4KPE

Novel fluoroquinolones in complex with topoisomerase IV from S. pneumoniae and E-site G-gate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.43 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Exploring the active site of the Streptococcus pneumoniae topoisomerase IV-DNA cleavage complex with novel 7,8-bridged fluoroquinolones.

Laponogov, I.Pan, X.S.Veselkov, D.A.Cirz, R.T.Wagman, A.Moser, H.E.Fisher, L.M.Sanderson, M.R.

(2016) Open Biol 6

  • DOI: 10.1098/rsob.160157
  • Primary Citation of Related Structures:  
    3RAD, 4KPE, 4KPF

  • PubMed Abstract: 
  • As part of a programme of synthesizing and investigating the biological properties of new fluoroquinolone antibacterials and their targeting of topoisomerase IV from Streptococcus pneumoniae, we have solved the X-ray structure of the complexes of two new 7,8-bridged fluoroquinolones (with restricted C7 group rotation favouring tight binding) in complex with the topoisomerase IV from S ...

    As part of a programme of synthesizing and investigating the biological properties of new fluoroquinolone antibacterials and their targeting of topoisomerase IV from Streptococcus pneumoniae, we have solved the X-ray structure of the complexes of two new 7,8-bridged fluoroquinolones (with restricted C7 group rotation favouring tight binding) in complex with the topoisomerase IV from S. pneumoniae and an 18-base-pair DNA binding site-the E-site-found by our DNA mapping studies to bind drug strongly in the presence of topoisomerase IV (Leo et al. 2005 J. Biol. Chem. 280, 14 252-14 263, doi:10.1074/jbc.M500156200). Although the degree of antibiotic resistance towards fluoroquinolones is much lower than that of β-lactams and a range of ribosome-bound antibiotics, there is a pressing need to increase the diversity of members of this successful clinically used class of drugs. The quinolone moiety of the new 7,8-bridged agents ACHN-245 and ACHN-454 binds similarly to that of clinafloxocin, levofloxacin, moxifloxacin and trovofloxacin but the cyclic scaffold offers the possibility of chemical modification to produce interactions with other topoisomerase residues at the active site.


    Organizational Affiliation

    Randall Division of Cell and Molecular Biophysics, King's College, Guy's Campus, London Bridge, London SE1 1UL, UK mark.sanderson@kcl.ac.uk.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 4 subunit AA, B496Streptococcus pneumoniae TIGR4Mutation(s): 1 
Gene Names: parCSP_0855
EC: 5.99.1.3 (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
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 4 subunit BC, D268Streptococcus pneumoniae TIGR4Mutation(s): 2 
Gene Names: parESP_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
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    E-site DNA1E7synthetic construct
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      E-site DNA2F11synthetic construct
      Protein Feature View
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      • Reference Sequence
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      • Entity ID: 5
        MoleculeChainsLengthOrganismImage
        E-site DNA3G7synthetic construct
        Protein Feature View
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        • Reference Sequence
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        • Entity ID: 6
          MoleculeChainsLengthOrganismImage
          E-site DNA4H11synthetic construct
          Protein Feature View
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          • Reference Sequence
          Small Molecules
          Ligands 2 Unique
          IDChainsName / Formula / InChI Key2D Diagram3D Interactions
          AF5
          Query on AF5

          Download Ideal Coordinates CCD File 
          O [auth F], P [auth H](7aR,8R)-8-amino-4-cyclopropyl-12-fluoro-1-oxo-4,7,7a,8,9,10-hexahydro-1H-pyrrolo[1',2':1,7]azepino[2,3-h]quinoline-2-carboxylic acid
          C20 H20 F N3 O3
          KZNQXATUOHSRHR-HZPDHXFCSA-N
           Ligand Interaction
          MG
          Query on MG

          Download Ideal Coordinates CCD File 
          I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth D]MAGNESIUM ION
          Mg
          JLVVSXFLKOJNIY-UHFFFAOYSA-N
           Ligand Interaction
          Experimental Data & Validation

          Experimental Data

          • Method: X-RAY DIFFRACTION
          • Resolution: 3.43 Å
          • R-Value Free: 0.195 
          • R-Value Work: 0.154 
          • R-Value Observed: 0.156 
          • Space Group: P 31 2 1
          Unit Cell:
          Length ( Å )Angle ( ˚ )
          a = 157.83α = 90
          b = 157.83β = 90
          c = 210.71γ = 120
          Software Package:
          Software NamePurpose
          GDEdata collection
          PHASERphasing
          PHENIXrefinement
          XDSdata reduction
          XSCALEdata scaling

          Structure Validation

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          Entry History 

          Deposition Data

          Revision History  (Full details and data files)

          • Version 1.0: 2014-11-26
            Type: Initial release
          • Version 1.1: 2018-10-03
            Changes: Data collection, Database references, Source and taxonomy
          • Version 1.2: 2020-01-29
            Changes: Data collection, Database references, Derived calculations