5J5Q | pdb_00005j5q

AMP-PNP-stabilized ATPase domain of topoisomerase IV from Streptococcus pneumoniae, complex type II

• PDB DOI: https://doi.org/10.2210/pdb5J5Q/pdb
• NAKB: 5J5Q

• Classification: ISOMERASE/DNA
• Organism(s): Streptococcus pneumoniae, synthetic construct
• Expression System: Escherichia coli BL21(DE3), synthetic construct
• Mutation(s): No 


• Deposited: 2016-04-03 Released: 2017-07-26 
• Deposition Author(s): Laponogov, I., Pan, X.-S., Skamrova, G., Umrekar, T., Fisher, L.M., Sanderson, M.R.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 
  0.263 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Trapping of the transport-segment DNA by the ATPase domains of a type II topoisomerase.

Laponogov, I., Pan, X.S., Veselkov, D.A., Skamrova, G.B., Umrekar, T.R., Fisher, L.M., Sanderson, M.R.

(2018) Nat Commun 9: 2579-2579

• PubMed: 29968711 
• DOI: https://doi.org/10.1038/s41467-018-05005-x
• Primary Citation of Related Structures:  
  5J5P, 5J5Q


• PubMed Abstract: 
  

  Type II topoisomerases alter DNA topology to control DNA supercoiling and chromosome segregation and are targets of clinically important anti-infective and anticancer therapeutics. They act as ATP-operated clamps to trap a DNA helix and transport it through a transient break in a second DNA. Here, we present the first X-ray crystal structure solved at 2.83 Å of a closed clamp complete with trapped T-segment DNA obtained by co-crystallizing the ATPase domain of S. pneumoniae topoisomerase IV with a nonhydrolyzable ATP analogue and 14-mer duplex DNA. The ATPase dimer forms a 22 Å protein hole occupied by the kinked DNA bound asymmetrically through positively charged residues lining the hole, and whose mutagenesis impacts the DNA decatenation, DNA relaxation and DNA-dependent ATPase activities of topo IV. These results and a side-bound DNA-ParE structure help explain how the T-segment DNA is captured and transported by a type II topoisomerase, and reveal a new enzyme-DNA interface for drug discovery.

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Organizational Affiliation: 
• Randall Centre for Cell and Molecular Biophysics, 3rd Floor New Hunt's House, Faculty of Life Sciences and Medicine, King's College London, London, SE1 1UL, UK.
Molecular and Clinical Sciences Research Institute, St. George's, University of London, Cranmer Terrace, London, SW17 0RE, UK.
Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London, SW7 2AZ, UK.
The Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet St., London, WC1E 7HX, UK.
Molecular and Clinical Sciences Research Institute, St. George's, University of London, Cranmer Terrace, London, SW17 0RE, UK. [e-mail].
Randall Centre for Cell and Molecular Biophysics, 3rd Floor New Hunt's House, Faculty of Life Sciences and Medicine, King's College London, London, SE1 1UL, UK. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 191.32 kDa 
• Atom Count: 12,155 
• Modeled Residue Count: 1,609 
• Deposited Residue Count: 1,664 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 4 subunit B	A, B, C, D	409	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: parE, SP_0852 EC: 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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*GP*C)-3')	E, F	14	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	G [auth A], I [auth B], K [auth C], M [auth D], O [auth F]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	H [auth A], J [auth B], L [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free:  0.263 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.95	α = 90
b = 72.74	β = 91.89
c = 222.96	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-07-26 
Deposition Author(s): Laponogov, I., Pan, X.-S., Skamrova, G., Umrekar, T., Fisher, L.M., Sanderson, M.R.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/K010069/1

Revision History  

• Version 1.0: 2017-07-26
  Type: Initial release
  
• Version 1.1: 2018-07-18
  Changes: Data collection, Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description