4I3H

A three-gate structure of topoisomerase IV from Streptococcus pneumoniae

• PDB DOI:  https://doi.org/10.2210/pdb4I3H/pdb
• NAKB: 4I3H

• Classification: ISOMERASE/DNA
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-11-26 Released: 2013-08-28 
• Deposition Author(s): Laponogov, I., Veselkov, D.A., Pan, X.-S., Crevel, I., Fisher, L.M., Sanderson, M.R.

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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 

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

• PubMed: 23965305 
• DOI: https://doi.org/10.1093/nar/gkt749
• Primary Citation of Related Structures:  
  4I3H, 4JUO


• 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. 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.

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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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 298.56 kDa 
• Atom Count: 16,228 
• Modelled Residue Count: 2,140 
• Deposited Residue Count: 2,424 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Topoisomerase IV subunit B, DNA topoisomerase 4 subunit A chimera	C [auth A], D [auth B]	1,144	Streptococcus pneumoniae TIGR4	Mutation(s): 0  Gene Names: parE, parC EC: 5.99.1 (PDB Primary Data), 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
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
UniProt Groups	Q59961P72525

Entity ID: 1
Molecule	Chains	Length	Organism	Image
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]	34	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
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]	34	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	G [auth A], H [auth B], I [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 160.6	α = 90
b = 160.6	β = 90
c = 280.56	γ = 90

Software Package:

Software Name	Purpose
GDE	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Laponogov, I., Veselkov, D.A., Pan, X.-S., Crevel, I., Fisher, L.M., Sanderson, M.R.

Revision History  

• 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
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description