PDBsum entry 2h7g

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protein dna_rna links
Isomerase/DNA PDB id
Protein chain
312 a.a. *
Waters ×395
* Residue conservation analysis
PDB id:
Name: Isomerase/DNA
Title: Structure of variola topoisomerase non-covalently bound to DNA
Structure: 5'-d( Tp Tp Gp Tp Cp Gp Cp Cp Cp Tp Tp A)-3'. Chain: y. Engineered: yes. 5'-d( Tp Ap Ap Tp Ap Ap Gp Gp Gp Cp Gp Ap Cp A)- 3'. Chain: z. Engineered: yes. DNA topoisomerase 1. Chain: x.
Source: Synthetic: yes. Variola virus. Organism_taxid: 10255. Gene: top1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Trimer (from PQS)
1.90Å     R-factor:   0.199     R-free:   0.243
Authors: K.Perry,Y.Hwang,F.D.Bushman,G.D.Van Duyne
Key ref:
K.Perry et al. (2006). Structural basis for specificity in the poxvirus topoisomerase. Mol Cell, 23, 343-354. PubMed id: 16885024 DOI: 10.1016/j.molcel.2006.06.015
02-Jun-06     Release date:   15-Aug-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P32989  (TOP1_VAR67) -  DNA topoisomerase 1
314 a.a.
312 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - 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   2 terms 
  Biochemical function     isomerase activity     5 terms  


DOI no: 10.1016/j.molcel.2006.06.015 Mol Cell 23:343-354 (2006)
PubMed id: 16885024  
Structural basis for specificity in the poxvirus topoisomerase.
K.Perry, Y.Hwang, F.D.Bushman, G.D.Van Duyne.
Although smallpox has been eradicated from the human population, it is presently feared as a possible agent of bioterrorism. The smallpox virus codes for its own topoisomerase enzyme that differs from its cellular counterpart by requiring a specific DNA sequence for activation of catalysis. Here we present crystal structures of the smallpox virus topoisomerase enzyme bound both covalently and noncovalently to a specific DNA sequence. These structures reveal the basis for site-specific DNA recognition, and they explain how catalysis is likely activated by formation of a specific enzyme-DNA interface. Unexpectedly, the poxvirus enzyme uses a major groove binding alpha helix that is not present in the human enzyme to recognize part of the core recognition sequence and activate the enzyme for catalysis. The topoisomerase-DNA complex structures also provide a three-dimensional framework that may facilitate the rational design of therapeutic agents to treat poxvirus infections.
  Selected figure(s)  
Figure 1.
Figure 1. The Type IB Topoisomerase Reaction and Electron Density for the Covalent vTopIB-DNA Complex
Figure 2.
Figure 2. The variola Virus TopIB-DNA Complex
  The above figures are reprinted by permission from Cell Press: Mol Cell (2006, 23, 343-354) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
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
20541502 L.Zechiedrich, and N.Osheroff (2010).
Topoisomerase IB-DNA interactions: X marks the spot.
  Structure, 18, 661-663.  
20187656 M.R.Stahley, and J.T.Stivers (2010).
Mechanism and specificity of DNA strand exchange catalyzed by vaccinia DNA topoisomerase type I.
  Biochemistry, 49, 2786-2795.  
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
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.  
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.  
19317906 T.Jain, B.J.Roper, and A.Grove (2009).
A functional type I topoisomerase from Pseudomonas aeruginosa.
  BMC Mol Biol, 10, 23.  
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.  
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.  
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.  
18417590 Y.C.Lin, J.Li, C.R.Irwin, H.Jenkins, L.DeLange, and D.H.Evans (2008).
Vaccinia virus DNA ligase recruits cellular topoisomerase II to sites of viral replication and assembly.
  J Virol, 82, 5922-5932.  
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.  
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.  
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.  
17198389 R.Nagarajan, and J.T.Stivers (2007).
Unmasking Anticooperative DNA-binding interactions of vaccinia DNA topoisomerase I.
  Biochemistry, 46, 192-199.  
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.  
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.  
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.  
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.