4NIL

Crystal structure of B. anthracis DHPS with compound 5: 4-[(trifluoromethyl)sulfanyl]benzamide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Identification and characterization of an allosteric inhibitory site on dihydropteroate synthase.

Hammoudeh, D.I., Date, M., Yun, M.K., Zhang, W., Boyd, V.A., Viacava Follis, A., Griffith, E., Lee, R.E., Bashford, D., White, S.W.

(2014) Acs Chem.Biol. 9: 1294-1302

  • DOI: 10.1021/cb500038g
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The declining effectiveness of current antibiotics due to the emergence of resistant bacterial strains dictates a pressing need for novel classes of antimicrobial therapies, preferably against molecular sites other than those in which resistance muta ...

    The declining effectiveness of current antibiotics due to the emergence of resistant bacterial strains dictates a pressing need for novel classes of antimicrobial therapies, preferably against molecular sites other than those in which resistance mutations have developed. Dihydropteroate synthase (DHPS) catalyzes a crucial step in the bacterial pathway of folic acid synthesis, a pathway that is absent in higher vertebrates. As the target of the sulfonamide class of drugs that were highly effective until resistance mutations arose, DHPS is known to be a valuable bacterial Achilles heel that is being further exploited for antibiotic development. Here, we report the discovery of the first known allosteric inhibitor of DHPS. NMR and crystallographic studies reveal that it engages a previously unknown binding site at the dimer interface. Kinetic data show that this inhibitor does not prevent substrate binding but rather exerts its effect at a later step in the catalytic cycle. Molecular dynamics simulations and quasi-harmonic analyses suggest that the effect of inhibitor binding is transmitted from the dimer interface to the active-site loops that are known to assume an obligatory ordered substructure during catalysis. Together with the kinetics results, these structural and dynamics data suggest an inhibitory mechanism in which binding at the dimer interface impacts loop movements that are required for product release. Our results potentially provide a novel target site for the development of new antibiotics.

    Organizational Affiliation: 

    Departments of †Structural Biology and ‡Chemical Biology and Therapeutics, St. Jude Children's Research Hospital , Memphis, Tennessee 38105, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydropteroate Synthase
A, B
297Bacillus anthracisMutation(s): 0 
Gene Names: folP
EC: 2.5.1.15
Find proteins for Q81VW8 (Bacillus anthracis)
Go to UniProtKB:  Q81VW8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
2O8
Query on 2O8
Download SDF File 
Download CCD File 
A, B
4-[(trifluoromethyl)sulfanyl]benzamide
C8 H6 F3 N O S
ILYWYSLTZOUSID-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.226 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 99.739α = 90.00
b = 99.739β = 90.00
c = 263.296γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
SERGUIdata collection
DENZOdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2014-08-06
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Advisory, Refinement description