PDBsum entry 3igc

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protein dna_rna ligands links
Isomerase/DNA PDB id
Protein chain
313 a.a. *
Waters ×426
* Residue conservation analysis
PDB id:
Name: Isomerase/DNA
Title: Smallpox virus topoisomerase-DNA transition state
Structure: DNA topoisomerase 1. Chain: a. Synonym: DNA topoisomerase i. Engineered: yes. Mutation: yes. 5'-d( Gp Tp Gp Tp Cp Gp Cp Cp Cp Tp T)-3'. Chain: b. Engineered: yes. Other_details: upstream DNA cleaved strand.
Source: Variola virus. Smallpox virus. Organism_taxid: 10255. Strain: western reserve. Gene: h6r, i6r, top1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: oligonucleotide synthesized by yale keck
2.10Å     R-factor:   0.180     R-free:   0.244
Authors: K.Perry,Y.Hwang,F.D.Bushman,G.D.Van Duyne
Key ref: K.Perry et al. (2010). Insights from the structure of a smallpox virus topoisomerase-DNA transition state mimic. Structure, 18, 127-137. PubMed id: 20152159
27-Jul-09     Release date:   02-Mar-10    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P32989  (TOP1_VAR67) -  DNA topoisomerase 1
314 a.a.
313 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  


Structure 18:127-137 (2010)
PubMed id: 20152159  
Insights from the structure of a smallpox virus topoisomerase-DNA transition state mimic.
K.Perry, Y.Hwang, F.D.Bushman, G.D.Van Duyne.
Poxviruses encode their own type IB topoisomerases (TopIBs), which release superhelical tension generated by replication and transcription of their genomes. To investigate the reaction catalyzed by viral TopIBs, we have determined the structure of a variola virus topoisomerase-DNA complex trapped as a vanadate transition state mimic. The structure reveals how the viral TopIB enzymes are likely to position the DNA duplex for ligation following relaxation of supercoils and identifies the sources of friction observed in single-molecule experiments that argue against free rotation. The structure also identifies a conformational change in the leaving group sugar that must occur prior to cleavage and reveals a mechanism for promoting ligation following relaxation of supercoils that involves an Asp-minor groove interaction. Overall, the new structural data support a common catalytic mechanism for the TopIB superfamily but indicate distinct methods for controlling duplex rotation in the small versus large enzyme subfamilies.

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
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.  
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.  
  21087076 W.Yang (2010).
Topoisomerases and site-specific recombinases: similarities in structure and mechanism.
  Crit Rev Biochem Mol Biol, 45, 520-534.  
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.