PDBsum entry 1cy9

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Isomerase PDB id
Protein chains
245 a.a. *
Waters ×509
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of the 30 kda fragment of e. Coli DNA topo i. Monoclinic form
Structure: DNA topoisomerase i. Chain: a, b. Fragment: 30 kda fragment comprising domains ii and iii. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.80Å     R-factor:   0.205     R-free:   0.242
Authors: H.Feinberg,C.Lima,A.Mondragon
Key ref:
H.Feinberg et al. (1999). Conformational changes in E. coli DNA topoisomerase I. Nat Struct Biol, 6, 918-922. PubMed id: 10504724 DOI: 10.1038/13283
31-Aug-99     Release date:   08-Mar-00    
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Protein chains
Pfam   ArchSchema ?
P06612  (TOP1_ECOLI) -  DNA topoisomerase 1
865 a.a.
245 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     DNA topological change   1 term 
  Biochemical function     DNA binding     3 terms  


DOI no: 10.1038/13283 Nat Struct Biol 6:918-922 (1999)
PubMed id: 10504724  
Conformational changes in E. coli DNA topoisomerase I.
H.Feinberg, C.D.Lima, A.Mondragón.
DNA topoisomerases are the enzymes responsible for maintaining the topological states of DNA. In order to change the topology of DNA, topoisomerases pass one or two DNA strands through transient single or double strand breaks in the DNA phosphodiester backbone. It has been proposed that both type IA and type II enzymes change conformation dramatically during the reaction cycle in order to accomplish these transformations. In the case of Escherichia coli DNA topoisomerase I, it has been suggested that a 30 kDa fragment moves away from the rest of the protein to create an entrance into the central hole in the protein. Structures of the 30 kDa fragment reveal that indeed this fragment can change conformation significantly. The fragment is composed of two domains, and while the domains themselves remain largely unchanged, their relative arrangement can change dramatically.
  Selected figure(s)  
Figure 2.
Figure 2. Stereo view of the structure of the 30 kDa fragment of E. coli DNA topoisomerase I. Two clearly different conformations of the 30 kDa fragment were observed. a, The structure of monomer A in the monoclinic crystal form, and b, the structure of monomer C in the hexagonal crystal form. The orientation of domain II is made identical in both panels to emphasize the large difference in conformation for the two monomers. Domain II is shown in red and domain III is in pink. Tyr 319, the active site tyrosine, and Arg 321 are shown in black. The loop comprising residues 358−364 is only ordered in monomer C and is shown in blue. Drawings were prepared using MOLSCRIPT^13.
Figure 3.
Figure 3. Stereo views of the active site region. a, Domain III of monomer C was superimposed on domain III of the 67 kDa fragment to illustrate the changes around Tyr 319. The structure of the 67 kDa fragment is colored by atom type; monomer C is colored green. Arg 321 is unable to interact with Tyr 319 in the 67 kDa fragment, as it forms hydrogen bonds to the acidic residues in domain I, but the arginine residue has moved in the 30 kDa fragment, and the side chain guanidinium group makes hydrogen bonds to the active site tyrosine. This suggests that Arg 321 could play a role in stabilizing an activated tyrosine. Water molecules were not drawn for clarity. This diagram was prepared using MOLSCRIPT^13 and RASTER3D^14, ^15. b, Electron density maps showing the active site region in the hexagonal crystal form. The 2F[o] - F[c] map is colored in cyan and is contoured at the 1.5 level, while the F[o] - F[c] map is colored in magenta and is contoured at the +3 level. The difference map clearly shows the presence of a second conformation for Arg 321. c, Electron density map showing the active site region in the monoclinic crystal form. The 2F[o] - F[c] map is colored in cyan and is contoured at the 1.5 level. Maps (b) and (c) were prepared using BOBSCRIPT^16 and RASTER3D^14, ^15.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 918-922) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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
17039546 N.Nagano, T.Noguchi, and Y.Akiyama (2007).
Systematic comparison of catalytic mechanisms of hydrolysis and transfer reactions classified in the EzCatDB database.
  Proteins, 66, 147-159.  
16395333 B.Taneja, A.Patel, A.Slesarev, and A.Mondragón (2006).
Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases.
  EMBO J, 25, 398-408.
PDB codes: 2csb 2csd
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.  
16314322 L.Sari, and I.Andricioaei (2005).
Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative supercoil relaxation.
  Nucleic Acids Res, 33, 6621-6634.  
14725760 A.C.Rodríguez, and D.Stock (2004).
Studying topoisomerases in the fourth dimension.
  Structure, 12, 7-9.  
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.  
12581655 A.Changela, K.Perry, B.Taneja, and A.Mondragón (2003).
DNA manipulators: caught in the act.
  Curr Opin Struct Biol, 13, 15-22.  
11823434 A.C.Rodríguez, and D.Stock (2002).
Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA.
  EMBO J, 21, 418-426.
PDB codes: 1gku 1gl9
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.  
11395412 J.J.Champoux (2001).
DNA topoisomerases: structure, function, and mechanism.
  Annu Rev Biochem, 70, 369-413.  
10574789 A.Mondragón, and R.DiGate (1999).
The structure of Escherichia coli DNA topoisomerase III.
  Structure, 7, 1373-1383.
PDB code: 1d6m
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