3STR

Strep Peptide Deformylase with a time dependent thiazolidine hydroxamic acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


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

Literature

Understanding the origins of time-dependent inhibition by polypeptide deformylase inhibitors.

Totoritis, R., Duraiswami, C., Taylor, A.N., Kerrigan, J.J., Campobasso, N., Smith, K.J., Ward, P., King, B.W., Murrayz-Thompson, M., Jones, A.D., Van Aller, G.S., Aubart, K.M., Zalacain, M., Thrall, S.H., Meek, T.D., Schwartz, B.

(2011) Biochemistry 50: 6642-6654

  • DOI: 10.1021/bi200655g
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The continual bacterial adaptation to antibiotics creates an ongoing medical need for the development of novel therapeutics. Polypeptide deformylase (PDF) is a highly conserved bacterial enzyme, which is essential for viability. It has previously bee ...

    The continual bacterial adaptation to antibiotics creates an ongoing medical need for the development of novel therapeutics. Polypeptide deformylase (PDF) is a highly conserved bacterial enzyme, which is essential for viability. It has previously been shown that PDF inhibitors represent a promising new area for the development of antimicrobial agents, and that many of the best PDF inhibitors demonstrate slow, time-dependent binding. To improve our understanding of the mechanistic origin of this time-dependent inhibition, we examined in detail the kinetics of PDF catalysis and inhibition by several different PDF inhibitors. Varying pH and solvent isotope led to clear changes in time-dependent inhibition parameters, as did inclusion of NaCl, which binds to the active site metal of PDF. Quantitative analysis of these results demonstrated that the observed time dependence arises from slow binding of the inhibitors to the active site metal. However, we also found several metal binding inhibitors that exhibited rapid, non-time-dependent onset of inhibition. By a combination of structural and chemical modification studies, we show that metal binding is only slow when the rest of the inhibitor makes optimal hydrogen bonds within the subsites of PDF. Both of these interactions between the inhibitor and enzyme were found to be necessary to observe time-dependent inhibition, as elimination of either leads to its loss.

    Organizational Affiliation: 

    Department of Biological Reagents, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide deformylase 3
P
203Streptococcus pneumoniaeMutation(s): 0 
Gene Names: defB (def, def_1, def_2, def_3)
EC: 3.5.1.88
Find proteins for Q939R9 (Streptococcus pneumoniae)
Go to UniProtKB:  Q939R9
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3LI
Query on 3LI
Download SDF File 
Download CCD File 
P
(4R)-3-(4-[4-(2-chlorophenyl)piperazin-1-yl]-6-{[2-methyl-6-(methylcarbamoyl)phenyl]amino}-1,3,5-triazin-2-yl)-N-[2-(hydroxyamino)-2-oxoethyl]-1,3-thiazolidine-4-carboxamide
C28 H33 Cl N10 O4 S
VJGKWQWGYXBKEJ-NRFANRHFSA-N
 Ligand Interaction
SO4
Query on SO4
Download SDF File 
Download CCD File 
P
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
P
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI
Download SDF File 
Download CCD File 
P
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3LIKi: 334 nM (100) BINDINGDB
3LIKi: 334 nM BINDINGMOAD
3LIKi: 3.96 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.192 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 50.274α = 90.00
b = 50.274β = 90.00
c = 91.486γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-27
    Type: Initial release
  • Version 1.1: 2011-08-17
    Type: Database references
  • Version 1.2: 2014-04-16
    Type: Other