PDBsum entry 2o59

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protein dna_rna ligands metals Protein-protein interface(s) links
Isomerase/DNA PDB id
Protein chains
619 a.a. *
_CL ×2
Waters ×142
* Residue conservation analysis
PDB id:
Name: Isomerase/DNA
Title: Structure of e. Coli topoisomerase iii in complex with an 8- base single stranded oligonucleotide. Frozen in glycerol ph 8.0
Structure: 5'-d( Cp Gp Cp Ap Ap Cp Tp T)-3'. Chain: c, d. Engineered: yes. DNA topoisomerase 3. Chain: a, b. Synonym: DNA topoisomerase iii. Engineered: yes
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562. Gene: topb. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
2.50Å     R-factor:   0.223     R-free:   0.258
Authors: A.Changela,R.J.Digate,A.Mondragon
Key ref:
A.Changela et al. (2007). Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate. J Mol Biol, 368, 105-118. PubMed id: 17331537 DOI: 10.1016/j.jmb.2007.01.065
05-Dec-06     Release date:   03-Apr-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P14294  (TOP3_ECOLI) -  DNA topoisomerase 3
653 a.a.
619 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 8 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     chromosome separation   3 terms 
  Biochemical function     isomerase activity     6 terms  


DOI no: 10.1016/j.jmb.2007.01.065 J Mol Biol 368:105-118 (2007)
PubMed id: 17331537  
Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate.
A.Changela, R.J.Digate, A.Mondragón.
Escherichia coli DNA topoisomerase III belongs to the type IA family of DNA topoisomerases, which transiently cleave single-stranded DNA (ssDNA) via a 5' phosphotyrosine intermediate. We have solved crystal structures of wild-type E. coli topoisomerase III bound to an eight-base ssDNA molecule in three different pH environments. The structures reveal the enzyme in three distinct conformational states while bound to DNA. One conformation resembles the one observed previously with a DNA-bound, catalytically inactive mutant of topoisomerase III where DNA binding realigns catalytic residues to form a functional active site. Another conformation represents a novel intermediate in which DNA is bound along the ssDNA-binding groove but does not enter the active site, which remains in a catalytically inactive, closed state. A third conformation shows an intermediate state where the enzyme is still in a closed state, but the ssDNA is starting to invade the active site. For the first time, the active site region in the presence of both the catalytic tyrosine and ssDNA substrate is revealed for a type IA DNA topoisomerase, although there is no evidence of ssDNA cleavage. Comparative analysis of the various conformational states suggests a sequence of domain movements undertaken by the enzyme upon substrate binding.
  Selected figure(s)  
Figure 1.
Figure 1. Overall structure of the open and closed complexes. (a) The diagram shows a schematic representation of the closed complex (Form I, pH 5.5). The four major domains of the protein are colored red, blue, purple, and green for domain I, II, III, and IV, respectively. The active site is found at the intersection of domains I and III. The ssDNA binding groove extends from domain IV to the active site. The ssDNA in the complex is shown in a ball and stick representation. (b) Schematic diagram of the open complex (Form II, pH 5.5), colored as in (a). (c) Stereo view showing the superposition of the closed (red), intermediate (blue), and open (green) complexes. The structures were aligned by superposing domain I only. The three structures correspond to Form I pH 5.5, Form II pH 8.0, and Form II, pH 5.5.
Figure 5.
Figure 5. Conformation of the ssDNA in the closed, intermediate, and closed forms. Stereo diagram of the ssDNA in the closed (red), intermediate (blue), and open (green) conformations. The diagram illustrates the differences in conformation of the ssDNA as it enters the active site. The first five nucleotides remain essentially unchanged, while nucleotides 6 and 7 change conformation to approach the active site. Nucleotide 8 is ordered only in the open conformation. Note the base of Thy 7, which is in a completely different conformation in the closed form. As the structure changes from the closed to the open forms, the phosphate of Thy 7, the scissile phosphate, approaches the active site. Nucleotides are numbered from the 5′ to the 3′ end starting at Cyt1.
  The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2007, 368, 105-118) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
20686482 B.D.Bax, P.F.Chan, D.S.Eggleston, A.Fosberry, D.R.Gentry, F.Gorrec, I.Giordano, M.M.Hann, A.Hennessy, M.Hibbs, J.Huang, E.Jones, J.Jones, K.K.Brown, C.J.Lewis, E.W.May, M.R.Saunders, O.Singh, C.E.Spitzfaden, C.Shen, A.Shillings, A.J.Theobald, A.Wohlkonig, N.D.Pearson, and M.N.Gwynn (2010).
Type IIA topoisomerase inhibition by a new class of antibacterial agents.
  Nature, 466, 935-940.
PDB codes: 2xco 2xcq 2xcr 2xcs 2xct
20623552 M.Mönnich, I.Hess, W.Wiest, C.Bachrati, I.D.Hickson, M.Schorpp, and T.Boehm (2010).
Developing T lymphocytes are uniquely sensitive to a lack of topoisomerase III alpha.
  Eur J Immunol, 40, 2379-2384.  
19222228 J.E.Deweese, A.M.Burch, A.B.Burgin, and N.Osheroff (2009).
Use of divalent metal ions in the dna cleavage reaction of human type II topoisomerases.
  Biochemistry, 48, 1862-1869.  
19106140 N.M.Baker, R.Rajan, and A.Mondragón (2009).
Structural studies of type I topoisomerases.
  Nucleic Acids Res, 37, 693-701.  
19742304 N.Temime-Smaali, L.Guittat, A.Sidibe, K.Shin-ya, C.Trentesaux, and J.F.Riou (2009).
The G-quadruplex ligand telomestatin impairs binding of topoisomerase IIIalpha to G-quadruplex-forming oligonucleotides and uncaps telomeres in ALT cells.
  PLoS One, 4, e6919.  
18755053 A.J.Schoeffler, and J.M.Berger (2008).
DNA topoisomerases: harnessing and constraining energy to govern chromosome topology.
  Q Rev Biophys, 41, 41.  
18096618 B.Cheng, E.P.Sorokin, and Y.C.Tse-Dinh (2008).
Mutation adjacent to the active site tyrosine can enhance DNA cleavage and cell killing by the TOPRIM Gly to Ser mutant of bacterial topoisomerase I.
  Nucleic Acids Res, 36, 1017-1025.  
18186484 B.Xiong, D.L.Burk, J.Shen, X.Luo, H.Liu, J.Shen, and A.M.Berghuis (2008).
The type IA topoisomerase catalytic cycle: A normal mode analysis and molecular dynamics simulation.
  Proteins, 71, 1984-1994.  
18653531 J.E.Deweese, A.B.Burgin, and N.Osheroff (2008).
Human topoisomerase IIalpha uses a two-metal-ion mechanism for DNA cleavage.
  Nucleic Acids Res, 36, 4883-4893.  
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 codes are shown on the right.