411
, pp. 1077-1081
-
-
Changela, A.1
Digate, R.J.2
Mondragon, A.3
-
25
-
-
33645826239
-
Experimental and computational investigations of Ser10 and Lys13 in the binding and cleavage of DNA substrates by Escherichia coli DNA topoisomerase i
-
Strahs, D., Zhu, C. X., Cheng, B., Chen, J. & Tse-Dinh, Y. C. Experimental and computational investigations of Ser10 and Lys13 in the binding and cleavage of DNA substrates by Escherichia coli DNA topoisomerase I. Nucleic Acids Res. 34, 1785-1797 (2006).
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 1785-1797
-
-
Strahs, D.1
Zhu, C.X.2
Cheng, B.3
Chen, J.4
Tse-Dinh, Y.C.5
-
26
-
-
58149083577
-
Asp-to-Asn substitution at the first position of the DxD TOPRIM motif of recombinant bacterial topoisomerase i is extremely lethal to E. coli
-
Cheng, B. et al. Asp-to-Asn substitution at the first position of the DxD TOPRIM motif of recombinant bacterial topoisomerase I is extremely lethal to E. coli. J. Mol. Biol. 385, 558-567 (2009).
-
(2009)
J. Mol. Biol.
, vol.385
, pp. 558-567
-
-
Cheng, B.1
-
27
-
-
0030045003
-
Structure and mechanism of DNA topoisomerase II
-
Berger, J. M., Gamblin, S. J., Harrison, S. C. & Wang, J. C. Structure and mechanism of DNA topoisomerase II. Nature 379, 225-232 (1996).
-
(1996)
Nature
, vol.379
, pp. 225-232
-
-
Berger, J.M.1
Gamblin, S.J.2
Harrison, S.C.3
Wang, J.C.4
-
28
-
-
0000301456
-
Crystal structure of the breakage-reunion domain of DNA gyrase
-
Morais Cabral, J. H. et al. Crystal structure of the breakage-reunion domain of DNA gyrase. Nature 388, 903-906 (1997).
-
(1997)
Nature
, vol.388
, pp. 903-906
-
-
Morais Cabral, J.H.1
-
29
-
-
0032947158
-
Quaternary changes in topoisomerase II may direct orthogonal movement of two DNA strands
-
Fass, D., Bogden, C. E. & Berger, J. M. Quaternary changes in topoisomerase II may direct orthogonal movement of two DNA strands. Nature Struct. Biol. 6, 322-326 (1999).
-
(1999)
Nature Struct. Biol.
, vol.6
, pp. 322-326
-
-
Fass, D.1
Bogden, C.E.2
Berger, J.M.3
-
30
-
-
41449103710
-
Using 39-bridging phosphorothiolates to isolate the forward DNA cleavage reaction of human topoisomerase IIa
-
Deweese, J. E., Burgin, A. B. & Osheroff, N. Using 39-bridging phosphorothiolates to isolate the forward DNA cleavage reaction of human topoisomerase IIa. Biochemistry 47, 4129-4140 (2008).
-
(2008)
Biochemistry
, vol.47
, pp. 4129-4140
-
-
Deweese, J.E.1
Burgin, A.B.2
Osheroff, N.3
-
32
-
-
1342264715
-
Synthesis of phosphorothioamidites derived from 39-thio-39-deoxythymidine and 39-thio-29,39-dideoxycytidine and the automated synthesis of oligodeoxynucleotides containing a 39-S-phosphorothiolate linkage
-
Sabbagh, G., Fettes, K. J., Gosain, R., O'Neil, I. A. & Cosstick, R. Synthesis of phosphorothioamidites derived from 39-thio-39-deoxythymidine and 39-thio-29,39-dideoxycytidine and the automated synthesis of oligodeoxynucleotides containing a 39-S-phosphorothiolate linkage. Nucleic Acids Res. 32, 495-501 (2004).
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 495-501
-
-
Sabbagh, G.1
Fettes, K.J.2
Gosain, R.3
O'Neil, I.A.4
Cosstick, R.5
-
33
-
-
11844305022
-
Suite of three protein crystallography beamlines with single superconducting bend magnet as the source
-
MacDowell, A. A. et al. Suite of three protein crystallography beamlines with single superconducting bend magnet as the source. J. Synchrotron Radiat. 11, 447-455 (2004).
-
(2004)
J. Synchrotron Radiat.
, vol.11
, pp. 447-455
-
-
MacDowell, A.A.1
-
34
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997).
-
(1997)
Methods Enzymol.
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
35
-
-
34447508216
-
Phaser crystallographic software
-
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Cryst. 40, 658-674 (2007).
-
(2007)
J. Appl. Cryst.
, vol.40
, pp. 658-674
-
-
McCoy, A.J.1
-
36
-
-
13244281317
-
Model-building tools for molecular graphics
-
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126-2132 (2004).
-
(2004)
Acta Crystallogr. D.
, vol.60
, pp. 2126-2132
-
-
Emsley, P.1
Coot, C.K.2
-
37
-
-
14244272868
-
PHENIX: Building new software for automated crystallographic structure determination
-
Adams, P. D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D 58, 1948-1954 (2002).
-
(2002)
Acta Crystallogr. D.
, vol.58
, pp. 1948-1954
-
-
Adams, P.D.1
-
38
-
-
3242886389
-
MOLPROBITY: Structure validation and all-atom contact analysis for nucleic acids and their complexes
-
Davis, I. W., Murray, L. W., Richardson, J. S. & Richardson, D. C. MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res. 32, W615-W619 (2004).
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Davis, I.W.1
Murray, L.W.2
Richardson, J.S.3
Richardson, D.C.4
-
40
-
-
0032577678
-
Crystal structure of a tyrosine phosphorylated STAT-1 dimer bound to DNA
-
Chen, X. et al. Crystal structure of a tyrosine phosphorylated STAT-1 dimer bound to DNA. Cell 93, 827-839 (1998).
-
(1998)
Cell
, vol.93
, pp. 827-839
-
-
Chen, X.1
-
41
-
-
0024339376
-
Double-stranded DNA cleavage/religation reaction of eukaryotic topoisomerase II: Evidence for a nicked DNA intermediate
-
Zechiedrich, E. L., Christiansen, K., Andersen, A. H., Westergaard, O. & Osheroff, N. Double-stranded DNA cleavage/religation reaction of eukaryotic topoisomerase II: evidence for a nicked DNA intermediate. Biochemistry 28, 6229-6236 (1989). (Pubitemid 19202012)
-
(1989)
Biochemistry
, vol.28
, Issue.15
, pp. 6229-6236
-
-
Zechiedrich, E.L.1
Christiansen, K.2
Andersen, A.H.3
Westergaard, O.4
Osheroff, N.5
|