1AJ6

NOVOBIOCIN-RESISTANT MUTANT (R136H) OF THE N-TERMINAL 24 KDA FRAGMENT OF DNA GYRASE B COMPLEXED WITH NOVOBIOCIN AT 2.3 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The entropic penalty of ordered water accounts for weaker binding of the antibiotic novobiocin to a resistant mutant of DNA gyrase: a thermodynamic and crystallographic study.

Holdgate, G.A.Tunnicliffe, A.Ward, W.H.Weston, S.A.Rosenbrock, G.Barth, P.T.Taylor, I.W.Pauptit, R.A.Timms, D.

(1997) Biochemistry 36: 9663-9673

  • DOI: 10.1021/bi970294+

  • PubMed Abstract: 
  • Novobiocin is an antibiotic which binds to a 24 kDa fragment from the B subunit of DNA gyrase. Naturally occurring resistance arises from mutation of Arg-136 which hydrogen bonds to the coumarin ring of novobiocin. We have applied calorimetry to char ...

    Novobiocin is an antibiotic which binds to a 24 kDa fragment from the B subunit of DNA gyrase. Naturally occurring resistance arises from mutation of Arg-136 which hydrogen bonds to the coumarin ring of novobiocin. We have applied calorimetry to characterize the binding of novobiocin to wild-type and R136H mutant 24 kDa fragments. Upon mutation, the Kd increases from 32 to 1200 nM at 300 K. The enthalpy of binding is more favorable for the mutant (DeltaH degrees shifts from -12.1 to -17.5 kcal/mol), and the entropy of binding is much less favorable (TDeltaS degrees changes from -1.8 to -9.4 kcal/mol). Both of these changes are in the direction opposite to that expected if the loss of the Arg residue reduces hydrogen bonding. The change in heat capacity at constant pressure upon binding (DeltaCp) shifts from -295 to -454 cal mol-1 K-1. We also report the crystal structure, at 2.3 A resolution, of a complex between the R136H 24 kDa fragment and novobiocin. Although the change in DeltaCp often would be interpreted as reflecting increased burial of hydrophobic surface on binding, this structure reveals a small decrease. Furthermore, an ordered water molecule is sequestered into the volume vacated by removal of the guanidinium group. There are large discrepancies when the measured thermodynamic parameters are compared to those estimated from the structural data using empirical relationships. These differences seem to arise from the effects of sequestering ordered water molecules upon complexation. The water-mediated hydrogen bonds linking novobiocin to the mutant protein make a favorable enthalpic contribution, whereas the immobilization of the water leads to an entropic cost and a reduction in the heat capacity of the system. Such a negative contribution to DeltaCp, DeltaH degrees , and TDeltaS degrees appears to be a general property of water molecules that are sequestered when ligands bind to proteins.


    Related Citations: 
    • The Nature of Inhibition of DNA Gyrase by the Coumarins and the Cyclothialidines Revealed by X-Ray Crystallography
      Lewis, R.J.,Singh, O.M.,Smith, C.V.,Skarzynski, T.,Maxwell, A.,Wonacott, A.J.,Wigley, D.B.
      (1996) Embo J. 15: 1412
    • The High-Resolution Crystal Structure of a 24-kDa Gyrase B Fragment from E. Coli Complexed with One of the Most Potent Coumarin Inhibitors, Clorobiocin
      Tsai, F.T.,Singh, O.M.,Skarzynski, T.,Wonacott, A.J.,Weston, S.,Tucker, A.,Pauptit, R.A.,Breeze, A.L.,Poyser, J.P.,O'Brien, R.,Ladbury, J.E.,Wigley, D.B.
      (1997) Proteins 28: 41
    • Antibacterial Design Based on the Structures of Gyrase-Inhibitor Complexes
      Pauptit, R.A.,Weston, S.A.,Breeze, A.L.,Derbyshire, D.J.,Tucker, A.D.,Hales, N.,Hollinshead, D.,Timms, D.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    ZENECA Pharmaceuticals, Macclesfield, Cheshire, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GYRASE
A
219Escherichia coli (strain K12)Gene Names: gyrB (acrB, cou, himB, hisU, nalC, parA, pcbA)
EC: 5.99.1.3
Find proteins for P0AES6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AES6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NOV
Query on NOV

Download SDF File 
Download CCD File 
A
NOVOBIOCIN
4-Hydroxy-3-[4-hydroxy-3-(3-methylbut-2-enyl)benzamido]-8-methylcoumarin-7-yl 3-O-carbamoyl-5,5-di-C-methyl-alpha-l-lyxofuranoside
C31 H36 N2 O11
YJQPYGGHQPGBLI-KGSXXDOSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.500α = 90.00
b = 47.720β = 90.00
c = 114.410γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4phasing
TNTrefinement
CCP4data scaling
CCP4model building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-05-20
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance