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PDBsum entry 1a41

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protein ligands links
Isomerase PDB id
1a41
Jmol
Contents
Protein chain
221 a.a. *
Ligands
SO4
Waters ×492
* Residue conservation analysis
PDB id:
1a41
Name: Isomerase
Title: Type 1-topoisomerase catalytic fragment from vaccinia virus
Structure: Topoisomerase i. Chain: a. Fragment: carboxy-terminal catalytic domain. Engineered: yes
Source: Vaccinia virus. Organism_taxid: 10245. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Resolution:
2.30Å     R-factor:   0.227     R-free:   0.309
Authors: C.Cheng,P.Kussie,N.Pavletich,S.Shuman
Key ref:
C.Cheng et al. (1998). Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases. Cell, 92, 841-850. PubMed id: 9529259 DOI: 10.1016/S0092-8674(00)81411-7
Date:
10-Feb-98     Release date:   01-Jun-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P68698  (TOP1_VACCW) -  DNA topoisomerase 1B
Seq:
Struc:
314 a.a.
221 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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!
  Biological process     DNA topological change   1 term 
  Biochemical function     DNA binding     3 terms  

 

 
DOI no: 10.1016/S0092-8674(00)81411-7 Cell 92:841-850 (1998)
PubMed id: 9529259  
 
 
Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases.
C.Cheng, P.Kussie, N.Pavletich, S.Shuman.
 
  ABSTRACT  
 
Vaccinia DNA topoisomerase breaks and rejoins DNA strands through a DNA-(3'-phosphotyrosyl)-enzyme intermediate. A C-terminal catalytic domain, Topo(81-314), suffices for transesterification chemistry. The domain contains a constellation of five amino acids, conserved in all eukaryotic type IB topoisomerases, that catalyzes attack of the tyrosine nucleophile on the scissile phosphate. The structure of the catalytic domain, consisting of ten alpha helices and a three-strand beta sheet, resembles the catalytic domains of site-specific recombinases that act via a topoisomerase IB-like mechanism. The topoisomerase catalytic pentad is conserved in the tertiary structures of the recombinases despite scant sequence similarity overall. This implies that the catalytic domains of type IB topoisomerases and recombinases derive from a common ancestral strand transferase.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Overall Fold of the Topoisomerase Catalytic DomainThe figure was prepared with the program MOLSCRIPT ([17]). The amino lobe of the protein (consisting of helices 1–3, a three-strand β sheet, and helices 4 and 5) is colored in purple; the carboxyl lobe (consisting of helices 6–10) is colored in cyan. Two anomalous electron density peaks that likely correspond to enzyme-bound sulfates are shown in red. Amino acid side chains that coordinate the sulfates (Arg-84, His-265, Ser-268, Ser-270, and Lys-271) are colored in yellow. Residues 129–137 that are not defined in the structure are depicted as a dashed purple line connecting helices 2 and 3.
Figure 4.
Figure 4. Superimposition of the Topoisomerase and Recombinase Structures from Helices 6–8(A) Topoisomerase (cyan) versus HP1 integrase (green).(B) Topoisomerase (cyan) versus Cre recombinase (green).Topoisomerase residues Lys-220, Arg-223, His-265, and Tyr-274 are colored yellow. The homologous residues of HP1 (His-280, Arg-283, His-306, and Tyr-315) and Cre (His-289, Arg-292, Trp-315, and Tyr-324 of the noncovalent Cre protomer) are colored red.
 
  The above figures are reprinted by permission from Cell Press: Cell (1998, 92, 841-850) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
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
19952068 J.Laprise, S.Yoneji, and J.F.Gardner (2010).
Homology-dependent interactions determine the order of strand exchange by IntDOT recombinase.
  Nucleic Acids Res, 38, 958-969.  
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
21087076 W.Yang (2010).
Topoisomerases and site-specific recombinases: similarities in structure and mechanism.
  Crit Rev Biochem Mol Biol, 45, 520-534.  
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.  
19188255 C.Sissi, and M.Palumbo (2009).
Effects of magnesium and related divalent metal ions in topoisomerase structure and function.
  Nucleic Acids Res, 37, 702-711.  
19118193 G.D.Van Duyne (2009).
Teaching Cre to follow directions.
  Proc Natl Acad Sci U S A, 106, 4-5.  
19946139 K.Van Vliet, M.R.Mohamed, L.Zhang, N.Y.Villa, S.J.Werden, J.Liu, and G.McFadden (2009).
Poxvirus proteomics and virus-host protein interactions.
  Microbiol Mol Biol Rev, 73, 730-749.  
19106140 N.M.Baker, R.Rajan, and A.Mondragón (2009).
Structural studies of type I topoisomerases.
  Nucleic Acids Res, 37, 693-701.  
19208647 P.Forterre, and D.Gadelle (2009).
Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms.
  Nucleic Acids Res, 37, 679-692.  
19317906 T.Jain, B.J.Roper, and A.Grove (2009).
A functional type I topoisomerase from Pseudomonas aeruginosa.
  BMC Mol Biol, 10, 23.  
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.  
18755053 A.J.Schoeffler, and J.M.Berger (2008).
DNA topoisomerases: harnessing and constraining energy to govern chromosome topology.
  Q Rev Biophys, 41, 41.  
19105819 C.Brochier-Armanet, S.Gribaldo, and P.Forterre (2008).
A DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya.
  Biol Direct, 3, 54.  
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.  
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.  
17720706 K.Malanowska, S.Yoneji, A.A.Salyers, and J.F.Gardner (2007).
CTnDOT integrase performs ordered homology-dependent and homology-independent strand exchanges.
  Nucleic Acids Res, 35, 5861-5873.  
17462694 N.Minkah, Y.Hwang, K.Perry, G.D.Van Duyne, R.Hendrickson, E.J.Lefkowitz, S.Hannenhalli, and F.D.Bushman (2007).
Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes.
  Virology, 365, 60-69.  
17192585 S.S.Broyles (2007).
The age of reverse biochemistry.
  Protein Sci, 16, 2-3.  
17531268 S.Subramaniam, H.B.Kamadurai, and M.P.Foster (2007).
Trans cooperativity by a split DNA recombinase: the central and catalytic domains of bacteriophage lambda integrase cooperate in cleaving DNA substrates when the two domains are not covalently linked.
  J Mol Biol, 370, 303-314.  
16368685 A.Patel, S.Shuman, and A.Mondragón (2006).
Crystal structure of a bacterial type IB DNA topoisomerase reveals a preassembled active site in the absence of DNA.
  J Biol Chem, 281, 6030-6037.
PDB code: 2f4q
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
16352556 D.Benarroch, J.M.Claverie, D.Raoult, and S.Shuman (2006).
Characterization of mimivirus DNA topoisomerase IB suggests horizontal gene transfer between eukaryal viruses and bacteria.
  J Virol, 80, 314-321.  
16996084 D.F.Fujimoto, C.Pinilla, and A.M.Segall (2006).
New peptide inhibitors of type IB topoisomerases: similarities and differences vis-a-vis inhibitors of tyrosine recombinases.
  J Mol Biol, 363, 891-907.  
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.  
16689798 K.Malanowska, A.A.Salyers, and J.F.Gardner (2006).
Characterization of a conjugative transposon integrase, IntDOT.
  Mol Microbiol, 60, 1228-1240.  
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
17005552 L.Yakovleva, J.Lai, E.T.Kool, and S.Shuman (2006).
Nonpolar nucleobase analogs illuminate requirements for site-specific DNA cleavage by vaccinia topoisomerase.
  J Biol Chem, 281, 35914-35921.  
17003057 S.Bolusani, C.H.Ma, A.Paek, J.H.Konieczka, M.Jayaram, and Y.Voziyanov (2006).
Evolution of variants of yeast site-specific recombinase Flp that utilize native genomic sequences as recombination target sites.
  Nucleic Acids Res, 34, 5259-5269.  
17032643 Y.Hwang, N.Minkah, K.Perry, G.D.Van Duyne, and F.D.Bushman (2006).
Regulation of catalysis by the smallpox virus topoisomerase.
  J Biol Chem, 281, 38052-38060.  
15837188 A.Mondragón (2005).
Unraveling the mechanistic details of topoisomerases.
  Structure, 13, 502-503.  
15711017 B.B.Das, N.Sen, S.B.Dasgupta, A.Ganguly, and H.K.Majumder (2005).
N-terminal region of the large subunit of Leishmania donovani bisubunit topoisomerase I is involved in DNA relaxation and interaction with the smaller subunit.
  J Biol Chem, 280, 16335-16344.  
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.  
16237128 F.Moreno-Herrero, L.Holtzer, D.A.Koster, S.Shuman, C.Dekker, and N.H.Dekker (2005).
Atomic force microscopy shows that vaccinia topoisomerase IB generates filaments on DNA in a cooperative fashion.
  Nucleic Acids Res, 33, 5945-5953.  
16242714 K.A.Gelato, S.S.Martin, and E.P.Baldwin (2005).
Reversed DNA strand cleavage specificity in initiation of Cre-LoxP recombination induced by the His289Ala active-site substitution.
  J Mol Biol, 354, 233-245.  
16408057 K.Ghosh, C.K.Lau, K.Gupta, and G.D.Van Duyne (2005).
Preferential synapsis of loxP sites drives ordered strand exchange in Cre-loxP site-specific recombination.
  Nat Chem Biol, 1, 275-282.  
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.  
14725760 A.C.Rodríguez, and D.Stock (2004).
Studying topoisomerases in the fourth dimension.
  Structure, 12, 7-9.  
15123675 C.Letzelter, M.Duguet, and M.C.Serre (2004).
Mutational analysis of the archaeal tyrosine recombinase SSV1 integrase suggests a mechanism of DNA cleavage in trans.
  J Biol Chem, 279, 28936-28944.  
14594810 H.Interthal, P.M.Quigley, W.G.Hol, and J.J.Champoux (2004).
The role of lysine 532 in the catalytic mechanism of human topoisomerase I.
  J Biol Chem, 279, 2984-2992.
PDB code: 1r49
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.  
14625310 J.L.Boldt, C.Pinilla, and A.M.Segall (2004).
Reversible inhibitors of lambda integrase-mediated recombination efficiently trap Holliday junction intermediates and form the basis of a novel assay for junction resolution.
  J Biol Chem, 279, 3472-3483.  
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.  
15252055 L.Tian, J.M.Sayer, D.M.Jerina, and S.Shuman (2004).
Individual nucleotide bases, not base pairs, are critical for triggering site-specific DNA cleavage by vaccinia topoisomerase.
  J Biol Chem, 279, 39718-39726.  
15044474 L.Yakovleva, C.J.Handy, J.M.Sayer, M.Pirrung, D.M.Jerina, and S.Shuman (2004).
Benzo[c]phenanthrene adducts and nogalamycin inhibit DNA transesterification by vaccinia topoisomerase.
  J Biol Chem, 279, 23335-23342.  
14990574 P.Fiorani, R.J.Reid, A.Schepis, H.R.Jacquiau, H.Guo, P.Thimmaiah, P.Benedetti, and M.A.Bjornsti (2004).
The deubiquitinating enzyme Doa4p protects cells from DNA topoisomerase I poisons.
  J Biol Chem, 279, 21271-21281.  
15218019 V.Petyuk, J.McDermott, M.Cook, and B.Sauer (2004).
Functional mapping of Cre recombinase by pentapeptide insertional mutagenesis.
  J Biol Chem, 279, 37040-37048.  
12810956 A.L.Bodley, A.K.Chakraborty, S.Xie, C.Burri, and T.A.Shapiro (2003).
An unusual type IB topoisomerase from African trypanosomes.
  Proc Natl Acad Sci U S A, 100, 7539-7544.  
12482574 C.Bailly (2003).
Homocamptothecins: potent topoisomerase I inhibitors and promising anticancer drugs.
  Crit Rev Oncol Hematol, 45, 91.  
14502574 E.Casanova, T.Lemberger, S.Fehsenfeld, T.Mantamadiotis, and G.Schütz (2003).
Alpha complementation in the Cre recombinase enzyme.
  Genesis, 37, 25-29.  
14652076 E.P.Baldwin, S.S.Martin, J.Abel, K.A.Gelato, H.Kim, P.G.Schultz, and S.W.Santoro (2003).
A specificity switch in selected cre recombinase variants is mediated by macromolecular plasticity and water.
  Chem Biol, 10, 1085-1094.
PDB codes: 1pvp 1pvq 1pvr
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
12851389 L.Lee, and P.D.Sadowski (2003).
Identification of Cre residues involved in synapsis, isomerization, and catalysis.
  J Biol Chem, 278, 36905-36915.  
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.  
12524450 L.Tian, J.M.Sayer, H.Kroth, G.Kalena, D.M.Jerina, and S.Shuman (2003).
Benzo[a]pyrene-dG adduct interference illuminates the interface of vaccinia topoisomerase with the DNA minor groove.
  J Biol Chem, 278, 9905-9911.  
12909623 L.Yakovleva, L.Tian, J.M.Sayer, G.P.Kalena, H.Kroth, D.M.Jerina, and S.Shuman (2003).
Site-specific DNA transesterification by vaccinia topoisomerase: effects of benzo[alpha]pyrene-dA, 8-oxoguanine, 8-oxoadenine and 2-aminopurine modifications.
  J Biol Chem, 278, 42170-42177.  
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.  
14633998 S.C.Ip, M.Bregu, F.X.Barre, and D.J.Sherratt (2003).
Decatenation of DNA circles by FtsK-dependent Xer site-specific recombination.
  EMBO J, 22, 6399-6407.  
12914783 S.S.Martin, S.Wachi, and E.P.Baldwin (2003).
Vanadate-based transition-state analog inhibitors of Cre-LoxP recombination.
  Biochem Biophys Res Commun, 308, 529-534.  
12779336 S.S.Martin, V.C.Chu, and E.Baldwin (2003).
Modulation of the active complex assembly and turnover rate by protein-DNA interactions in Cre-LoxP recombination.
  Biochemistry, 42, 6814-6826.
PDB code: 1ma7
12670991 T.M.Bankhead, B.J.Etzel, F.Wolven, S.Bordenave, J.L.Boldt, T.A.Larsen, and A.M.Segall (2003).
Mutations at residues 282, 286, and 293 of phage lambda integrase exert pathway-specific effects on synapsis and catalysis in recombination.
  J Bacteriol, 185, 2653-2666.  
12716882 Y.Chen, and P.A.Rice (2003).
The role of the conserved Trp330 in Flp-mediated recombination. Functional and structural analysis.
  J Biol Chem, 278, 24800-24807.
PDB code: 1p4e
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.  
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
11756402 B.O.Krogh, and S.Shuman (2002).
Proton relay mechanism of general acid catalysis by DNA topoisomerase IB.
  J Biol Chem, 277, 5711-5714.  
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.  
11733530 G.I.Belova, R.Prasad, I.V.Nazimov, S.H.Wilson, and A.I.Slesarev (2002).
The domain organization and properties of individual domains of DNA topoisomerase V, a type 1B topoisomerase with DNA repair activities.
  J Biol Chem, 277, 4959-4965.  
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
11861912 L.Debéthune, G.Kohlhagen, A.Grandas, and Y.Pommier (2002).
Processing of nucleopeptides mimicking the topoisomerase I-DNA covalent complex by tyrosyl-DNA phosphodiesterase.
  Nucleic Acids Res, 30, 1198-1204.  
11875075 M.C.Serre, C.Letzelter, J.R.Garel, and M.Duguet (2002).
Cleavage properties of an archaeal site-specific recombinase, the SSV1 integrase.
  J Biol Chem, 277, 16758-16767.  
11809802 R.L.Diaz, A.D.Alcid, J.M.Berger, and S.Keeney (2002).
Identification of residues in yeast Spo11p critical for meiotic DNA double-strand break formation.
  Mol Cell Biol, 22, 1106-1115.  
12051940 S.S.Martin, E.Pulido, V.C.Chu, T.S.Lechner, and E.P.Baldwin (2002).
The order of strand exchanges in Cre-LoxP recombination and its basis suggested by the crystal structure of a Cre-LoxP Holliday junction complex.
  J Mol Biol, 319, 107-127.
PDB code: 1kbu
12077150 Z.Yang, and J.J.Champoux (2002).
Reconstitution of enzymatic activity by the association of the cap and catalytic domains of human topoisomerase I.
  J Biol Chem, 277, 30815-30823.  
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.  
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.  
11395412 J.J.Champoux (2001).
DNA topoisomerases: structure, function, and mechanism.
  Annu Rev Biochem, 70, 369-413.  
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.  
11238985 K.S.Makarova, L.Aravind, Y.I.Wolf, R.L.Tatusov, K.W.Minton, E.V.Koonin, and M.J.Daly (2001).
Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics.
  Microbiol Mol Biol Rev, 65, 44-79.  
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.  
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.  
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.  
10809761 J.Fertala, J.R.Vance, P.Pourquier, Y.Pommier, and M.A.Bjornsti (2000).
Substitutions of Asn-726 in the active site of yeast DNA topoisomerase I define novel mechanisms of stabilizing the covalent enzyme-DNA intermediate.
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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.
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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.
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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.  
  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
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.
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10361305 A.J.Spiers, and D.J.Sherratt (1999).
C-terminal interactions between the XerC and XerD site-specific recombinases.
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10491013 A.K.Larsen, and C.Gobert (1999).
DNA topoisomerase I in oncology: Dr Jekyll or Mr Hyde?
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10377377 A.Landy (1999).
Coming or going it's another pretty picture for the lambda-Int family album.
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10574789 A.Mondragón, and R.DiGate (1999).
The structure of Escherichia coli DNA topoisomerase III.
  Structure, 7, 1373-1383.
PDB code: 1d6m
10600122 C.Cheng, and S.Shuman (1999).
Site-specific DNA transesterification by vaccinia topoisomerase: role of specific phosphates and nucleosides.
  Biochemistry, 38, 16599-16612.  
10468612 C.Gobert, A.Skladanowski, and A.K.Larsen (1999).
The interaction between p53 and DNA topoisomerase I is regulated differently in cells with wild-type and mutant p53.
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10047575 D.N.Gopaul, and G.D.Duyne (1999).
Structure and mechanism in site-specific recombination.
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10377382 F.Guo, D.N.Gopaul, and G.D.Van Duyne (1999).
Asymmetric DNA bending in the Cre-loxP site-specific recombination synapse.
  Proc Natl Acad Sci U S A, 96, 7143-7148.
PDB codes: 4crx 5crx
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.
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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.
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PDB code: 1d3y
10047584 M.R.Redinbo, J.J.Champoux, and W.G.Hol (1999).
Structural insights into the function of type IB topoisomerases.
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10092587 Y.Hwang, A.Burgin, and F.Bushman (1999).
DNA contacts stimulate catalysis by a poxvirus topoisomerase.
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9804830 C.J.Xu, Y.T.Ahn, S.Pathania, and M.Jayaram (1998).
Flp ribonuclease activities. Mechanistic similarities and contrasts to site-specific DNA recombination.
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9813066 C.L.Hann, A.L.Carlberg, and M.A.Bjornsti (1998).
Intragenic suppressors of mutant DNA topoisomerase I-induced lethality diminish enzyme binding of DNA.
  J Biol Chem, 273, 31519-31527.  
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.  
9670032 D.N.Gopaul, F.Guo, and G.D.Van Duyne (1998).
Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination.
  EMBO J, 17, 4175-4187.
PDB codes: 2crx 3crx
9748476 J.M.Berger (1998).
Structure of DNA topoisomerases.
  Biochim Biophys Acta, 1400, 3.  
9722641 L.Aravind, D.D.Leipe, and E.V.Koonin (1998).
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.  
9722507 M.Hartung, and B.Kisters-Woike (1998).
Cre mutants with altered DNA binding properties.
  J Biol Chem, 273, 22884-22891.  
9660957 S.Shuman (1998).
Polynucleotide ligase activity of eukaryotic topoisomerase I.
  Mol Cell, 1, 741-748.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.