3K9F

Detailed structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis of Gate-DNA Breakage and Resealing by Type II Topoisomerases

Laponogov, I.Pan, X.-S.Veselkov, D.A.McAuley, K.E.Fisher, L.M.Sanderson, M.R.

(2010) PLoS One 5: e11338-e11338

  • DOI: 10.1371/journal.pone.0011338
  • Primary Citation of Related Structures:  
    3KSA, 3KSB, 3LTN, 3K9F

  • PubMed Abstract: 
  • Type II DNA topoisomerases are ubiquitous enzymes with essential functions in DNA replication, recombination and transcription. They change DNA topology by forming a transient covalent cleavage complex with a gate-DNA duplex that allows transport of a second duplex though the gate ...

    Type II DNA topoisomerases are ubiquitous enzymes with essential functions in DNA replication, recombination and transcription. They change DNA topology by forming a transient covalent cleavage complex with a gate-DNA duplex that allows transport of a second duplex though the gate. Despite its biological importance and targeting by anticancer and antibacterial drugs, cleavage complex formation and reversal is not understood for any type II enzyme. To address the mechanism, we have used X-ray crystallography to study sequential states in the formation and reversal of a DNA cleavage complex by topoisomerase IV from Streptococcus pneumoniae, the bacterial type II enzyme involved in chromosome segregation. A high resolution structure of the complex captured by a novel antibacterial dione reveals two drug molecules intercalated at a cleaved B-form DNA gate and anchored by drug-specific protein contacts. Dione release generated drug-free cleaved and resealed DNA complexes in which the DNA gate instead adopts an unusual A/B-form helical conformation with a Mg(2+) ion repositioned to coordinate each scissile phosphodiester group and promote reversible cleavage by active-site tyrosines. These structures, the first for putative reaction intermediates of a type II topoisomerase, suggest how a type II enzyme reseals DNA during its normal reaction cycle and illuminate aspects of drug arrest important for the development of new topoisomerase-targeting therapeutics.


    Related Citations: 
    • Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases
      Laponogov, I., Sohi, M.K., Veselkov, D.A., Pan, X.-S., Sawhney, R., Thompson, A.W., McAuley, K.E., Fisher, L.M., Sanderson, M.R.
      (2009) Nat Struct Mol Biol 16: 667

    Organizational Affiliation

    Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 4 subunit AA, B496Streptococcus pneumoniaeMutation(s): 0 
Gene Names: parC
EC: 5.99.1 (PDB Primary Data), 5.6.2.2 (UniProt)
Find proteins for P72525 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore P72525 
Go to UniProtKB:  P72525
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 4 subunit BC, D268Streptococcus pneumoniaeMutation(s): 0 
Gene Names: parE
EC: 5.99.1 (PDB Primary Data), 5.6.2.2 (UniProt)
Find proteins for Q59961 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore Q59961 
Go to UniProtKB:  Q59961
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*CP*CP*AP*AP*GP*GP*T*CP*AP*TP*GP*AP*AP*T)-3')E15N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*GP*AP*CP*CP*TP*TP*GP*GP*T)-3')F19N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 5
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(*CP*TP*GP*TP*TP*TP*TP*A*CP*GP*TP*GP*CP*AP*T)-3')G15N/A
        • Find similar nucleic acids by:  Sequence   |   Structure
        • Entity ID: 6
          MoleculeChainsLengthOrganismImage
          DNA (5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*AP*G)-3')H19N/A
          Small Molecules
          Ligands 2 Unique
          IDChainsName / Formula / InChI Key2D Diagram3D Interactions
          LFX
          Query on LFX

          Download Ideal Coordinates CCD File 
          K [auth F], L [auth H](3S)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid
          C18 H20 F N3 O4
          GSDSWSVVBLHKDQ-JTQLQIEISA-N
           Ligand Interaction
          MG
          Query on MG

          Download Ideal Coordinates CCD File 
          I [auth C], J [auth D]MAGNESIUM ION
          Mg
          JLVVSXFLKOJNIY-UHFFFAOYSA-N
           Ligand Interaction
          Experimental Data & Validation

          Experimental Data

          • Method: X-RAY DIFFRACTION
          • Resolution: 2.90 Å
          • R-Value Free: 0.218 
          • R-Value Work: 0.183 
          • R-Value Observed: 0.187 
          • Space Group: P 32
          Unit Cell:
          Length ( Å )Angle ( ˚ )
          a = 122.407α = 90
          b = 122.407β = 90
          c = 178.287γ = 120
          Software Package:
          Software NamePurpose
          GDAdata collection
          PHASERphasing
          PHENIXrefinement
          HKL-2000data reduction
          HKL-2000data scaling

          Structure Validation

          View Full Validation Report



          Entry History 

          Deposition Data

          Revision History  (Full details and data files)

          • Version 1.0: 2009-10-27
            Type: Initial release
          • Version 1.1: 2011-07-13
            Changes: Version format compliance