PDBsum entry 1vev

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Hydrolase PDB id
Protein chains
171 a.a. *
MES ×3
FMT ×2
_ZN ×2
Waters ×210
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of peptide deformylase from leptospira interrogans (lipdf) at ph6.5
Structure: Peptide deformylase. Chain: a, b. Synonym: lipdf, pdf, polypeptide deformylase. Engineered: yes
Source: Leptospira interrogans. Organism_taxid: 173. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PDB file)
2.51Å     R-factor:   0.258     R-free:   0.290
Authors: Z.Zhou,X.Song,Y.Li,W.Gong
Key ref:
Z.Zhou et al. (2005). Novel conformational states of peptide deformylase from pathogenic bacterium Leptospira interrogans: implications for population shift. J Biol Chem, 280, 42391-42396. PubMed id: 16239225 DOI: 10.1074/jbc.M506370200
06-Apr-04     Release date:   23-Aug-05    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q93LE9  (DEF_LEPIN) -  Peptide deformylase
178 a.a.
171 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Peptide deformylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Formyl-L-methionyl peptide + H2O = formate + methionyl peptide
Formyl-L-methionyl peptide
+ H(2)O
Bound ligand (Het Group name = FMT)
corresponds exactly
+ methionyl peptide
      Cofactor: Fe(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     translation   1 term 
  Biochemical function     hydrolase activity     4 terms  


DOI no: 10.1074/jbc.M506370200 J Biol Chem 280:42391-42396 (2005)
PubMed id: 16239225  
Novel conformational states of peptide deformylase from pathogenic bacterium Leptospira interrogans: implications for population shift.
Z.Zhou, X.Song, W.Gong.
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.
  Selected figure(s)  
Figure 1.
FIGURE 1. Closed and half-open states of LiPDF. A, the closed state within the active pH range represented by the structure determined at pH 7.5. B, the half-open state bound with actinonin. Shown on the right halves of both A and B, dimer is formed through hydrophobic interactions (Phe^164, Phe^166, Met^108, and Met^9 shown in stick model) between two subunits colored in blue and brown, respectively. Shown on the left halves of A and B are close-up pictures for the closed and half-open pockets, respectively (viewed from same direction). The CD-loop (residue 65-76) is highlighted in red, and the active zinc ion is in pink. In the closed state (A), the substrate pocket is blocked and hydrogen bonds are shown by a green dashed line. For clarity, the formate group is shown as a star. In the half-open state (B), the bound competitive inhibitor actinonin is shown in stick-and-dots model. In this state, Arg^71 is completely solvent-exposed and thus disordered. This figure and Fig. 3 were prepared using Pymol.
Figure 2.
FIGURE 2. Superposition of all LiPDF structures. A, all observed conformational states of LiPDF are superimposed to reveal the differences around the substrate pocket. Pink, closed state at pH 3.0; brown, all closed states within pH values 6.5-8.0; blue, half-open state; cyan, open state at pH 3.0. Residues Tyr^72 and Arg^109 (ball-and-stick model) undergo significant conformational change during the conversion between different states. The competitive inhibitor actinonin (black), which was bound to the half-open state (blue) would collide with the pocket in the closed states. With the opening of the substrate pocket, the side chain of Arg^109 swung up toward the molecular surface. Compared with the closed state at pH 3.0, the closed states within the pH range 6.5-8.0 displayed a slightly open pocket. B, a schematic is shown to help compare these different states. The color scheme is consistent in both panels. This figure was prepared using Molscript (30) and Raster3D (31).
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 42391-42396) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20656778 P.Lin, T.Hu, J.Hu, W.Yu, C.Han, J.Zhang, G.Qin, K.Yu, F.Götz, X.Shen, H.Jiang, and D.Qu (2010).
Characterization of peptide deformylase homologues from Staphylococcus epidermidis.
  Microbiology, 156, 3194-3202.  
19236878 S.Escobar-Alvarez, Y.Goldgur, G.Yang, O.Ouerfelli, Y.Li, and D.A.Scheinberg (2009).
Structure and activity of human mitochondrial peptide deformylase, a novel cancer target.
  J Mol Biol, 387, 1211-1228.
PDB codes: 3g5k 3g5p
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