PDBsum entry 1d6m

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Isomerase PDB id
Protein chain
603 a.a. *
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of e. Coli DNA topoisomerase iii
Structure: DNA topoisomerase iii. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
3.00Å     R-factor:   0.239     R-free:   0.268
Authors: A.Mondragon,R.Digate
Key ref:
A.Mondragón and R.DiGate (1999). The structure of Escherichia coli DNA topoisomerase III. Structure, 7, 1373-1383. PubMed id: 10574789 DOI: 10.1016/S0969-2126(00)80027-1
14-Oct-99     Release date:   14-Oct-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P14294  (TOP3_ECOLI) -  DNA topoisomerase 3
653 a.a.
603 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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/S0969-2126(00)80027-1 Structure 7:1373-1383 (1999)
PubMed id: 10574789  
The structure of Escherichia coli DNA topoisomerase III.
A.Mondragón, R.DiGate.
BACKGROUND: DNA topoisomerases are enzymes that change the topology of DNA. Type IA topoisomerases transiently cleave one DNA strand in order to pass another strand or strands through the break. In this manner, they can relax negatively supercoiled DNA and catenate and decatenate DNA molecules. Structural information on Escherichia coli DNA topoisomerase III is important for understanding the mechanism of this type of enzyme and for studying the mechanistic differences among different members of the same subfamily. RESULTS: The structure of the intact and fully active E. coli DNA topoisomerase III has been solved to 3.0 A resolution. The structure shows the characteristic fold of the type IA topoisomerases that is formed by four domains, creating a toroidal protein. There is remarkable structural similarity to the 67 kDa N-terminal fragment of E. coli DNA topoisomerase I, although the relative arrangement of the four domains is significantly different. A major difference is the presence of a 17 amino acid insertion in topoisomerase III that protrudes from the side of the central hole and could be involved in the catenation and decatenation reactions. The active site is formed by highly conserved amino acids, but the structural information and existing biochemical and mutagenesis data are still insufficient to assign specific roles to most of them. The presence of a groove in one side of the protein is suggestive of a single-stranded DNA (ssDNA)-binding region. CONCLUSIONS: The structure of E. coli DNA topoisomerase III resembles the structure of E. coli DNA topoisomerase I except for the presence of a positively charged loop that may be involved in catenation and decatenation. A groove on the side of the protein leads to the active site and is likely to be involved in DNA binding. The structure helps to establish the overall mechanism for the type IA subfamily of topoisomerases with greater confidence and expands the structural basis for understanding these proteins.
  Selected figure(s)  
Figure 5.
Figure 5. Stereo representation of the active site of E. coli DNA topoisomerase III. The mainchain of the protein is colored using the same color scheme as in Figure 1. This region contains some of the most highly conserved residues among all type IA topoisomerases. The active-site tyrosine, Tyr328, is surrounded by several acidic residues in domain I. In the open conformation, these acidic residues may serve to bind magnesium and through it ssDNA. The drawing was made with the program MolScript [38].
  The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 1373-1383) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20194637 R.Kawamura, L.H.Pope, M.O.Christensen, M.Sun, K.Terekhova, F.Boege, C.Mielke, A.H.Andersen, and J.F.Marko (2010).
Mitotic chromosomes are constrained by topoisomerase II-sensitive DNA entanglements.
  J Cell Biol, 188, 653-663.  
21087076 W.Yang (2010).
Topoisomerases and site-specific recombinases: similarities in structure and mechanism.
  Crit Rev Biochem Mol Biol, 45, 520-534.  
19106140 N.M.Baker, R.Rajan, and A.Mondragón (2009).
Structural studies of type I topoisomerases.
  Nucleic Acids Res, 37, 693-701.  
19150358 R.D.Shereda, N.J.Reiter, S.E.Butcher, and J.L.Keck (2009).
Identification of the SSB binding site on E. coli RecQ reveals a conserved surface for binding SSB's C terminus.
  J Mol Biol, 386, 612-625.  
18755053 A.J.Schoeffler, and J.M.Berger (2008).
DNA topoisomerases: harnessing and constraining energy to govern chromosome topology.
  Q Rev Biophys, 41, 41.  
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.  
17331537 A.Changela, R.J.DiGate, and A.Mondragón (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.
PDB codes: 2o19 2o54 2o59 2o5c 2o5e
16192570 Z.Li, H.Hiasa, and R.DiGate (2005).
Bacillus cereus DNA topoisomerase I and IIIalpha: purification, characterization and complementation of Escherichia coli TopoIII activity.
  Nucleic Acids Res, 33, 5415-5425.  
14711811 B.Cheng, J.Feng, S.Gadgil, and Y.C.Tse-Dinh (2004).
Flexibility at Gly-194 is required for DNA cleavage and relaxation activity of Escherichia coli DNA topoisomerase I.
  J Biol Chem, 279, 8648-8654.  
15215234 B.Cheng, J.Feng, V.Mulay, S.Gadgil, and Y.C.Tse-Dinh (2004).
Site-directed mutagenesis of residues involved in G Strand DNA binding by Escherichia coli DNA topoisomerase I.
  J Biol Chem, 279, 39207-39213.  
14691242 J.Shapiro, and D.Brutlag (2004).
FoldMiner: structural motif discovery using an improved superposition algorithm.
  Protein Sci, 13, 278-294.  
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.  
15140883 T.Viard, R.Cossard, M.Duguet, and La Tour (2004).
Thermotoga maritima-Escherichia coli chimeric topoisomerases. Answers about involvement of the carboxyl-terminal domain in DNA topoisomerase I-mediated catalysis.
  J Biol Chem, 279, 30073-30080.  
12581655 A.Changela, K.Perry, B.Taneja, and A.Mondragón (2003).
DNA manipulators: caught in the act.
  Curr Opin Struct Biol, 13, 15-22.  
14527324 G.L.Verdine, and D.P.Norman (2003).
Covalent trapping of protein-DNA complexes.
  Annu Rev Biochem, 72, 337-366.  
12769857 M.Kato, T.Ito, G.Wagner, C.C.Richardson, and T.Ellenberger (2003).
Modular architecture of the bacteriophage T7 primase couples RNA primer synthesis to DNA synthesis.
  Mol Cell, 11, 1349-1360.
PDB code: 1nui
12052259 A.Ahumada, and Y.C.Tse-Dinh (2002).
The role of the Zn(II) binding domain in the mechanism of E. coli DNA topoisomerase I.
  BMC Biochem, 3, 13.  
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.  
11809772 K.Perry, and A.Mondragón (2002).
Biochemical characterization of an invariant histidine involved in Escherichia coli DNA topoisomerase I catalysis.
  J Biol Chem, 277, 13237-13245.  
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.  
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.  
11239459 Z.Li, A.Mondragón, and R.J.DiGate (2001).
The mechanism of type IA topoisomerase-mediated DNA topological transformations.
  Mol Cell, 7, 301-307.  
11006548 M.J.Davey, and M.O'Donnell (2000).
Mechanisms of DNA replication.
  Curr Opin Chem Biol, 4, 581-586.  
10692165 Z.Li, A.Mondragón, H.Hiasa, K.J.Marians, and R.J.DiGate (2000).
Identification of a unique domain essential for Escherichia coli DNA topoisomerase III-catalysed decatenation of replication intermediates.
  Mol Microbiol, 35, 888-895.  
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.