PDBsum entry 1mw9

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Isomerase PDB id
Protein chain
556 a.a. *
SO4 ×9
Waters ×577
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of h365r mutant of 67 kda n-terminal fragment of e. Coli DNA topoisomerase i
Structure: DNA topoisomerase i. Chain: x. Fragment: 67 kda n-terminal fragment. Synonym: omega-protein, relaxing enzyme, untwisting enzyme, swivelase. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: topa. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.67Å     R-factor:   0.209     R-free:   0.216
Authors: K.Perry,A.Mondragon
Key ref:
K.Perry and A.Mondragón (2003). Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA. Structure, 11, 1349-1358. PubMed id: 14604525 DOI: 10.1016/j.str.2003.09.013
27-Sep-02     Release date:   14-Oct-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P06612  (TOP1_ECOLI) -  DNA topoisomerase 1
865 a.a.
556 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   1 term 
  Biochemical function     DNA binding     3 terms  


DOI no: 10.1016/j.str.2003.09.013 Structure 11:1349-1358 (2003)
PubMed id: 14604525  
Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA.
K.Perry, A.Mondragón.
In order to gain insights into the mechaism of ssDNA binding and recognition by Escherichia coli DNA topoisomerase I, the structure of the 67 kDa N-terminal fragment of topoisomerase I was solved in complex with ssDNA. The structure reveals a new conformational stage in the multistep catalytic cycle of type IA topoisomerases. In the structure, the ssDNA binding groove leading to the active site is occupied, but the active site is not fully formed. Large conformational changes are not seen; instead, a single helix parallel to the ssDNA binding groove shifts to clamp the ssDNA. The structure helps clarify the temporal sequence of conformational events, starting from an initial empty enzyme and proceeding to a ssDNA-occupied and catalytically competent active site.
  Selected figure(s)  
Figure 4.
Figure 4. Diagram of Specific Hydrogen Bonds Made between the Oligonucleotide and the Protein in the DNA Binding Groove and at Site IThe coloring of the domains is the same as in Figure 2. Starting at the visible 5' end of the oligonucleotide, the nucleotides are Cyt2, Thy3, Thy4, Cyt5, Gua6, and Gua7. Hydrogen bonds are shown as dashed lines.Top: The shifted a helix has been made transparent, as it directly overlays the oligonucleotide and would prevent visualization of the bonds. The ring stacking between Tyr177 and Thy3, as well as the stacking interaction between Cyt2 and Trp184, are shown.Bottom: Superposition of the topoisomerase III/ssDNA complex on the T67-H365R/11 complex to show the location of the stacking tryptophans. The topoisomerase III/ssDNA complex is colored blue: the protein is dark blue, the ssDNA is light blue, and Trp61 is light blue. The T67-H365R protein is colored green, the ssDNA is in colors, and Trp184 is colored in magenta. The tryptophans are labeled in red, while the ssDNA nucleotides are labeled in black. It can be seen that Trp61 in topoisomerase III comes in from a strand below the base of the 5' nucleotide while Trp184 in topoisomerase I comes in from a helix above the base of the 5' nucleotide.
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 1349-1358) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20920291 G.Narula, J.Becker, B.Cheng, N.Dani, M.V.Abrenica, and Y.C.Tse-Dinh (2010).
The DNA relaxation activity and covalent complex accumulation of Mycobacterium tuberculosis topoisomerase I can be assayed in Escherichia coli: application for identification of potential FRET-dye labeling sites.
  BMC Biochem, 11, 41.  
19013470 B.Cheng, T.Annamalai, E.Sorokin, M.Abrenica, S.Aedo, and Y.C.Tse-Dinh (2009).
Asp-to-Asn substitution at the first position of the DxD TOPRIM motif of recombinant bacterial topoisomerase I is extremely lethal to E. coli.
  J Mol Biol, 385, 558-567.  
19106140 N.M.Baker, R.Rajan, and A.Mondragón (2009).
Structural studies of type I topoisomerases.
  Nucleic Acids Res, 37, 693-701.  
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.  
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
16582104 D.Strahs, C.X.Zhu, B.Cheng, J.Chen, and Y.C.Tse-Dinh (2006).
Experimental and computational investigations of Ser10 and Lys13 in the binding and cleavage of DNA substrates by Escherichia coli DNA topoisomerase I.
  Nucleic Acids Res, 34, 1785-1797.  
15699629 G.V.Tolstonog, G.Li, R.L.Shoeman, and P.Traub (2005).
Interaction in vitro of type III intermediate filament proteins with higher order structures of single-stranded DNA, particularly with G-quadruplex DNA.
  DNA Cell Biol, 24, 85.  
14725760 A.C.Rodríguez, and D.Stock (2004).
Studying topoisomerases in the fourth dimension.
  Structure, 12, 7-9.  
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.  
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.  
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.