4I3H

A three-gate structure of topoisomerase IV from Streptococcus pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of an 'open' clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport.

Laponogov, I.Veselkov, D.A.Crevel, I.M.Pan, X.S.Fisher, L.M.Sanderson, M.R.

(2013) Nucleic Acids Res 41: 9911-9923

  • DOI: 10.1093/nar/gkt749
  • Primary Citation of Related Structures:  
    4JUO, 4I3H

  • PubMed Abstract: 
  • Type II topoisomerases regulate DNA supercoiling and chromosome segregation. They act as ATP-operated clamps that capture a DNA duplex and pass it through a transient DNA break in a second DNA segment via the sequential opening and closure of ATPase-, G-DNA- and C-gates ...

    Type II topoisomerases regulate DNA supercoiling and chromosome segregation. They act as ATP-operated clamps that capture a DNA duplex and pass it through a transient DNA break in a second DNA segment via the sequential opening and closure of ATPase-, G-DNA- and C-gates. Here, we present the first 'open clamp' structures of a 3-gate topoisomerase II-DNA complex, the seminal complex engaged in DNA recognition and capture. A high-resolution structure was solved for a (full-length ParE-ParC55)2 dimer of Streptococcus pneumoniae topoisomerase IV bound to two DNA molecules: a closed DNA gate in a B-A-B form double-helical conformation and a second B-form duplex associated with closed C-gate helices at a novel site neighbouring the catalytically important β-pinwheel DNA-binding domain. The protein N gate is present in an 'arms-wide-open' state with the undimerized N-terminal ParE ATPase domains connected to TOPRIM domains via a flexible joint and folded back allowing ready access both for gate and transported DNA segments and cleavage-stabilizing antibacterial drugs. The structure shows the molecular conformations of all three gates at 3.7 Å, the highest resolution achieved for the full complex to date, and illuminates the mechanism of DNA capture and transport by a type II topoisomerase.


    Organizational Affiliation

    Randall Division of Cell and Molecular Biophysics, 3rd floor New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK and Division of Biomedical Sciences, St. George's, University of London, Cranmer Terrace, London, SW17 0RE, UK.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Topoisomerase IV subunit B, DNA topoisomerase 4 subunit A chimeraC [auth A], D [auth B]1144Streptococcus pneumoniae TIGR4Mutation(s): 0 
Gene Names: parEparC
EC: 5.99.1 (PDB Primary Data), 5.99.1.3 (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
Find proteins for P72525 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore P72525 
Go to UniProtKB:  P72525
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*AP*AP*AP*GP*GP*CP*GP*GP*TP*AP*AP*TP*AP*CP*GP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*GP*AP*AP*TP*CP*AP*GP*G)-3')A [auth E], E [auth G]34N/A
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*CP*TP*GP*AP*TP*TP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*CP*GP*TP*AP*TP*TP*AP*CP*CP*GP*CP*CP*TP*TP*TP*G)-3')B [auth F], F [auth H]34N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A], H [auth B], I [auth H]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.6α = 90
b = 160.6β = 90
c = 280.56γ = 90
Software Package:
Software NamePurpose
GDEdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-28
    Type: Initial release
  • Version 1.1: 2013-09-04
    Changes: Database references
  • Version 1.2: 2013-12-04
    Changes: Database references
  • Version 1.3: 2017-07-26
    Changes: Data collection, Refinement description, Source and taxonomy