Molecola del Mese
di David S. Goodsell
Trad. di Mauro Tonellato
Topoisomerasi

Indice 2006

PDB
ID  		 Title Authors Publication
Year 		Journal Name Volume
Id 		First Page Pubmed
1A31 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. 		1998 Science 279 1504 9488644
1A35 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. 		1998 Science 279 1504 9488644
1A36 A model for the mechanism of human topoisomerase
I. 		Stewart, L., Redinbo, M.R., Qiu, X., Hol,
W.G., Champoux, J.J. 		1998 Science 279 1534 9488652
1A41 Conservation of structure and mechanism between
eukaryotic topoisomerase I and site-specific
recombinases. 		Cheng, C., Kussie, P., Pavletich, N., Shuman,
S. 		1998 Cell 92 841 9529259
1AB4 Crystal structure of the breakage-reunion
domain of DNA gyrase. 		Cabral, J.H., Jackson, A.P., Smith, C.V.,
Shikotra, N., Maxwell, A., Liddington, R.C. 		1997 Nature 388 903 9278055
1AJ6 The entropic penalty of ordered water accounts
for weaker binding of the antibiotic novobiocin
to a resistant mutant of DNA gyrase: a thermodynamic
and crystallographic study. 		Holdgate, G.A., Tunnicliffe, A., Ward, W.H.,
Weston, S.A., Rosenbrock, G., Barth, P.T.,
Taylor, I.W., Pauptit, R.A., Timms, D. 		1997 Biochemistry 36 9663 9245398
1AM2 Crystal structure of GyrA intein from Mycobacterium
xenopi reveals structural basis of protein
splicing. 		Klabunde, T., Sharma, S., Telenti, A., Jacobs
Jr., W.R., Sacchettini, J.C. 		1998 Nat.Struct.Biol. 5 31 9437427
1BGW Structure and mechanism of DNA topoisomerase
II. 		Berger, J.M., Gamblin, S.J., Harrison, S.C.,
Wang, J.C. 		1996 Nature 379 225 8538787
1BJT Quaternary changes in topoisomerase II may
direct orthogonal movement of two DNA strands. 		Fass, D., Bogden, C.E., Berger, J.M. 1999 Nat.Struct.Biol. 6 322 10201398
1CX3 Solution structure and dynamics of a complex
between DNA and the antitumor bisnaphthalimide
LU-79553: intercalated ring flipping on
the millisecond time scale. 		Gallego, J., Reid, B.R. 1999 Biochemistry 38 15104 10563793
1CY0 Protein-nucleotide interactions in E. coli
DNA topoisomerase I. 		Feinberg, H., Changela, A., Mondragon, A. 1999 Nat.Struct.Biol. 6 961 10504732
1CY1 Protein-nucleotide interactions in E. coli
DNA topoisomerase I. 		Feinberg, H., Changela, A., Mondragon, A. 1999 Nat.Struct.Biol. 6 961 10504732
1CY2 Protein-nucleotide interactions in E. coli
DNA topoisomerase I. 		Feinberg, H., Changela, A., Mondragon, A. 1999 Nat.Struct.Biol. 6 961 10504732
1CY4 Protein-nucleotide interactions in E. coli
DNA topoisomerase I. 		Feinberg, H., Changela, A., Mondragon, A. 1999 Nat.Struct.Biol. 6 961 10504732
1CY6 Protein-nucleotide interactions in E. coli
DNA topoisomerase I. 		Feinberg, H., Changela, A., Mondragon, A. 1999 Nat.Struct.Biol. 6 961 10504732
1CY7 Protein-nucleotide interactions in E. coli
DNA topoisomerase I. 		Feinberg, H., Changela, A., Mondragon, A. 1999 Nat.Struct.Biol. 6 961 10504732
1CY8 Protein-nucleotide interactions in E. coli
DNA topoisomerase I. 		Feinberg, H., Changela, A., Mondragon, A. 1999 Nat.Struct.Biol. 6 961 10504732
1CY9 Conformational changes in E. coli DNA topoisomerase
I. 		Feinberg, H., Lima, C.D., Mondragon, A. 1999 Nat.Struct.Biol. 6 918 10504724
1CYY Conformational changes in E. coli DNA topoisomerase
I. 		Feinberg, H., Lima, C.D., Mondragon, A. 1999 Nat.Struct.Biol. 6 918 10504724
1D3Y 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. 		1999 EMBO J. 18 6177 10545127
1D6M The structure of Escherichia coli DNA topoisomerase
III. 		Mondragon, A., DiGate, R. 1999 Structure Fold.Des. 7 1373 10574789
1DL8 Acridinecarboxamide topoisomerase poisons:
structural and kinetic studies of the DNA
complexes of 5-substituted 9-amino-(N-(2-dimethylamino)
ethyl)acridine-4-carboxamides. 		Adams, A., Guss, J.M., Collyer, C.A., Denny,
W.A., Prakash, A.S., Wakelin, L.P. 		2000 Mol.Pharmacol. 58 649 10953060
1ECL Three-dimensional structure of the 67K N-terminal
fragment of E. coli DNA topoisomerase I. 		Lima, C.D., Wang, J.C., Mondragon, A. 1994 Nature 367 138 8114910
1EG6 Guanine specific binding at a DNA junction
formed by d[CG(5-BrU)ACG](2) with a topoisomerase
poison in the presence of Co(2+) ions. 		Thorpe, J.H., Hobbs, J.R., Todd, A.K., Denny,
W.A., Charlton, P., Cardin, C.J. 		2000 Biochemistry 39 15055 11106483
1EI1 Dimerization of Escherichia coli DNA-gyrase
B provides a structural mechanism for activating
the ATPase catalytic center. 		Brino, L., Urzhumtsev, A., Mousli, M., Bronner,
C., Mitschler, A., Oudet, P., Moras, D. 		2000 J.Biol.Chem. 275 9468 10734094
1EJ9 Novel insights into catalytic mechanism from
a crystal structure of human topoisomerase
I in complex with DNA. 		Redinbo, M.R., Champoux, J.J., Hol, W.G. 2000 Biochemistry 39 6832 10841763
1EV7 Crystal structure of NaeI-an evolutionary
bridge between DNA endonuclease and topoisomerase. 		Huai, Q., Colandene, J.D., Chen, Y., Luo,
F., Zhao, Y., Topal, M.D., Ke, H. 		2000 EMBO J. 19 3110 10856254
1FV8 NMR study of a heterochiral DNA hairpin:impact
of L-enantiomery in the loop. 		El Amri, C., Mauffret, O., Santamariar, F.,
Tevanian, G., Rayner, B., Fermandjian, S. 		2001 J.Biomol.Struct.Dyn. 19 459 11790144
1GKU Crystal structure of reverse gyrase: insights
into the positive supercoiling of DNA. 		Rodriguez, A.C., Stock, D. 2002 EMBO J. 21 418 11823434
1GL9 Crystal structure of reverse gyrase: insights
into the positive supercoiling of DNA. 		Rodriguez, A.C., Stock, D. 2002 EMBO J. 21 418 11823434
1I7D Crystal structure of a complex of a type
IA DNA topoisomerase with a single-stranded
DNA molecule. 		Changela, A., DiGate, R.J., Mondragon, A. 2001 Nature 411 1077 11429611
1K4S The mechanism of topoisomerase I poisoning
by a camptothecin analog 		Staker, B.L., Hjerrild, K., Feese, M.D.,
Behnke, C.A., Burgin Jr., A.B., Stewart,
L.J. 		2002 Proc.Natl.Acad.Sci.USA 99 15387 12426403
1K4T The mechanism of topoisomerase I poisoning
by a camptothecin analog 		Staker, B.L., Hjerrild, K., Feese, M.D.,
Behnke, C.A., Burgin Jr., A.B., Stewart,
L.J. 		2002 Proc.Natl.Acad.Sci.USA 99 15387 12426403
1KCI Crystal structure of 9-amino-N-[2-(4-morpholinyl)ethyl]
-4-acridinecarboxamide bound to d(CGTACG)2:
implications for structure-activity relationships of
acridinecarboxamide topoisomerase
poisons. 		Adams, A., Guss, J.M., Denny, W.A., Wakelin,
L.P. 		2002 Nucleic Acids Res. 30 719 11809884
1KIJ An open conformation of the Thermus thermophilus
gyrase B ATP-binding domain. 		Lamour, V., Hoermann, L., Jeltsch, J.M.,
Oudet, P., Moras, D. 		2002 J.Biol.Chem. 277 18947 11850422
1KZN DNA gyrase interaction with coumarin-based
inhibitors: the role of the hydroxybenzoate
isopentenyl moiety and the 5'-methyl group
of the noviose. 		Lafitte, D., Lamour, V., Tsvetkov, P.O.,
Makarov, A.A., Klich, M., Deprez, P., Moras,
D., Briand, C., Gilli, R. 		2002 Biochemistry 41 7217 12044152
1LPQ 8-Oxoguanine rearranges the active site of
human topoisomerase I 		Lesher, D.T., Pommier, Y., Stewart, L., Redinbo,
M.R. 		2002 Proc.Natl.Acad.Sci.USA 99 12102 12209008
1M69 Heavy Going: the Atomic Resolution Structure
of a Topoisomerase II Poison Intercalating
into DNA in Multiple Orientations Also Reveals
a Multiple Adenine-Thymine Hydrogen Bonding
Pattern 		Teixeira, S.C.M., Thorpe, J.H., Todd, A.K.,
Cardin, C.J. 		n/a To be Published n/a n/a n/a
1MU5 Structure of the topoisomerase VI-B subunit:
implications for type II topoisomerase mechanism
and evolution 		Corbett, K.D., Berger, J.M. 2003 Embo J. 22 151 12505993
1MW8 Structure of a Complex between E. coli DNA
Topoisomerase I and Single-Stranded DNA. 		Perry, K., Mondragon, A. 2003 Structure 11 1349 14604525
1MW9 Structure of a Complex between E. coli DNA
Topoisomerase I and Single-Stranded DNA. 		Perry, K., Mondragon, A. 2003 Structure 11 1349 14604525
1MX0 Structure of the topoisomerase VI-B subunit:
implications for type II topoisomerase mechanism
and evolution 		Corbett, K.D., Berger, J.M. 2003 Embo J. 22 151 12505993
1NH3 Structural Impact of the Leukemia Drug 1-beta-D-
Arabinofuranosylcytosine
(Ara-C) on the Covalent Human Topoisomerase
I-DNA Complex 		Chrencik, J.E., Burgin, A.B., Pommier, Y.,
Stewart, L., Redinbo, M.R. 		2003 J.Biol.Chem. 278 12461 12533542
1NOP Crystal structure of a transition state mimic
for Tdp1 assembled from vanadate, DNA, and
a topoisomerase I-derived peptide 		Davies, D.R., Interthal, H., Champoux, J.J.,
Hol, W.G.J. 		2003 Chem.Biol. 10 139 12618186
1OIS A 26 kDa yeast DNA topoisomerase I fragment:
crystallographic structure and mechanistic
implications. 		Lue, N., Sharma, A., Mondragon, A., Wang,
J.C. 		1995 Structure 3 1315 8747458
1PVG Structure of the topoisomerase II ATPase
region and its mechanism of inhibition by
the chemotherapeutic agent ICRF-187 		Classen, S., Olland, S., Berger, J.M. 2003 Proc.Natl.Acad.Sci.USA 100 10629 12963818
1QZR Structure of the topoisomerase II ATPase
region and its mechanism of inhibition by
the chemotherapeutic agent ICRF-187 		Classen, S., Olland, S., Berger, J.M. 2003 Proc.Natl.Acad.Sci.USA 100 10629 12963818
1R49 The role of lysine 532 in the catalytic mechanism
of human topoisomerase I. 		Interthal, H., Quigley, P.M., Hol, W.G.,
Champoux, J.J. 		2004 J.Biol.Chem. 279 2984 14594810
1RFF Explorations of peptide and oligonucleotide
binding sites of tyrosyl-DNA phosphodiesterase
using vanadate complexes. 		Davies, D.R., Interthal, H., Champoux, J.J.,
Hol, W.G. 		2004 J.Med.Chem. 47 829 14761185
1RFI Explorations of peptide and oligonucleotide
binding sites of tyrosyl-DNA phosphodiesterase
using vanadate complexes. 		Davies, D.R., Interthal, H., Champoux, J.J.,
Hol, W.G. 		2004 J.Med.Chem. 47 829 14761185
1RG1 Explorations of peptide and oligonucleotide
binding sites of tyrosyl-DNA phosphodiesterase
using vanadate complexes. 		Davies, D.R., Interthal, H., Champoux, J.J.,
Hol, W.G. 		2004 J.Med.Chem. 47 829 14761185
1RG2 Explorations of peptide and oligonucleotide
binding sites of tyrosyl-DNA phosphodiesterase
using vanadate complexes. 		Davies, D.R., Interthal, H., Champoux, J.J.,
Hol, W.G. 		2004 J.Med.Chem. 47 829 14761185
1RGT Explorations of peptide and oligonucleotide
binding sites of tyrosyl-DNA phosphodiesterase
using vanadate complexes. 		Davies, D.R., Interthal, H., Champoux, J.J.,
Hol, W.G. 		2004 J.Med.Chem. 47 829 14761185
1RGU Explorations of peptide and oligonucleotide
binding sites of tyrosyl-DNA phosphodiesterase
using vanadate complexes. 		Davies, D.R., Interthal, H., Champoux, J.J.,
Hol, W.G. 		2004 J.Med.Chem. 47 829 14761185
1RH0 Explorations of peptide and oligonucleotide
binding sites of tyrosyl-DNA phosphodiesterase
using vanadate complexes. 		Davies, D.R., Interthal, H., Champoux, J.J.,
Hol, W.G. 		2004 J.Med.Chem. 47 829 14761185
1RR8 Mechanisms of camptothecin resistance by
human topoisomerase I mutations 		Chrencik, J.E., Staker, B.L., Burgin, A.B.,
Pourquier, P., Pommier, Y., Stewart, L.,
Redinbo, M.R. 		2004 J.Mol.Biol. 339 773 15165849
1RRJ Mechanisms of camptothecin resistance by
human topoisomerase I mutations 		Chrencik, J.E., Staker, B.L., Burgin, A.B.,
Pourquier, P., Pommier, Y., Stewart, L.,
Redinbo, M.R. 		2004 J.Mol.Biol. 339 773 15165849
1S14 Crystal Structures of Escherichia coli Topoisomerase
IV ParE Subunit (24 and 43 Kilodaltons):
a Single Residue Dictates Differences in
Novobiocin Potency against Topoisomerase
IV and DNA Gyrase 		Bellon, S., Parsons, J.D., Wei, Y., Hayakawa,
K., Swenson, L.L., Charifson, P.S., Lippke,
J.A., Aldape, R., Gross, C.H. 		2004 ANTIMICROB.AGENTS
CHEMOTHER. 		48 1856 n/a
1S16 Crystal Structures of Escherichia coli Topoisomerase
IV ParE Subunit (24 and 43 Kilodaltons):
a Single Residue Dictates Differences in
Novobiocin Potency against Topoisomerase
IV and DNA Gyrase 		Bellon, S., Parsons, J.D., Wei, Y., Hayakawa,
K., Swenson, L.L., Charifson, P.S., Lippke,
J.A., Aldape, R., Gross, C.H. 		2004 ANTIMICROB.AGENTS
CHEMOTHER. 		48 1856 n/a
1SC7 Structures of three classes of anticancer
agents bound to the human topoisomerase
I-DNA covalent complex 		Staker, B.L., Feese, M.D., Cushman, M., Pommier,
Y., Zembower, D., Stewart, L., Burgin, A.B. 		2005 J.Med.Chem. 48 2336 15801827
1SEU Structures of three classes of anticancer
agents bound to the human topoisomerase
I-DNA covalent complex 		Staker, B.L., Feese, M.D., Cushman, M., Pommier,
Y., Zembower, D., Stewart, L., Burgin, A.B. 		2005 J.Med.Chem. 48 2336 15801827
1SUU The C-terminal domain of DNA gyrase A adopts
a DNA-bending beta-pinwheel fold. 		Corbett, K.D., Shultzaberger, R.K., Berger,
J.M. 		2004 Proc.Natl.Acad.
Sci.USA 		101 7293 n/a
1T8I Structures of three classes of anticancer
agents bound to the human topoisomerase
I-DNA covalent complex 		Staker, B.L., Feese, M.D., Cushman, M., Pommier,
Y., Zembower, D., Stewart, L., Burgin, A.B. 		2005 J.Med.Chem. 48 2336 15801827
1TL8 Synthesis and Mechanism of Action Studies
of a Series of Norindenoisoquinoline Topoisomerase
I Poisons Reveal an Inhibitor with a Flipped
Orientation in the Ternary DNA-Enzyme-Inhibitor
Complex As Determined by X-ray Crystallographic
Analysis 		Ioanoviciu, A., Antony, S., Pommier, Y.,
Staker, B.L., Stewart, L., Cushman, M. 		2005 J.Med.Chem. 48 4803 16033260
1VCC Crystal structure of the amino-terminal fragment
of vaccinia virus DNA topoisomerase I at
1.6 A resolution. 		Sharma, A., Hanai, R., Mondragon, A. 1994 Structure 2 767 7994576
1VUB Crystal structure of CcdB, a topoisomerase
poison from E. coli. 		Loris, R., Dao-Thi, M.H., Bahassi, E.M.,
Van Melderen, L., Poortmans, F., Liddington,
R., Couturier, M., Wyns, L. 		1999 J.Mol.Biol. 285 1667 9917404
1WF6 The third BRCA1 C-terminus (BRCT) domain
of Similar to S.pombe rad4+/cut5+ product 		Nagashima, T., Hayashi, F., Yokoyama, S. n/a TO BE PUBL n/a n/a n/a
1WP5 Structure of the topoisomerase IV C-terminal
domain: a broken beta-propeller implies
a role as geometry facilitator in catalysis 		Hsieh, T.-J., Farh, L., Huang, W.M., Chan,
N.-L. 		2004 J.Biol.Chem. 279 55587 15466871
1X75 Molecular Basis of Gyrase Poisoning by the
Addiction Toxin CcdB 		Dao-Thi, M.H., Van Melderen, L., De Genst,
E., Afif, H., Buts, L., Wyns, L., Loris,
R. 		2005 J.Mol.Biol. 348 1091 15854646
1YO5 Analysis of the 2.0 A Crystal Structure of
the Protein-DNA Complex of the Human PDEF
Ets Domain Bound to the Prostate Specific
Antigen Regulatory Site 		Wang, Y., Feng, L., Said, M., Balderman,
S., Fayazi, Z., Liu, Y., Ghosh, D., Gulick,
A.M. 		2005 Biochemistry 44 7095 15882048
1YUA Solution structure of the C-terminal single-stranded
DNA-binding domain of Escherichia coli topoisomerase
I. 		Yu, L., Zhu, C.X., Tse-Dinh, Y.C., Fesik,
S.W. 		1995 Biochemistry 34 7622 7779808
1Z59 Structural dissection of ATP turnover in
the prototypical GHL ATPase topo VI 		Corbett, K.D., Berger, J.M. 2005 Structure 13 873 n/a
1Z5A Structural dissection of ATP turnover in
the prototypical GHL ATPase topo VI 		Corbett, K.D., Berger, J.M. 2005 Structure 13 873 n/a
1Z5B Structural dissection of ATP turnover in
the prototypical GHL ATPase topo VI 		Corbett, K.D., Berger, J.M. 2005 Structure 13 873 n/a
1Z5C Structural dissection of ATP turnover in
the prototypical GHL ATPase topo VI 		Corbett, K.D., Berger, J.M. 2005 Structure 13 873 n/a
1ZI0 A superhelical spiral in the Escherichia
coli DNA gyrase A C-terminal domain imparts
unidirectional supercoiling bias 		Ruthenburg, A.J., Graybosch, D.M., Huetsch,
J.C., Verdine, G.L. 		2005 J.Biol.Chem. 280 26177 15897198
1ZVT The Structural Basis for Substrate Specificity
in DNA Topoisomerase IV. 		Corbett, K.D., Schoeffler, A.J., Thomsen,
N.D., Berger, J.M. 		2005 J.Mol.Biol. 351 545 16023670
1ZVU The Structural Basis for Substrate Specificity
in DNA Topoisomerase IV. 		Corbett, K.D., Schoeffler, A.J., Thomsen,
N.D., Berger, J.M. 		2005 J.Mol.Biol. 351 545 16023670
1ZXM Nucleotide-dependent Domain Movement in the
ATPase Domain of a Human Type IIA DNA
Topoisomerase. 		Wei, H., Ruthenburg, A.J., Bechis, S.K.,
Verdine, G.L. 		2005 J.Biol.Chem. 280 37041 16100112
1ZXN Nucleotide-dependent Domain Movement in the
ATPase Domain of a Human Type IIA DNA
Topoisomerase. 		Wei, H., Ruthenburg, A.J., Bechis, S.K.,
Verdine, G.L. 		2005 J.Biol.Chem. 280 37041 16100112
2F4Q Crystal Structure of a Bacterial Type IB
DNA Topoisomerase Reveals a Preassembled
Active Site in the Absence of DNA 		Patel, A., Shuman, S., Mondragon, A. n/a J.Biol.Chem. n/a n/a n/a
2VUB Crystal structure of CcdB, a topoisomerase
poison from E. coli. 		Loris, R., Dao-Thi, M.-H., Bahassi, E.M.,
Van Melderen, L., Poortmans, F., Liddington,
R., Couturier, M., Wyns, L. 		1999 J.Mol.Biol. 285 1667 9917404
366D Major groove binding and 'DNA-induced' fit
in the intercalation of a derivative of
the mixed topoisomerase I/II poison N-(2-(dimethylamino)
ethyl)acridine-4-carboxamide
(DACA) into DNA: X-ray structure complexed
to d(CG(5-BrU)ACG)2 at 1.3-A resolution. 		Todd, A.K., Adams, A., Thorpe, J.H., Denny,
W.A., Wakelin, L.P., Cardin, C.J. 		1999 J.Med.Chem. 42 536 10052960
367D Major groove binding and 'DNA-induced' fit
in the intercalation of a derivative of
the mixed topoisomerase I/II poison N-(2-(dimethlyamino)
ethyl)acridine-4-carboxamide
(DACA) into DNA: X-ray structure complexed
to d(CG(5Br-U)ACG)2 at 1.3-angstrom resolution 		Todd, A.K., Adams, A., Thorpe, J.H., Denny,
W.A., Wakelin, L.P.G., Cardin, C.J. 		1999 J.Med.Chem. 42 536 10052960
3VUB Crystal structure of CcdB, a topoisomerase
poison from E. coli. 		Loris, R., Dao-Thi, M.-H., Bahassi, E.M.,
Van Melderen, L., Poortmans, F., Liddington,
R., Couturier, M., Wyns, L. 		1999 J.Mol.Biol. 285 1667 9917404
452D Major groove binding and 'DNA-induced' fit
in the intercalation of a derivative of
the mixed topoisomerase I/II poison N-(2-(dimethlyamino)
ethyl)acridine-4-carboxamide
(DACA) into DNA: X-ray structure complexed
to d(CG(5Br-U)ACG)2 at 1.3-angstrom resolution 		Todd, A.K., Adams, A., Thorpe, J.H., Denny,
W.A., Wakelin, L.P.G., Cardin, C.J. 		1999 J.Med.Chem. 42 536 10052960
465D Crystal structure of the topoisomerase II
poison 9-amino-[N-(2-dimethylamino)ethyl]acridine-4-
carboxamide
bound to the DNA hexanucleotide d(CGTACG)2. 		Adams, A., Guss, J.M., Collyer, C.A., Denny,
W.A., Wakelin, L.P. 		1999 Biochemistry 38 9221 10413496
4VUB Crystal structure of CcdB, a topoisomerase
poison from E. coli. 		Loris, R., Dao-Thi, M.-H., Bahassi, E.M.,
Van Melderen, L., Poortmans, F., Liddington,
R., Couturier, M., Wyns, L. 		1999 J.Mol.Biol. 285 1667 9917404

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