3FOF | pdb_00003fof

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

• PDB DOI: https://doi.org/10.2210/pdb3FOF/pdb
• NAKB: 3FOF

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


• Deposited: 2008-12-30 Released: 2009-02-24 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.00 Å
• R-Value Free: 
  0.289 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Starting Models: experimental

Literature

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: 667-669

• PubMed: 19448616 
• DOI: https://doi.org/10.1038/nsmb.1604
• Primary Citation Related Structures: 
  3FOE, 3FOF


• PubMed Abstract: 
  

  Type II topoisomerases alter DNA topology by forming a covalent DNA-cleavage complex that allows DNA transport through a double-stranded DNA break. We present the structures of cleavage complexes formed by the Streptococcus pneumoniae ParC breakage-reunion and ParE TOPRIM domains of topoisomerase IV stabilized by moxifloxacin and clinafloxacin, two antipneumococcal fluoroquinolones. These structures reveal two drug molecules intercalated at the highly bent DNA gate and help explain antibacterial quinolone action and resistance.

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Organizational Affiliation: 
• Randall Division of Cell and Molecular Biophysics, King's College London, University of London, London, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content 

• Total Structure Weight: 195.37 kDa 
• Atom Count: 8,452 
• Modeled Residue Count: 1,330 
• Deposited Residue Count: 1,596 
• Unique protein chains: 2
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 4 subunit A	A, B	496	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: parC, SP_0855 EC: 5.99.1 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P72525 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore P72525  Go to UniProtKB:  P72525

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 4 subunit B	C, D	268	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: parE, SP_0852 EC: 5.99.1 (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: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*CP*AP*AP*GP*GP*TP*CP*AP*TP*GP*AP*AP*T)-3')	E	15	N/A

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*GP*AP*CP*CP*TP*TP*GP*GP*T)-3')	F	19	N/A

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*TP*GP*TP*TP*TP*TP*AP*CP*GP*TP*GP*CP*AP*T)-3')	G	15	N/A

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*AP*G)-3')	H	19	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MFX	I [auth F], J [auth H]	1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid C21 H24 F N3 O4 FABPRXSRWADJSP-MEDUHNTESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.00 Å
• R-Value Free:  0.289 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.601	α = 90
b = 121.601	β = 90
c = 178.699	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-24 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2009-02-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description