2Y3P

Crystal structure of N-terminal domain of GyrA with the antibiotic simocyclinone D8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A Crystal Structure of the Bifunctional Antibiotic Simocyclinone D8, Bound to DNA Gyrase.

Edwards, M.J.Flatman, R.H.Mitchenall, L.A.Stevenson, C.E.M.Le, T.B.K.Clarke, T.A.Mckay, A.R.Fiedler, H.-P.Buttner, M.J.Lawson, D.M.Maxwell, A.

(2009) Science 326: 1415

  • DOI: 10.1126/science.1179123
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Simocyclinones are bifunctional antibiotics that inhibit bacterial DNA gyrase by preventing DNA binding to the enzyme. We report the crystal structure of the complex formed between the N-terminal domain of the Escherichia coli gyrase A subunit and si ...

    Simocyclinones are bifunctional antibiotics that inhibit bacterial DNA gyrase by preventing DNA binding to the enzyme. We report the crystal structure of the complex formed between the N-terminal domain of the Escherichia coli gyrase A subunit and simocyclinone D8, revealing two binding pockets that separately accommodate the aminocoumarin and polyketide moieties of the antibiotic. These are close to, but distinct from, the quinolone-binding site, consistent with our observations that several mutations in this region confer resistance to both agents. Biochemical studies show that the individual moieties of simocyclinone D8 are comparatively weak inhibitors of gyrase relative to the parent compound, but their combination generates a more potent inhibitor. Our results should facilitate the design of drug molecules that target these unexploited binding pockets.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Analysis of a Complex Formed between the Antibiotic Simocyclinone D8 and the DNA Breakage-Reunion Domain of Escherichia Coli DNA Gyrase.
      Edwards, M.J.,Flatman, R.H.,Mitchenall, L.A.,Stevenson, C.E.M.,Maxwell, A.,Lawson, D.M.
      (2009) Acta Crystallogr.,Sect.F 65: 846


    Organizational Affiliation

    Department of Biological Chemistry, John Innes Centre, Colney, Norwich NR4 7UH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA GYRASE SUBUNIT A
A, B
522Shigella flexneriMutation(s): 0 
Gene Names: gyrA
EC: 5.6.2.3
Find proteins for P0AES5 (Shigella flexneri)
Go to UniProtKB:  P0AES5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SM8
Query on SM8

Download SDF File 
Download CCD File 
A, B
SIMOCYCLINONE D8
C46 H42 Cl N O18
PLEGMCYXNQPJNV-VHSVXIAXSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SM8Kd: 1300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.202 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 143.910α = 90.00
b = 153.090β = 90.00
c = 177.700γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-29
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-07-12
    Type: Data collection