3KSB

Detailed structural insight into the DNA cleavage complex of type IIA topoisomerases (re-sealed form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.181 

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:  3K9F, 3KSA, 3LTN

  • 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 ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase 4 subunit A
A, B
496Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)Gene Names: parC
EC: 5.99.1.3
Find proteins for P72525 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  P72525
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase 4 subunit B
C, D
268Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)Gene Names: parE
EC: 5.99.1.3
Find proteins for Q59961 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  Q59961
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*AP*CP*CP*AP*AP*GP*GP*T*CP*AP*TP*GP*AP*AP*TP*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*AP*G)-3'E34N/A
Entity ID: 4
MoleculeChainsLengthOrganism
5'-D(*CP*TP*GP*TP*TP*TP*TP*A*CP*GP*TP*GP*CP*AP*TP*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*GP*AP*CP*CP*TP*TP*GP*GP*T)-3'F34N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.181 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 116.757α = 90.00
b = 116.757β = 90.00
c = 182.811γ = 120.00
Software Package:
Software NamePurpose
GDAdata collection
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance