2NOV

Breakage-reunion domain of S.pneumoniae topo IV: crystal structure of a gram-positive quinolone target


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Breakage-Reunion Domain of Streptococcus pneumoniae Topoisomerase IV: Crystal Structure of a Gram-Positive Quinolone Target.

Laponogov, I.Veselkov, D.A.Sohi, M.K.Pan, X.S.Achari, A.Yang, C.Ferrara, J.D.Fisher, L.M.Sanderson, M.R.

(2007) PLoS ONE 2: e301-e301

  • DOI: 10.1371/journal.pone.0000301

  • PubMed Abstract: 
  • The 2.7 A crystal structure of the 55-kDa N-terminal breakage-reunion domain of topoisomerase (topo) IV subunit A (ParC) from Streptococcus pneumoniae, the first for the quinolone targets from a gram-positive bacterium, has been solved and reveals a ...

    The 2.7 A crystal structure of the 55-kDa N-terminal breakage-reunion domain of topoisomerase (topo) IV subunit A (ParC) from Streptococcus pneumoniae, the first for the quinolone targets from a gram-positive bacterium, has been solved and reveals a 'closed' dimer similar in fold to Escherichia coli DNA gyrase subunit A (GyrA), but distinct from the 'open' gate structure of Escherichia coli ParC. Unlike GyrA whose DNA binding groove is largely positively charged, the DNA binding site of ParC exhibits a distinct pattern of alternating positively and negatively charged regions coincident with the predicted positions of the grooves and phosphate backbone of DNA. Based on the ParC structure, a new induced-fit model for sequence-specific recognition of the gate (G) segment by ParC has been proposed. These features may account for the unique DNA recognition and quinolone targeting properties of pneumococcal type II topoisomerases compared to their gram-negative counterparts.


    Related Citations: 
    • The Structure of the ParC Subunit of Topoisomerase IV from Streptococcus pneumoniae
      Laponogov, I.,Veselkov, D.A.,Sohi, M.K.,Pan, X.S.,Fisher, L.M.,Sanderson, M.R.
      (2005) Acta Crystallogr.,Sect.A 61: 176


    Organizational Affiliation

    Randall Division of Cell and Molecular Biophysics, School of Biomedical and Health Sciences, King's College London, London, United Kindgom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase 4 subunit A
A, B, C, D
496Streptococcus pneumoniaeGene Names: parC
EC: 5.99.1.3
Find proteins for Q3HYJ3 (Streptococcus pneumoniae)
Go to UniProtKB:  Q3HYJ3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.224 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 136.920α = 90.00
b = 137.850β = 90.00
c = 326.020γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XSCALEdata scaling
XDSdata reduction
CNSrefinement
MAR345data collection
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description