3SW8

Strep Peptide Deformylase with a time dependent dichlorobenzamide-reverse hydroxamic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.702 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.193 

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.


    Related Citations: 
    • Structural variation and inhibitor binding in polypeptide deformylase from four different bacterial species.
      Smith, K.J.,Petit, C.M.,Aubart, K.,Smyth, M.,McManus, E.,Jones, J.,Fosberry, A.,Lewis, C.,Lonetto, M.,Christensen, S.B.
      (2003) Protein Sci. 12: 349


    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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
P
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
5LI
Query on 5LI

Download SDF File 
Download CCD File 
P
2,3-dichloro-N-{2-[formyl(hydroxy)amino]ethyl}benzamide
C10 H10 Cl2 N2 O3
QOBOQKAHMKWYEE-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 %)
5LIKi: 25910 nM BINDINGMOAD
5LIKi: 31720 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.702 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.193 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 50.015α = 90.00
b = 50.015β = 90.00
c = 91.605γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
PHENIXrefinement
MAR345dtbdata collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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