Crystal Structure of Peptide Deformylase from Leptospira Interrogans (LiPDF) at pH7.5

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 

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Novel conformational states of peptide deformylase from pathogenic bacterium Leptospira interrogans: implications for population shift

Zhou, Z.Song, X.Gong, W.

(2005) J Biol Chem 280: 42391-42396

  • DOI: https://doi.org/10.1074/jbc.M506370200
  • Primary Citation of Related Structures:  
    1SV2, 1SZZ, 1VEV, 1VEY, 1VEZ

  • PubMed Abstract: 

    Peptide deformylase is an attractive target for developing novel antibiotics. Previous studies at pH 3.0 showed peptide deformylase from Leptospira interrogans (LiPDF) exists as a dimer in which one monomer is in a closed form and the other is in an open form, with different conformations of the CD-loop controlling the entrance to the active pocket. Here we present structures of LiPDF at its active pH range. LiPDF forms a similar dimer at pH values 6.5-8.0 as it does at pH 3.0. Interestingly, both of the monomers are almost in the same closed form as that observed at pH 3.0. However, when the enzyme is complexed with the natural inhibitor actinotin, the conformation of the CD-loop is half-open. Two pairs of Arg109-mediated cation-pi interactions, as well as hydrogen bonds, have been identified to stabilize the different CD-loop conformations. These results indicate that LiPDF may be found in different structural states, a feature that has never before been observed in the peptide deformylase family. Based on our results, a novel substrate binding model, featured by an equilibrium between the closed and the open forms, is proposed. Our results present crystallographic evidence supporting population shift theory, which is distinguished from the conventional lock-and-key or induced-fit models. These results not only facilitate the development of peptide deformylase-targeted drugs but also provide structural insights into the mechanism of an unusual type of protein binding event.

  • Organizational Affiliation

    National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide deformylase
A, B
177Leptospira interrogansMutation(s): 0 
Find proteins for Q93LE9 (Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601))
Explore Q93LE9 
Go to UniProtKB:  Q93LE9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93LE9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.914α = 90
b = 83.914β = 90
c = 204.411γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-09
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance