1LRU

Crystal Structure of E.coli Peptide Deformylase Complexed with Antibiotic Actinonin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 

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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

  • DOI: 10.1016/s0022-2836(02)00549-1
  • Primary Citation of Related Structures:  
    1LQW, 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 therefore considered an attractive target for developing new antibacterial agents ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDE DEFORMYLASEA, B, C168Escherichia coliMutation(s): 0 
EC: 3.5.1.88
UniProt
Find proteins for P0A6K3 (Escherichia coli (strain K12))
Explore P0A6K3 
Go to UniProtKB:  P0A6K3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6K3
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
BB2 BindingDB:  1LRU IC50: min: 6, max: 140 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.04α = 90
b = 63.608β = 123.35
c = 83.494γ = 90
Software Package:
Software NamePurpose
SHARPphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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