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PDBsum entry 1a35

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protein dna_rna links
Isomerase/DNA PDB id
1a35
Jmol
Contents
Protein chain
474 a.a. *
DNA/RNA
Waters ×273
* Residue conservation analysis
PDB id:
1a35
Name: Isomerase/DNA
Title: Human topoisomerase i/DNA complex
Structure: DNA (5'- d( Ap Ap Ap Ap Ap Gp Ap Cp Tp Tp Ap Gp Ap Ap Ap Ap Ap (Bru) p (Bru)p Tp Tp T)-3'). Chain: c. Engineered: yes. DNA (5'- d( Ap Ap Ap Ap Ap Tp +Up +Up +Up +Up Cp +Up Ap Ap Gp Tp Cp Tp Tp Tp + Up T)-3'). Chain: d.
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Cellular_location: nucleus. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.
Biol. unit: Monomer (from PDB file)
Resolution:
2.50Å     R-factor:   0.209     R-free:   0.308
Authors: M.R.Redinbo,L.Stewart,P.Kuhn,J.J.Champoux,W.G.Hol
Key ref:
M.R.Redinbo et al. (1998). Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. Science, 279, 1504-1513. PubMed id: 9488644 DOI: 10.1126/science.279.5356.1504
Date:
29-Jan-98     Release date:   28-Aug-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P11387  (TOP1_HUMAN) -  DNA topoisomerase 1
Seq:
Struc:
 
Seq:
Struc:
765 a.a.
474 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.5.99.1.2  - Dna topoisomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     chromosome   1 term 
  Biological process     DNA topological change   1 term 
  Biochemical function     DNA binding     3 terms  

 

 
DOI no: 10.1126/science.279.5356.1504 Science 279:1504-1513 (1998)
PubMed id: 9488644  
 
 
Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA.
M.R.Redinbo, L.Stewart, P.Kuhn, J.J.Champoux, W.G.Hol.
 
  ABSTRACT  
 
Topoisomerases I promote the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination. The crystal structures at 2.1 and 2.5 angstrom resolution of reconstituted human topoisomerase I comprising the core and carboxyl-terminal domains in covalent and noncovalent complexes with 22-base pair DNA duplexes reveal an enzyme that "clamps" around essentially B-form DNA. The core domain and the first eight residues of the carboxyl-terminal domain of the enzyme, including the active-site nucleophile tyrosine-723, share significant structural similarity with the bacteriophage family of DNA integrases. A binding mode for the anticancer drug camptothecin is proposed on the basis of chemical and biochemical information combined with these three-dimensional structures of topoisomerase I-DNA complexes.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Structural similarities between human topo I and HP1 integrase. (A) The sequence and secondary structural elements of reconstituted human topo I are indicated in the standard coloring scheme of the domain architecture of the enzyme (Fig. 1A), and^ the structurally similar regions of HP1 integrase are shown in red with gray background. Catalytically relevant residues of human topo I are highlighted in cyan, and the positions of known CPT-resistant mutations in human, hamster, and yeast topoisomerases I are shown in gray. -Helices 18 and 19 are not depicted because these correspond^ to the linker domain (20), which is not present in the reconstituted^ enzyme. (B) Stereoview of the superposition of core subdomain III (red) and the COOH-terminal domain (green) of human topo I and bacteriophage HP1 integrase (gray) (38). The active-site^ residues of each enzyme are shown, with the human topo I residues in cyan and the integrase residues in gray. Helices 8, 10, 15, and 17 of core subdomain III of topo I are also indicated. There^ is no structural equivalent in the integrase for the topo I COOH-terminal domain past the first eight residues, which contain the catalytic^ Tyr723. The C positions of the active-site residues Arg488 and Arg590 of topo I (20) superimpose within 0.6 and 1.9 Å, respectively, of the C positions of Arg207 and Arg283 in the integrase. His306 of the integrase superimposes within 3.3 Å on His632 of human topo I, but the putative catalytic His280 of the integrase superimposes on a noncatalytic residue of human topo I, Lys587. Abbreviations for the amino acid residues are as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; and Y, Tyr.
Figure 6.
Fig. 6. Proposed CPT binding mode. (A) A schematic representation of the key hydrogen bond and ring-stacking interactions made between the human topo I-DNA covalent complex and CPT in the proposed CPT binding mode. The atomic nomenclature for CPT is also indicated. (B) Stereoview of the proposed binding mode of CPT to the covalent human topo I DNA complex. The active^ lactone form of CPT (20-S-camptothecin, in green) is shown stacked^ between the terminal +1 guanine nucleotide from the cleaved strand^ (+1 Gua, in yellow, which is reoriented from the observed position as described below), and the side chain of Asn722, which provides interactions with the A-ring of CPT (the cleaved^ strand is rendered in light and dark magenta upstream and downstream of the cleavage site, respectively). The carbonyl oxygen at the^ 17 position in CPT makes a hydrogen bond with the NH[2] group on the pyrimidine ring of the +1 cytosine. The side chains of active-site^ residues Tyr723, Arg488, and Arg590 are shown in cyan. The side chain residues that, if singly mutated, result in a CPT-resistant phenotype [Phe^361, Gly363, and Arg364 of region 1 (see text); Asp533 and Asn722 of region 2] are shown in tan. The side chain conformations of^ Arg364 and Asp533 have been altered slightly from the final structure of the covalent complex to allow for optimal hydrogen bonding to the double-bonded^ lactone oxygen and the hydroxyl at the 20-S chiral center of CPT, respectively. Modifications to the 10 and 11 positions of CPT may require some minor shifts in the positions of residues Lys720 and Leu721 of topo I, which exhibit relatively high temperature factors (for example, 55 to 65 Å2) in the structure of the covalent complex. The proposed conformation of the +1 Gua nucleotide was inspired by flipped-out bases observed^ experimentally by Sussman and co-workers (62), but was further optimized by rotations about bonds in the intact phosphate between the +1 and +2 nucleotides. Because this base is now a terminal nucleotide in the cleaved strand, it is less contrained by the^ ribose-phosphate backbone and is more free to rotate to positions outside the DNA duplex.
 
  The above figures are reprinted by permission from the AAAs: Science (1998, 279, 1504-1513) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21132352 O.M.Koo, I.Rubinstein, and H.Onyüksel (2011).
Actively targeted low-dose camptothecin as a safe, long-acting, disease-modifying nanomedicine for rheumatoid arthritis.
  Pharm Res, 28, 776-787.  
22108601 S.M.Vos, E.M.Tretter, B.H.Schmidt, and J.M.Berger (2011).
All tangled up: how cells direct, manage and exploit topoisomerase function.
  Nat Rev Mol Cell Biol, 12, 827-841.  
21504738 T.D.Lillian, M.Taranova, J.Wereszczynski, I.Andricioaei, and N.C.Perkins (2011).
A multiscale dynamic model of DNA supercoil relaxation by topoisomerase IB.
  Biophys J, 100, 2016-2023.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
21406310 Y.A.Chen, H.C.Kuo, Y.M.Chen, S.Y.Huang, Y.R.Liu, S.C.Lin, H.L.Yang, and T.Y.Chen (2011).
A gene delivery system based on the N-terminal domain of human topoisomerase I.
  Biomaterials, 32, 4174-4184.  
21482796 Z.Zhang, B.Cheng, and Y.C.Tse-Dinh (2011).
Crystal structure of a covalent intermediate in DNA cleavage and rejoining by Escherichia coli DNA topoisomerase I.
  Proc Natl Acad Sci U S A, 108, 6939-6944.  
20511594 A.H.Kachroo, C.H.Ma, P.A.Rowley, A.D.Maciaszek, P.Guga, and M.Jayaram (2010).
Restoration of catalytic functions in Cre recombinase mutants by electrostatic compensation between active site and DNA substrate.
  Nucleic Acids Res, 38, 6589-6601.  
20541510 A.Patel, L.Yakovleva, S.Shuman, and A.Mondragón (2010).
Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site.
  Structure, 18, 725-733.
PDB code: 3m4a
20462863 B.Gibb, K.Gupta, K.Ghosh, R.Sharp, J.Chen, and G.D.Van Duyne (2010).
Requirements for catalysis in the Cre recombinase active site.
  Nucleic Acids Res, 38, 5817-5832.
PDB code: 3mgv
20485342 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: 3l4j 3l4k
  21092135 B.Khurana, L.Zhuang, P.K.Moitra, T.S.Stantchev, C.C.Broder, M.L.Cutler, and P.D'Arpa (2010).
Human TOP1 residues implicated in species specificity of HIV-1 infection are required for interaction with BTBD2, and RNAi of BTBD2 in old world monkey and human cells increases permissiveness to HIV-1 infection.
  Virol J, 7, 332.  
20200034 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.  
19883377 C.Tesauro, P.Fiorani, I.D'Annessa, G.Chillemi, G.Turchi, and A.Desideri (2010).
Erybraedin C, a natural compound from the plant Bituminaria bituminosa, inhibits both the cleavage and religation activities of human topoisomerase I.
  Biochem J, 425, 531-539.  
20723754 D.A.Koster, A.Crut, S.Shuman, M.A.Bjornsti, and N.H.Dekker (2010).
Cellular strategies for regulating DNA supercoiling: a single-molecule perspective.
  Cell, 142, 519-530.  
20532182 G.Mancini, I.D'Annessa, A.Coletta, N.Sanna, G.Chillemi, and A.Desideri (2010).
Structural and dynamical effects induced by the anticancer drug topotecan on the human topoisomerase I - DNA complex.
  PLoS One, 5, e10934.  
20152159 K.Perry, Y.Hwang, F.D.Bushman, and G.D.Van Duyne (2010).
Insights from the structure of a smallpox virus topoisomerase-DNA transition state mimic.
  Structure, 18, 127-137.
PDB code: 3igc
20637419 R.Rajan, B.Taneja, and A.Mondragón (2010).
Structures of minimal catalytic fragments of topoisomerase V reveals conformational changes relevant for DNA binding.
  Structure, 18, 829-838.
PDB codes: 3m6k 3m6z 3m7d 3m7g
20603643 T.H.Huang, H.C.Chen, S.M.Chou, Y.C.Yang, J.R.Fan, and T.K.Li (2010).
Cellular processing determinants for the activation of damage signals in response to topoisomerase I-linked DNA breakage.
  Cell Res, 20, 1060-1075.  
20482798 T.Norambuena, and F.Melo (2010).
The Protein-DNA Interface database.
  BMC Bioinformatics, 11, 262.  
20097655 T.S.Dexheimer, A.G.Stephen, M.J.Fivash, R.J.Fisher, and Y.Pommier (2010).
The DNA binding and 3'-end preferential activity of human tyrosyl-DNA phosphodiesterase.
  Nucleic Acids Res, 38, 2444-2452.  
21087076 W.Yang (2010).
Topoisomerases and site-specific recombinases: similarities in structure and mechanism.
  Crit Rev Biochem Mol Biol, 45, 520-534.  
19789629 C.H.Ma, A.H.Kachroo, A.Macieszak, T.Y.Chen, P.Guga, and M.Jayaram (2009).
Reactions of Cre with methylphosphonate DNA: similarities and contrasts with Flp and vaccinia topoisomerase.
  PLoS One, 4, e7248.  
19440204 C.H.Ma, P.A.Rowley, A.Macieszak, P.Guga, and M.Jayaram (2009).
Active site electrostatics protect genome integrity by blocking abortive hydrolysis during DNA recombination.
  EMBO J, 28, 1745-1756.  
19472416 C.Punchihewa, M.Carver, and D.Yang (2009).
DNA sequence selectivity of human topoisomerase I-mediated DNA cleavage induced by camptothecin.
  Protein Sci, 18, 1326-1331.  
19211583 D.Simon, T.Czömpöly, T.Berki, T.Minier, A.Peti, E.Tóth, L.Czirják, and P.Németh (2009).
Naturally occurring and disease-associated auto-antibodies against topoisomerase I: a fine epitope mapping study in systemic sclerosis and systemic lupus erythematosus.
  Int Immunol, 21, 415-422.  
19589806 J.Malina, O.Vrana, and V.Brabec (2009).
Mechanistic studies of the modulation of cleavage activity of topoisomerase I by DNA adducts of mono- and bi-functional PtII complexes.
  Nucleic Acids Res, 37, 5432-5442.  
19551725 L.Shuai, S.Wang, L.Zhang, B.Fu, and X.Zhou (2009).
Cationic porphyrins and analogues as new DNA topoisomerase I and II inhibitors.
  Chem Biodivers, 6, 827-837.  
19151088 M.C.de la Loza, and R.E.Wellinger (2009).
A novel approach for organelle-specific DNA damage targeting reveals different susceptibility of mitochondrial DNA to the anticancer drugs camptothecin and topotecan.
  Nucleic Acids Res, 37, e26.  
19106140 N.M.Baker, R.Rajan, and A.Mondragón (2009).
Structural studies of type I topoisomerases.
  Nucleic Acids Res, 37, 693-701.  
19452556 O.Szklarczyk, K.Staroń, and M.Cieplak (2009).
Native state dynamics and mechanical properties of human topoisomerase I within a structure-based coarse-grained model.
  Proteins, 77, 420-431.  
19767617 P.Fiorani, C.Tesauro, G.Mancini, G.Chillemi, I.D'Annessa, G.Graziani, L.Tentori, A.Muzi, and A.Desideri (2009).
Evidence of the crucial role of the linker domain on the catalytic activity of human topoisomerase I by experimental and simulative characterization of the Lys681Ala mutant.
  Nucleic Acids Res, 37, 6849-6858.  
19317906 T.Jain, B.J.Roper, and A.Grove (2009).
A functional type I topoisomerase from Pseudomonas aeruginosa.
  BMC Mol Biol, 10, 23.  
19688808 Z.Liu, R.Meng, Y.Zu, Q.Li, and L.Yao (2009).
Imaging and studying human topoisomerase I on mica surfaces in air and in liquid by atomic force microscopy.
  Scanning, 31, 160-166.  
19740104 Z.Yang, J.F.Carey, and J.J.Champoux (2009).
Mutational analysis of the preferential binding of human topoisomerase I to supercoiled DNA.
  FEBS J, 276, 5906-5919.  
18458338 A.Crut, P.A.Nair, D.A.Koster, S.Shuman, and N.H.Dekker (2008).
Dynamics of phosphodiester synthesis by DNA ligase.
  Proc Natl Acad Sci U S A, 105, 6894-6899.  
18755053 A.J.Schoeffler, and J.M.Berger (2008).
DNA topoisomerases: harnessing and constraining energy to govern chromosome topology.
  Q Rev Biophys, 41, 41.  
18772225 C.Losasso, E.Cretaio, P.Fiorani, I.D'Annessa, G.Chillemi, and P.Benedetti (2008).
A single mutation in the 729 residue modulates human DNA topoisomerase IB DNA binding and drug resistance.
  Nucleic Acids Res, 36, 5635-5644.  
18157856 F.Animati, M.Berettoni, M.Bigioni, M.Binaschi, P.Felicetti, L.Gontrani, O.Incani, A.Madami, E.Monteagudo, L.Olivieri, S.Resta, C.Rossi, and A.Cipollone (2008).
Synthesis, biological evaluation, and molecular modeling studies of rebeccamycin analogues modified in the carbohydrate moiety.
  ChemMedChem, 3, 266-279.  
18765473 G.Chillemi, I.D'Annessa, P.Fiorani, C.Losasso, P.Benedetti, and A.Desideri (2008).
Thr729 in human topoisomerase I modulates anti-cancer drug resistance by altering protein domain communications as suggested by molecular dynamics simulations.
  Nucleic Acids Res, 36, 5645-5651.  
18215123 G.S.Laco, and Y.Pommier (2008).
Role of a tryptophan anchor in human topoisomerase I structure, function and inhibition.
  Biochem J, 411, 523-530.  
18508107 H.Kim, J.H.Cardellina, R.Akee, J.J.Champoux, and J.T.Stivers (2008).
Arylstibonic acids: novel inhibitors and activators of human topoisomerase IB.
  Bioorg Chem, 36, 190-197.  
18318502 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.  
18408216 J.S.Hackbarth, M.Galvez-Peralta, N.T.Dai, D.A.Loegering, K.L.Peterson, X.W.Meng, L.M.Karnitz, and S.H.Kaufmann (2008).
Mitotic phosphorylation stimulates DNA relaxation activity of human topoisomerase I.
  J Biol Chem, 283, 16711-16722.  
18693244 K.Palle, L.Pattarello, M.van der Merwe, C.Losasso, P.Benedetti, and M.A.Bjornsti (2008).
Disulfide cross-links reveal conserved features of DNA topoisomerase I architecture and a role for the N terminus in clamp closure.
  J Biol Chem, 283, 27767-27775.  
18367446 L.Yakovleva, S.Chen, S.M.Hecht, and S.Shuman (2008).
Chemical and traditional mutagenesis of vaccinia DNA topoisomerase provides insights to cleavage site recognition and transesterification chemistry.
  J Biol Chem, 283, 16093-16103.  
18443285 S.Sirikantaramas, M.Yamazaki, and K.Saito (2008).
Mutations in topoisomerase I as a self-resistance mechanism coevolved with the production of the anticancer alkaloid camptothecin in plants.
  Proc Natl Acad Sci U S A, 105, 6782-6786.  
18473723 T.S.Dexheimer, S.Antony, C.Marchand, and Y.Pommier (2008).
Tyrosyl-DNA phosphodiesterase as a target for anticancer therapy.
  Anticancer Agents Med Chem, 8, 381-389.  
18451142 X.Chen, S.Zhong, X.Zhu, B.Dziegielewska, T.Ellenberger, G.M.Wilson, A.D.MacKerell, and A.E.Tomkinson (2008).
Rational design of human DNA ligase inhibitors that target cellular DNA replication and repair.
  Cancer Res, 68, 3169-3177.  
17222179 B.B.Das, S.Bose Dasgupta, A.Ganguly, S.Mazumder, A.Roy, and H.K.Majumder (2007).
Leishmania donovani bisubunit topoisomerase I gene fusion leads to an active enzyme with conserved type IB enzyme function.
  FEBS J, 274, 150-163.  
17804808 B.Taneja, B.Schnurr, A.Slesarev, J.F.Marko, and A.Mondragón (2007).
Topoisomerase V relaxes supercoiled DNA by a constrained swiveling mechanism.
  Proc Natl Acad Sci U S A, 104, 14670-14675.  
17434318 C.Punchihewa, J.Dai, M.Carver, and D.Yang (2007).
Human topoisomerase I C-terminal domain fragment containing the active site tyrosine is a molten globule: implication for the formation of competent productive complex.
  J Struct Biol, 159, 111-121.  
17589503 D.A.Koster, K.Palle, E.S.Bot, M.A.Bjornsti, and N.H.Dekker (2007).
Antitumour drugs impede DNA uncoiling by topoisomerase I.
  Nature, 448, 213-217.  
17439970 G.Chillemi, A.Bruselles, P.Fiorani, S.Bueno, and A.Desideri (2007).
The open state of human topoisomerase I as probed by molecular dynamics simulation.
  Nucleic Acids Res, 35, 3032-3038.  
17157316 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.  
17889664 H.Aihara, W.M.Huang, and T.Ellenberger (2007).
An interlocked dimer of the protelomerase TelK distorts DNA structure for the formation of hairpin telomeres.
  Mol Cell, 27, 901-913.
PDB code: 2v6e
18022919 L.Liqing, G.Lin, S.Ming, and S.Hanwen (2007).
Determination of hydroxycamptothecinum by flow injection analysis with chemiluminescence detection.
  J Clin Lab Anal, 21, 356-362.  
18033877 M.Nakata, G.Zanchetta, B.D.Chapman, C.D.Jones, J.O.Cross, R.Pindak, T.Bellini, and N.A.Clark (2007).
End-to-end stacking and liquid crystal condensation of 6 to 20 base pair DNA duplexes.
  Science, 318, 1276-1279.  
17024403 N.R.Jena, and P.C.Mishra (2007).
A theoretical study of some new analogues of the anti-cancer drug camptothecin.
  J Mol Model, 13, 267-274.  
17827209 R.F.Frøhlich, C.Veigaard, F.F.Andersen, A.K.McClendon, A.C.Gentry, A.H.Andersen, N.Osheroff, T.Stevnsner, and B.R.Knudsen (2007).
Tryptophane-205 of human topoisomerase I is essential for camptothecin inhibition of negative but not positive supercoil removal.
  Nucleic Acids Res, 35, 6170-6180.  
16488884 B.B.Das, N.Sen, A.Roy, S.B.Dasgupta, A.Ganguly, B.C.Mohanta, B.Dinda, and H.K.Majumder (2006).
Differential induction of Leishmania donovani bi-subunit topoisomerase I-DNA cleavage complex by selected flavones and camptothecin: activity of flavones against camptothecin-resistant topoisomerase I.
  Nucleic Acids Res, 34, 1121-1132.  
16395333 B.Taneja, A.Patel, A.Slesarev, and A.Mondragón (2006).
Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases.
  EMBO J, 25, 398-408.
PDB codes: 2csb 2csd
16505102 C.Marchand, S.Antony, K.W.Kohn, M.Cushman, A.Ioanoviciu, B.L.Staker, A.B.Burgin, L.Stewart, and Y.Pommier (2006).
A novel norindenoisoquinoline structure reveals a common interfacial inhibitor paradigm for ternary trapping of the topoisomerase I-DNA covalent complex.
  Mol Cancer Ther, 5, 287-295.  
16151810 D.J.Adams, M.W.da Silva, J.L.Flowers, G.Kohlhagen, Y.Pommier, O.M.Colvin, G.Manikumar, and M.C.Wani (2006).
Camptothecin analogs with enhanced activity against human breast cancer cells. I. Correlation of potency with lipophilicity and persistence in the cleavage complex.
  Cancer Chemother Pharmacol, 57, 135-144.  
16286315 G.Roja (2006).
Comparative studies on the camptothecin content from Nothapodytes foetida and Ophiorrhiza species.
  Nat Prod Res, 20, 85-88.  
16895336 J.T.Stivers, and R.Nagarajan (2006).
Probing enzyme phosphoester interactions by combining mutagenesis and chemical modification of phosphate ester oxygens.
  Chem Rev, 106, 3443-3467.  
16556227 J.W.Schmidt, L.Rajeev, A.A.Salyers, and J.F.Gardner (2006).
NBU1 integrase: evidence for an altered recombination mechanism.
  Mol Microbiol, 60, 152-164.  
16885024 K.Perry, Y.Hwang, F.D.Bushman, and G.D.Van Duyne (2006).
Structural basis for specificity in the poxvirus topoisomerase.
  Mol Cell, 23, 343-354.
PDB codes: 2h7f 2h7g
16756503 N.D.Grindley, K.L.Whiteson, and P.A.Rice (2006).
Mechanisms of site-specific recombination.
  Annu Rev Biochem, 75, 567-605.  
16990249 P.Fiorani, G.Chillemi, C.Losasso, S.Castelli, and A.Desideri (2006).
The different cleavage DNA sequence specificity explains the camptothecin resistance of the human topoisomerase I Glu418Lys mutant.
  Nucleic Acids Res, 34, 5093-5100.  
16650908 P.Forterre (2006).
DNA topoisomerase V: a new fold of mysterious origin.
  Trends Biotechnol, 24, 245-247.  
16311843 S.Pinel, P.Chastagner, J.L.Merlin, C.Marchal, A.Taghian, and M.Barberi-Heyob (2006).
Topotecan can compensate for protracted radiation treatment time effects in high grade glioma xenografts.
  J Neurooncol, 76, 31-38.  
16488610 S.Zhang, X.Li, F.Zhang, P.Yang, X.Gao, and Q.Song (2006).
Preparation of yuanhuacine and relative daphne diterpene esters from Daphne genkwa and structure-activity relationship of potent inhibitory activity against DNA topoisomerase I.
  Bioorg Med Chem, 14, 3888-3895.  
15837188 A.Mondragón (2005).
Unraveling the mechanistic details of topoisomerases.
  Structure, 13, 502-503.  
15800630 D.A.Koster, V.Croquette, C.Dekker, S.Shuman, and N.H.Dekker (2005).
Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB.
  Nature, 434, 671-674.  
15895231 E.L.Lund, L.T.Hansen, and P.E.Kristjansen (2005).
Augmenting tumor sensitivity to topotecan by transient hypoxia.
  Cancer Chemother Pharmacol, 56, 473-480.  
15944452 G.Chillemi, P.Fiorani, S.Castelli, A.Bruselles, P.Benedetti, and A.Desideri (2005).
Effect on DNA relaxation of the single Thr718Ala mutation in human topoisomerase I: a functional and molecular dynamics study.
  Nucleic Acids Res, 33, 3339-3350.  
15641118 G.I.Giles, and R.P.Sharma (2005).
Solid phase synthesis of anthraquinone peptides and their evaluation as topoisomerase I inhibitors.
  J Pept Sci, 11, 417-423.  
16141202 H.Interthal, H.J.Chen, and J.J.Champoux (2005).
Human Tdp1 cleaves a broad spectrum of substrates, including phosphoamide linkages.
  J Biol Chem, 280, 36518-36528.  
15830206 J.B.Leppard, and J.J.Champoux (2005).
Human DNA topoisomerase I: relaxation, roles, and damage control.
  Chromosoma, 114, 75-85.  
15793124 J.F.Marquis, I.Hardy, and M.Olivier (2005).
Topoisomerase I amino acid substitutions, Gly185Arg and Asp325Glu, confer camptothecin resistance in Leishmania donovani.
  Antimicrob Agents Chemother, 49, 1441-1446.  
16314322 L.Sari, and I.Andricioaei (2005).
Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative supercoil relaxation.
  Nucleic Acids Res, 33, 6621-6634.  
15837190 L.Tian, C.D.Claeboe, S.M.Hecht, and S.Shuman (2005).
Mechanistic plasticity of DNA topoisomerase IB: phosphate electrostatics dictate the need for a catalytic arginine.
  Structure, 13, 513-520.  
15959561 M.Malanga, and F.R.Althaus (2005).
The role of poly(ADP-ribose) in the DNA damage signaling network.
  Biochem Cell Biol, 83, 354-364.  
16271076 M.Yanagihara, N.Sasaki-Takahashi, T.Sugahara, S.Yamamoto, M.Shinomi, I.Yamashita, M.Hayashida, B.Yamanoha, A.Numata, T.Yamori, and T.Andoh (2005).
Leptosins isolated from marine fungus Leptoshaeria species inhibit DNA topoisomerases I and/or II and induce apoptosis by inactivation of Akt/protein kinase B.
  Cancer Sci, 96, 816-824.  
15670945 N.J.Rahier, B.M.Eisenhauer, R.Gao, S.J.Thomas, and S.M.Hecht (2005).
On the role of E-ring oxygen atoms in the binding of camptothecin to the topoisomerase I-DNA covalent binary complex.
  Bioorg Med Chem, 13, 1381-1386.  
17292061 O.M.Koo, I.Rubinstein, and H.Onyuksel (2005).
Camptothecin in sterically stabilized phospholipid micelles: a novel nanomedicine.
  Nanomedicine, 1, 77-84.  
16132345 Q.Tian, J.Zhang, T.M.Tan, E.Chan, W.Duan, S.Y.Chan, U.A.Boelsterli, P.C.Ho, H.Yang, J.S.Bian, M.Huang, Y.Z.Zhu, W.Xiong, X.Li, and S.Zhou (2005).
Human multidrug resistance associated protein 4 confers resistance to camptothecins.
  Pharm Res, 22, 1837-1853.  
16160819 T.Ishikawa, A.Tamura, H.Saito, K.Wakabayashi, and H.Nakagawa (2005).
Pharmacogenomics of the human ABC transporter ABCG2: from functional evaluation to drug molecular design.
  Naturwissenschaften, 92, 451-463.  
16011334 X.Xiao, and M.Cushman (2005).
An ab initio quantum mechanics calculation that correlates with ligand orientation and DNA cleavage site selectivity in camptothecin-DNA-topoisomerase I ternary cleavage complexes.
  J Am Chem Soc, 127, 9960-9961.  
15948034 Z.Hu, X.Yang, P.C.Ho, E.Chan, S.Y.Chan, C.Xu, X.Li, Y.Z.Zhu, W.Duan, X.Chen, M.Huang, H.Yang, and S.Zhou (2005).
St. John's Wort modulates the toxicities and pharmacokinetics of CPT-11 (irinotecan) in rats.
  Pharm Res, 22, 902-914.  
14725760 A.C.Rodríguez, and D.Stock (2004).
Studying topoisomerases in the fourth dimension.
  Structure, 12, 7-9.  
15112237 E.Staub, P.Fiziev, A.Rosenthal, and B.Hinzmann (2004).
Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire.
  Bioessays, 26, 567-581.  
15347588 G.Chillemi, M.Redinbo, A.Bruselles, and A.Desideri (2004).
Role of the linker domain and the 203-214 N-terminal residues in the human topoisomerase I DNA complex dynamics.
  Biophys J, 87, 4087-4097.  
15096574 H.Zhang, L.H.Meng, D.B.Zimonjic, N.C.Popescu, and Y.Pommier (2004).
Thirteen-exon-motif signature for vertebrate nuclear and mitochondrial type IB topoisomerases.
  Nucleic Acids Res, 32, 2087-2092.  
14967139 J.C.Connelly, and D.R.Leach (2004).
Repair of DNA covalently linked to protein.
  Mol Cell, 13, 307-316.  
15494452 J.J.Vermeersch, S.Christmann-Franck, L.V.Karabashyan, S.Fermandjian, G.Mirambeau, and P.A.Der Garabedian (2004).
Pyridoxal 5'-phosphate inactivates DNA topoisomerase IB by modifying the lysine general acid.
  Nucleic Acids Res, 32, 5649-5657.  
15139806 K.D.Corbett, and J.M.Berger (2004).
Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases.
  Annu Rev Biophys Biomol Struct, 33, 95.  
14725763 L.Tian, C.D.Claeboe, S.M.Hecht, and S.Shuman (2004).
Remote phosphate contacts trigger assembly of the active site of DNA topoisomerase IB.
  Structure, 12, 31-40.  
15469908 S.Antony, P.B.Arimondo, J.S.Sun, and Y.Pommier (2004).
Position- and orientation-specific enhancement of topoisomerase I cleavage complexes by triplex DNA structures.
  Nucleic Acids Res, 32, 5163-5173.  
16075310 V.Kettmann, D.Kost'álová, and H.D.Höltje (2004).
Human topoisomerase I poisoning: docking protoberberines into a structure-based binding site model.
  J Comput Aided Mol Des, 18, 785-796.  
15472946 W.Bocian, R.Kawecki, E.Bednarek, J.Sitkowski, A.Pietrzyk, M.P.Williamson, P.E.Hansen, and L.Kozerski (2004).
Multiple binding modes of the camptothecin family to DNA oligomers.
  Chemistry, 10, 5776-5787.  
12482574 C.Bailly (2003).
Homocamptothecins: potent topoisomerase I inhibitors and promising anticancer drugs.
  Crit Rev Oncol Hematol, 45, 91.  
12618186 D.R.Davies, H.Interthal, J.J.Champoux, and W.G.Hol (2003).
Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide.
  Chem Biol, 10, 139-147.
PDB code: 1nop
12595561 G.Chillemi, P.Fiorani, P.Benedetti, and A.Desideri (2003).
Protein concerted motions in the DNA-human topoisomerase I complex.
  Nucleic Acids Res, 31, 1525-1535.  
14527324 G.L.Verdine, and D.P.Norman (2003).
Covalent trapping of protein-DNA complexes.
  Annu Rev Biochem, 72, 337-366.  
12887904 H.Aihara, H.J.Kwon, S.E.Nunes-Düby, A.Landy, and T.Ellenberger (2003).
A conformational switch controls the DNA cleavage activity of lambda integrase.
  Mol Cell, 12, 187-198.
PDB code: 1p7d
12711735 J.F.Carey, S.J.Schultz, L.Sisson, T.G.Fazzio, and J.J.Champoux (2003).
DNA relaxation by human topoisomerase I occurs in the closed clamp conformation of the protein.
  Proc Natl Acad Sci U S A, 100, 5640-5645.  
14602918 K.Søe, and F.Grosse (2003).
p53 stimulates human topoisomerase I activity by modulating its DNA binding.
  Nucleic Acids Res, 31, 6585-6592.  
12887905 L.Tian, C.D.Claeboe, S.M.Hecht, and S.Shuman (2003).
Guarding the genome: electrostatic repulsion of water by DNA suppresses a potent nuclease activity of topoisomerase IB.
  Mol Cell, 12, 199-208.  
14585933 M.H.Woo, C.Losasso, H.Guo, L.Pattarello, P.Benedetti, and M.A.Bjornsti (2003).
Locking the DNA topoisomerase I protein clamp inhibits DNA rotation and induces cell lethality.
  Proc Natl Acad Sci U S A, 100, 13767-13772.  
14654701 M.O.Christensen, H.U.Barthelmes, F.Boege, and C.Mielke (2003).
Residues 190-210 of human topoisomerase I are required for enzyme activity in vivo but not in vitro.
  Nucleic Acids Res, 31, 7255-7263.  
12853620 P.B.Arimondo, S.Angenault, L.Halby, A.Boutorine, F.Schmidt, C.Monneret, T.Garestier, J.S.Sun, C.Bailly, and C.Hélène (2003).
Spatial organization of topoisomerase I-mediated DNA cleavage induced by camptothecin-oligonucleotide conjugates.
  Nucleic Acids Res, 31, 4031-4040.  
14523238 Q.A.Khan, G.Kohlhagen, R.Marshall, C.A.Austin, G.P.Kalena, H.Kroth, J.M.Sayer, D.M.Jerina, and Y.Pommier (2003).
Position-specific trapping of topoisomerase II by benzo[a]pyrene diol epoxide adducts: implications for interactions with intercalating anticancer agents.
  Proc Natl Acad Sci U S A, 100, 12498-12503.  
12941889 R.Roy, P.Trowbridge, Z.Yang, J.J.Champoux, and D.T.Simmons (2003).
The cap region of topoisomerase I binds to sites near both ends of simian virus 40 T antigen.
  J Virol, 77, 9809-9816.  
12598365 Y.Chen, and P.A.Rice (2003).
New insight into site-specific recombination from Flp recombinase-DNA structures.
  Annu Rev Biophys Biomol Struct, 32, 135-159.  
12191478 A.B.Hickman, D.R.Ronning, R.M.Kotin, and F.Dyda (2002).
Structural unity among viral origin binding proteins: crystal structure of the nuclease domain of adeno-associated virus Rep.
  Mol Cell, 10, 327-337.
PDB code: 1m55
11809893 A.Das, C.Mandal, A.Dasgupta, T.Sengupta, and H.K.Majumder (2002).
An insight into the active site of a type I DNA topoisomerase from the kinetoplastid protozoan Leishmania donovani.
  Nucleic Acids Res, 30, 794-802.
PDB code: 1juw
12135490 B.Kowalska-Loth, A.Girstun, A.Piekiełko, and K.Staroń (2002).
SF2/ASF protein inhibits camptothecin-induced DNA cleavage by human topoisomerase I.
  Eur J Biochem, 269, 3504-3510.  
12426403 B.L.Staker, K.Hjerrild, M.D.Feese, C.A.Behnke, A.B.Burgin, and L.Stewart (2002).
The mechanism of topoisomerase I poisoning by a camptothecin analog.
  Proc Natl Acad Sci U S A, 99, 15387-15392.
PDB codes: 1k4s 1k4t
11830640 B.O.Krogh, and S.Shuman (2002).
A poxvirus-like type IB topoisomerase family in bacteria.
  Proc Natl Acad Sci U S A, 99, 1853-1858.  
12209008 D.T.Lesher, Y.Pommier, L.Stewart, and M.R.Redinbo (2002).
8-Oxoguanine rearranges the active site of human topoisomerase I.
  Proc Natl Acad Sci U S A, 99, 12102-12107.
PDB code: 1lpq
11814334 G.S.Laco, J.R.Collins, B.T.Luke, H.Kroth, J.M.Sayer, D.M.Jerina, and Y.Pommier (2002).
Human topoisomerase I inhibition: docking camptothecin and derivatives into a structure-based active site model.
  Biochemistry, 41, 1428-1435.  
12042765 J.C.Wang (2002).
Cellular roles of DNA topoisomerases: a molecular perspective.
  Nat Rev Mol Cell Biol, 3, 430-440.  
12007989 J.J.Champoux (2002).
A first view of the structure of a type IA topoisomerase with bound DNA.
  Trends Pharmacol Sci, 23, 199-201.  
11904406 J.M.Wojciak, D.Sarkar, A.Landy, and R.T.Clubb (2002).
Arm-site binding by lambda -integrase: solution structure and functional characterization of its amino-terminal domain.
  Proc Natl Acad Sci U S A, 99, 3434-3439.
PDB code: 1kjk
12368472 J.R.Vance, and T.E.Wilson (2002).
Yeast Tdp1 and Rad1-Rad10 function as redundant pathways for repairing Top1 replicative damage.
  Proc Natl Acad Sci U S A, 99, 13669-13674.  
  11818025 L.Xu, L.Yang, K.Hashimoto, M.Anderson, G.Kohlhagen, Y.Pommier, and P.D'Arpa (2002).
Characterization of BTBD1 and BTBD2, two similar BTB-domain-containing Kelch-like proteins that interact with Topoisomerase I.
  BMC Genomics, 3, 1.  
12069967 R.T.van Dross, and M.M.Sanders (2002).
Molecular characterization of recombinant Pneumocystis carinii topoisomerase I: differential interactions with human topoisomerase I poisons and pentamidine.
  Antimicrob Agents Chemother, 46, 2145-2154.  
12209444 V.Oleinikov, A.Sukhanova, K.Mochalov, O.Ustinova, I.Kudelina, I.Bronstein, and I.Nabiev (2002).
DNA binding induces conformational transition within human DNA topoisomerase I in solution.
  Biopolymers, 67, 369-375.  
11861910 Z.Morávek, S.Neidle, and B.Schneider (2002).
Protein and drug interactions in the minor groove of DNA.
  Nucleic Acids Res, 30, 1182-1191.  
11459959 A.Kuzminov (2001).
Single-strand interruptions in replicating chromosomes cause double-strand breaks.
  Proc Natl Acad Sci U S A, 98, 8241-8246.  
11230143 D.Sarkar, M.Radman-Livaja, and A.Landy (2001).
The small DNA binding domain of lambda integrase is a context-sensitive modulator of recombinase functions.
  EMBO J, 20, 1203-1212.  
11446589 D.V.Bugreev, E.L.Vasyutina, V.A.Ryabinin, A.N.Sinyakov, V.N.Buneva, and G.A.Nevinsky (2001).
Inhibition of human DNA topoisomerase I by new DNA minor groove ligands: derivatives of oligo-1,3-thiazolecarboxamides.
  Antisense Nucleic Acid Drug Dev, 11, 137-147.  
11423431 G.Chillemi, T.Castrignanò, and A.Desideri (2001).
Structure and hydration of the DNA-human topoisomerase I covalent complex.
  Biophys J, 81, 490-500.  
11340053 G.D.Van Duyne (2001).
A structural view of cre-loxp site-specific recombination.
  Annu Rev Biophys Biomol Struct, 30, 87.  
11353838 G.I.Belova, R.Prasad, S.A.Kozyavkin, J.A.Lake, S.H.Wilson, and A.I.Slesarev (2001).
A type IB topoisomerase with DNA repair activities.
  Proc Natl Acad Sci U S A, 98, 6015-6020.  
11526219 H.Zhang, J.M.Barceló, B.Lee, G.Kohlhagen, D.B.Zimonjic, N.C.Popescu, and Y.Pommier (2001).
Human mitochondrial topoisomerase I.
  Proc Natl Acad Sci U S A, 98, 10608-10613.  
11395412 J.J.Champoux (2001).
DNA topoisomerases: structure, function, and mechanism.
  Annu Rev Biochem, 70, 369-413.  
11532027 J.J.Pouliot, C.A.Robertson, and H.A.Nash (2001).
Pathways for repair of topoisomerase I covalent complexes in Saccharomyces cerevisiae.
  Genes Cells, 6, 677-687.  
11470877 K.Søe, G.Dianov, H.P.Nasheuer, V.A.Bohr, F.Grosse, and T.Stevnsner (2001).
A human topoisomerase I cleavage complex is recognized by an additional human topisomerase I molecule in vitro.
  Nucleic Acids Res, 29, 3195-3203.  
11222763 L.Kozerski, A.P.Mazurek, R.Kawecki, W.Bocian, P.Krajewski, E.Bednarek, J.Sitkowski, M.P.Williamson, A.J.Moir, and P.E.Hansen (2001).
A nicked duplex decamer DNA with a PEG(6) tether.
  Nucleic Acids Res, 29, 1132-1143.
PDB code: 1g1n
11459977 M.A.Trakselis, S.C.Alley, E.Abel-Santos, and S.J.Benkovic (2001).
Creating a dynamic picture of the sliding clamp during T4 DNA polymerase holoenzyme assembly by using fluorescence resonance energy transfer.
  Proc Natl Acad Sci U S A, 98, 8368-8375.  
11250198 M.J.van der Woerd, J.J.Pelletier, S.Xu, and A.M.Friedman (2001).
Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis.
  Structure, 9, 133-144.
PDB code: 1dc1
11212094 S.Dallavalle, A.Ferrari, L.Merlini, S.Penco, N.Carenini, M.De Cesare, P.Perego, G.Pratesi, and F.Zunino (2001).
Novel cytotoxic 7-iminomethyl and 7-aminomethyl derivatives of camptothecin.
  Bioorg Med Chem Lett, 11, 291-294.  
11564555 S.Scaldaferro, S.Tinelli, M.E.Borgnetto, A.Azzini, and G.Capranico (2001).
Directed evolution to increase camptothecin sensitivity of human DNA topoisomerase I.
  Chem Biol, 8, 871-881.  
11264450 T.K.Li, and L.F.Liu (2001).
Tumor cell death induced by topoisomerase-targeting drugs.
  Annu Rev Pharmacol Toxicol, 41, 53-77.  
10828956 B.O.Krogh, and S.Shuman (2000).
DNA strand transfer catalyzed by vaccinia topoisomerase: peroxidolysis and hydroxylaminolysis of the covalent protein-DNA intermediate.
  Biochemistry, 39, 6422-6432.  
10911997 B.O.Krogh, and S.Shuman (2000).
Catalytic mechanism of DNA topoisomerase IB.
  Mol Cell, 5, 1035-1041.  
10756188 C.Cheng, and S.Shuman (2000).
DNA strand transfer catalyzed by vaccinia topoisomerase: ligation of DNAs containing a 3' mononucleotide overhang.
  Nucleic Acids Res, 28, 1893-1898.  
11027276 C.Cheng, and S.Shuman (2000).
Recombinogenic flap ligation pathway for intrinsic repair of topoisomerase IB-induced double-strand breaks.
  Mol Cell Biol, 20, 8059-8068.  
10805740 D.Strumberg, A.A.Pilon, M.Smith, R.Hickey, L.Malkas, and Y.Pommier (2000).
Conversion of topoisomerase I cleavage complexes on the leading strand of ribosomal DNA into 5'-phosphorylated DNA double-strand breaks by replication runoff.
  Mol Cell Biol, 20, 3977-3987.  
10954601 G.Woodfield, C.Cheng, S.Shuman, and A.B.Burgin (2000).
Vaccinia topoisomerase and Cre recombinase catalyze direct ligation of activated DNA substrates containing a 3'-para-nitrophenyl phosphate ester.
  Nucleic Acids Res, 28, 3323-3331.  
10908320 J.Sekiguchi, C.Cheng, and S.Shuman (2000).
Resolution of a Holliday junction by vaccinia topoisomerase requires a spacer DNA segment 3' of the CCCTT/ cleavage sites.
  Nucleic Acids Res, 28, 2658-2663.  
10820030 J.T.Stivers, G.J.Jagadeesh, B.Nawrot, W.J.Stec, and S.Shuman (2000).
Stereochemical outcome and kinetic effects of Rp- and Sp-phosphorothioate substitutions at the cleavage site of vaccinia type I DNA topoisomerase.
  Biochemistry, 39, 5561-5572.  
10841763 M.R.Redinbo, J.J.Champoux, and W.G.Hol (2000).
Novel insights into catalytic mechanism from a crystal structure of human topoisomerase I in complex with DNA.
  Biochemistry, 39, 6832-6840.
PDB code: 1ej9
10871343 N.V.Grishin (2000).
Two tricks in one bundle: helix-turn-helix gains enzymatic activity.
  Nucleic Acids Res, 28, 2229-2233.  
11145031 P.A.Henry, S.P.Atamas, V.V.Yurovsky, I.Luzina, F.M.Wigley, and B.White (2000).
Diversity and plasticity of the anti-DNA topoisomerase I autoantibody response in scleroderma.
  Arthritis Rheum, 43, 2733-2742.  
11121473 P.B.Arimondo, J.F.Riou, J.L.Mergny, J.Tazi, J.S.Sun, T.Garestier, and C.Hélène (2000).
Interaction of human DNA topoisomerase I with G-quartet structures.
  Nucleic Acids Res, 28, 4832-4838.  
10677551 P.Pourquier, Y.Takebayashi, Y.Urasaki, C.Gioffre, G.Kohlhagen, and Y.Pommier (2000).
Induction of topoisomerase I cleavage complexes by 1-beta -D-arabinofuranosylcytosine (ara-C) in vitro and in ara-C-treated cells.
  Proc Natl Acad Sci U S A, 97, 1885-1890.  
10861727 Q.Li, L.A.Mitscher, and L.L.Shen (2000).
The 2-pyridone antibacterial agents: bacterial topoisomerase inhibitors.
  Med Res Rev, 20, 231-293.  
10933812 S.P.Sim, D.S.Pilch, and L.F.Liu (2000).
Site-specific topoisomerase I-mediated DNA cleavage induced by nogalamycin: a potential role of ligand-induced DNA bending at a distal site.
  Biochemistry, 39, 9928-9934.  
10801498 S.Suresh, S.Turley, F.R.Opperdoes, P.A.Michels, and W.G.Hol (2000).
A potential target enzyme for trypanocidal drugs revealed by the crystal structure of NAD-dependent glycerol-3-phosphate dehydrogenase from Leishmania mexicana.
  Structure, 8, 541-552.
PDB codes: 1evy 1evz
10998231 X.L.Yang, H.Robinson, Y.G.Gao, and A.H.Wang (2000).
Binding of a macrocyclic bisacridine and ametantrone to CGTACG involves similar unusual intercalation platforms.
  Biochemistry, 39, 10950-10957.
PDB codes: 1fd5 1fdg
  11090626 Y.Chen, U.Narendra, L.E.Iype, M.M.Cox, and P.A.Rice (2000).
Crystal structure of a Flp recombinase-Holliday junction complex: assembly of an active oligomer by helix swapping.
  Mol Cell, 6, 885-897.
PDB code: 1flo
11121479 Y.Hwang, D.Rhodes, and F.Bushman (2000).
Rapid microtiter assays for poxvirus topoisomerase, mammalian type IB topoisomerase and HIV-1 integrase: application to inhibitor isolation.
  Nucleic Acids Res, 28, 4884-4892.  
10688881 Y.Pommier, G.Kohlhagen, P.Pourquier, J.M.Sayer, H.Kroth, and D.M.Jerina (2000).
Benzo[a]pyrene diol epoxide adducts in DNA are potent suppressors of a normal topoisomerase I cleavage site and powerful inducers of other topoisomerase I cleavages.
  Proc Natl Acad Sci U S A, 97, 2040-2045.  
10995470 Y.Pommier, G.S.Laco, G.Kohlhagen, J.M.Sayer, H.Kroth, and D.M.Jerina (2000).
Position-specific trapping of topoisomerase I-DNA cleavage complexes by intercalated benzo[a]- pyrene diol epoxide adducts at the 6-amino group of adenine.
  Proc Natl Acad Sci U S A, 97, 10739-10744.  
10377377 A.Landy (1999).
Coming or going it's another pretty picture for the lambda-Int family album.
  Proc Natl Acad Sci U S A, 96, 7122-7124.  
10574789 A.Mondragón, and R.DiGate (1999).
The structure of Escherichia coli DNA topoisomerase III.
  Structure, 7, 1373-1383.
PDB code: 1d6m
10569939 C.Bailly, A.Lansiaux, L.Dassonneville, D.Demarquay, H.Coulomb, M.Huchet, O.Lavergne, and D.C.Bigg (1999).
Homocamptothecin, an E-ring-modified camptothecin analogue, generates new topoisomerase I-mediated DNA breaks.
  Biochemistry, 38, 15556-15563.  
10393535 C.Bailly, C.Carrasco, F.Hamy, H.Vezin, M.Prudhomme, A.Saleem, and E.Rubin (1999).
The camptothecin-resistant topoisomerase I mutant F361S is cross-resistant to antitumor rebeccamycin derivatives. A model for topoisomerase I inhibition by indolocarbazoles.
  Biochemistry, 38, 8605-8611.  
10600122 C.Cheng, and S.Shuman (1999).
Site-specific DNA transesterification by vaccinia topoisomerase: role of specific phosphates and nucleosides.
  Biochemistry, 38, 16599-16612.  
10450093 D.J.Diller, E.Pohl, M.R.Redinbo, B.T.Hovey, and W.G.Hol (1999).
A rapid method for positioning small flexible molecules, nucleic acids, and large protein fragments in experimental electron density maps.
  Proteins, 36, 512-525.  
10450094 D.J.Diller, M.R.Redinbo, E.Pohl, and W.G.Hol (1999).
A database method for automated map interpretation in protein crystallography.
  Proteins, 36, 526-541.  
10577069 I.Grainge, and M.Jayaram (1999).
The integrase family of recombinase: organization and function of the active site.
  Mol Microbiol, 33, 449-456.  
9927438 J.Lee, M.Jayaram, and I.Grainge (1999).
Wild-type Flp recombinase cleaves DNA in trans.
  EMBO J, 18, 784-791.  
10077164 K.Yanase, Y.Sugimoto, T.Andoh, and T.Tsuruo (1999).
Retroviral expression of a mutant (Gly-533) human DNA topoisomerase I cDNA confers a dominant form of camptothecin resistance.
  Int J Cancer, 81, 134-140.  
10545127 M.D.Nichols, K.DeAngelis, J.L.Keck, and J.M.Berger (1999).
Structure and function of an archaeal topoisomerase VI subunit with homology to the meiotic recombination factor Spo11.
  EMBO J, 18, 6177-6188.
PDB code: 1d3y
  10224251 M.Del Poeta, D.L.Toffaletti, T.H.Rude, C.C.Dykstra, J.Heitman, and J.R.Perfect (1999).
Topoisomerase I is essential in Cryptococcus neoformans: role In pathobiology and as an antifungal target.
  Genetics, 152, 167-178.  
  10582872 M.Del Poeta, S.F.Chen, D.Von Hoff, C.C.Dykstra, M.C.Wani, G.Manikumar, J.Heitman, M.E.Wall, and J.R.Perfect (1999).
Comparison of in vitro activities of camptothecin and nitidine derivatives against fungal and cancer cells.
  Antimicrob Agents Chemother, 43, 2862-2868.  
  10515904 M.E.Cardenas, M.C.Cruz, M.Del Poeta, N.Chung, J.R.Perfect, and J.Heitman (1999).
Antifungal activities of antineoplastic agents: Saccharomyces cerevisiae as a model system to study drug action.
  Clin Microbiol Rev, 12, 583-611.  
10047584 M.R.Redinbo, J.J.Champoux, and W.G.Hol (1999).
Structural insights into the function of type IB topoisomerases.
  Curr Opin Struct Biol, 9, 29-36.  
10194356 X.Wang, X.Zhou, and S.M.Hecht (1999).
Role of the 20-hydroxyl group in camptothecin binding by the topoisomerase I-DNA binary complex.
  Biochemistry, 38, 4374-4381.  
11504505 Y.Pommier, P.Pourquier, Y.Urasaki, J.Wu, and G.S.Laco (1999).
Topoisomerase I inhibitors: selectivity and cellular resistance.
  Drug Resist Updat, 2, 307-318.  
9634692 D.B.Wigley (1998).
Teaching a new dog old tricks?
  Structure, 6, 543-548.  
9568707 D.J.Sherratt, and D.B.Wigley (1998).
Conserved themes but novel activities in recombinases and topoisomerases.
  Cell, 93, 149-152.  
9772192 F.Fleury, A.Ianoul, E.Kryukov, A.Sukhanova, I.Kudelina, A.Wynne-Jones, I.B.Bronstein, M.Maizieres, M.Berjot, G.G.Dodson, A.J.Wilkinson, J.A.Holden, A.V.Feofanov, A.J.Alix, J.C.Jardillier, and I.Nabiev (1998).
Raman and CD spectroscopy of recombinant 68-kDa DNA human topoisomerase I and its complex with suicide DNA-substrate.
  Biochemistry, 37, 14630-14642.  
9748476 J.M.Berger (1998).
Structure of DNA topoisomerases.
  Biochim Biophys Acta, 1400, 3.  
9699610 J.M.Grimes, and D.I.Stuart (1998).
Large unit cells and cellular mechanics.
  Nat Struct Biol, 5, 630-634.  
9692972 M.Lisby, B.O.Krogh, F.Boege, O.Westergaard, and B.R.Knudsen (1998).
Camptothecins inhibit the utilization of hydrogen peroxide in the ligation step of topoisomerase I catalysis.
  Biochemistry, 37, 10815-10827.  
9649322 X.Wang, L.K.Wang, W.D.Kingsbury, R.K.Johnson, and S.M.Hecht (1998).
Differential effects of camptothecin derivatives on topoisomerase I-mediated DNA structure modification.
  Biochemistry, 37, 9399-9408.  
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