1LQW

Crystal Structure of S.aureus Peptide Deformylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structures of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: a platform for the structure-based design of antibacterial agents.

Guilloteau, J.P.Mathieu, M.Giglione, C.Blanc, V.Dupuy, A.Chevrier, M.Gil, P.Famechon, A.Meinnel, T.Mikol, V.

(2002) J.Mol.Biol. 320: 951-962

  • Primary Citation of Related Structures:  1LQY, 1LRU, 1LRY

  • PubMed Abstract: 
  • Bacterial peptide deformylase (PDF) belongs to a sub-family of metalloproteases that catalyse the removal of the N-terminal formyl group from newly synthesised proteins. PDF is essential in prokaryotes and conserved throughout the eubacteria. It is t ...

    Bacterial peptide deformylase (PDF) belongs to a sub-family of metalloproteases that catalyse the removal of the N-terminal formyl group from newly synthesised proteins. PDF is essential in prokaryotes and conserved throughout the eubacteria. It is therefore considered an attractive target for developing new antibacterial agents. Here, we report the crystal structures of four bacterial deformylases, free or bound to the naturally occurring antibiotic actinonin, including two from the major bacterial pathogens Pseudomonas aeruginosa and Staphylococcus aureus. The overall tertiary structure is essentially conserved but shows significant differences, namely at the C terminus, which are directly related to the deformylase type (i.e. I or II) they belong to. The geometry around the catalytic metal ion exhibits a high level of similarity within the different enzymes, as does the binding mode of actinonin to the various deformylases. However, some significant structural differences are found in the vicinity of the active site, highlighting the structural and molecular requirements for the design of a deformylase inhibitor active against a broad spectrum of bacterial strains.


    Organizational Affiliation

    Drug Innovation & Approval, Aventis Pharma, 13 Quai Jules Guesde, BP.14, F-94403, Vitry-sur-Seine, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE DEFORMYLASE PDF1
A, B
183Staphylococcus aureusGene Names: def (def1, pdf1)
EC: 3.5.1.88
Find proteins for P68826 (Staphylococcus aureus)
Go to UniProtKB:  P68826
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.231 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.210α = 90.00
b = 42.190β = 98.67
c = 101.670γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
MOSFLMdata reduction
CCP4data scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2002-05-14 
  • Released Date: 2002-07-24 
  • Deposition Author(s): Mikol, V.

Revision History 

  • Version 1.0: 2002-07-24
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance