PDBsum entry 1cy0

Go to PDB code: 
protein ligands links
Isomerase PDB id
Jmol PyMol
Protein chain
534 a.a. *
Waters ×123
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Complex of e.Coli DNA topoisomerase i with 3'-5'-adenosine d
Structure: DNA topoisomerase i. Chain: a. Fragment: 67 kda n-terminal fragment of e.Coli topoisomeras engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.45Å     R-factor:   0.220     R-free:   0.274
Authors: H.Feinberg,A.Changela,A.Mondragon
Key ref:
H.Feinberg et al. (1999). Protein-nucleotide interactions in E. coli DNA topoisomerase I. Nat Struct Biol, 6, 961-968. PubMed id: 10504732 DOI: 10.1038/13333
31-Aug-99     Release date:   08-Mar-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P06612  (TOP1_ECOLI) -  DNA topoisomerase 1
865 a.a.
534 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: 10.1038/13333 Nat Struct Biol 6:961-968 (1999)
PubMed id: 10504732  
Protein-nucleotide interactions in E. coli DNA topoisomerase I.
H.Feinberg, A.Changela, A.Mondragón.
DNA topoisomerases are the enzymes responsible for controlling and maintaining the topological states of DNA. Type IA enzymes work by transiently breaking the phosphodiester backbone of one strand to allow passage of another strand through the break. The protein has to perform complex rearrangements of the DNA, and hence it is likely that different regions of the enzyme bind DNA with different affinities. In order to identify some of the DNA binding sites in the protein, we have solved the structures of several complexes of the 67 kDa N-terminal fragment of Escherichia coli DNA topoisomerase I with mono- and trinucleotides. There are five different binding sites in the complexes, one of which is adjacent to the active site. Two other sites are in the central hole of the protein and may represent general DNA binding regions. The positions of these sites allow us to identify different DNA binding regions and to understand their possible roles in the catalytic cycle.
  Selected figure(s)  
Figure 3.
Figure 3. Models showing different conformations of the loop region in domain III. a, Overall view illustrating three different conformations of a loop consisting of residues 357−364 located near the active site. The green model represents the structure of the 3'5'ADP complex showing an ordered loop in a closed conformation. A structure of the 30 kDa fragment of E. coli DNA topoisomerase I^10, which contains an ordered loop, is shown in red. The loop in this model of the 30 kDa fragment is in an open conformation. The structure of the 5'pTTT complex is in blue. The loop is mostly disordered in the 5'pTTT model although two ordered residues (Glu 363 and Ala 364) can be seen. This structure of this loop seems to be in between the open and the closed conformations. The structures of domain III from all three models were superimposed in this panel. b, A stereo closeup view of the loop region. The model of the 5'pTTT complex is in blue, the 3'5'ADP model is in green, and the 30 kDa fragment is colored red. The different orientations of His 365 with respect to the nucleotide in site I can be seen. In the open conformation, represented by the structure of the 30 kDa fragment, His 365 points towards the nucleotide in site I. In the closed conformation depicted by the 3'5'ADP model, His 365 points away from the nucleotide. In the model of the 5'pTTT complex, His 365 is directed towards the nucleotide. Drawings were prepared using MOLSCRIPT^30.
Figure 4.
Figure 4. Stereo view of the active site region. The model of the 5'pT complex shows the location of the nucleotide at site I with respect to the active site region. Conserved residues in the active site region are labeled; hydrogen bonds and salt bridges are shown as dotted lines. The 5'pT molecule makes contacts with Arg 114 and Arg 161. The extensive hydrogen bond network found in the interface between domains I and III is also illustrated. Tyr 319 contacts Asp 111 through a water molecule, which also contacts Glu 115 . Arg 321 makes salt bridges to both Asp 113 and Glu 115. Clearly, a single stranded DNA molecule could bind in the same site and extend to the active site if the protein is in the open conformation. Site I appears to be one or two nucleotides away from the active site. The drawing was prepared using MOLSCRIPT^30 and RASTER3D^32, ^33.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 961-968) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.  
15454610 N.F.Lue, and S.Jiang (2004).
Reverse transcriptase at bacterial telomeres.
  Proc Natl Acad Sci U S A, 101, 14307-14308.  
15094797 Y.Zheng, R.J.Roberts, and S.Kasif (2004).
Segmentally variable genes: a new perspective on adaptation.
  PLoS Biol, 2, E81.  
14527324 G.L.Verdine, and D.P.Norman (2003).
Covalent trapping of protein-DNA complexes.
  Annu Rev Biochem, 72, 337-366.  
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.  
11395412 J.J.Champoux (2001).
DNA topoisomerases: structure, function, and mechanism.
  Annu Rev Biochem, 70, 369-413.  
11455562 J.L.Beck, M.L.Colgrave, S.F.Ralph, and M.M.Sheil (2001).
Electrospray ionization mass spectrometry of oligonucleotide complexes with drugs, metals, and proteins.
  Mass Spectrom Rev, 20, 61-87.  
10574789 A.Mondragón, and R.DiGate (1999).
The structure of Escherichia coli DNA topoisomerase III.
  Structure, 7, 1373-1383.
PDB code: 1d6m
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.