PDBsum entry 2aia

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Hydrolase PDB id
Protein chain
192 a.a. *
Waters ×211
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: S.Pneumoniae pdf complexed with sb-543668
Structure: Peptide deformylase. Chain: a. Synonym: pdf, polypeptide deformylase. Engineered: yes
Source: Streptococcus pneumoniae. Organism_taxid: 1313. Strain: atcc baa-255-r6. Gene: def. Expressed in: escherichia coli. Expression_system_taxid: 562
1.70Å     R-factor:   0.235     R-free:   0.268
Authors: K.J.Smith,C.M.Petit,K.Aubart,M.Smyth,E.Mcmanus,J.Jones, A.Fosberry,C.Lewis,M.Lonetto,S.B.Christensen
Key ref:
K.J.Smith et al. (2003). Structural variation and inhibitor binding in polypeptide deformylase from four different bacterial species. Protein Sci, 12, 349-360. PubMed id: 12538898 DOI: 10.1110/ps.0229303
29-Jul-05     Release date:   06-Sep-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q8DP79  (DEF_STRR6) -  Peptide deformylase
203 a.a.
192 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 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
= formate
+ 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: 10.1110/ps.0229303 Protein Sci 12:349-360 (2003)
PubMed id: 12538898  
Structural variation and inhibitor binding in polypeptide deformylase from four different bacterial species.
K.J.Smith, C.M.Petit, K.Aubart, M.Smyth, E.McManus, J.Jones, A.Fosberry, C.Lewis, M.Lonetto, S.B.Christensen.
Polypeptide deformylase (PDF) catalyzes the deformylation of polypeptide chains in bacteria. It is essential for bacterial cell viability and is a potential antibacterial drug target. Here, we report the crystal structures of polypeptide deformylase from four different species of bacteria: Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, and Escherichia coli. Comparison of these four structures reveals significant overall differences between the two Gram-negative species (E. coli and H. influenzae) and the two Gram-positive species (S. pneumoniae and S. aureus). Despite these differences and low overall sequence identity, the S1' pocket of PDF is well conserved among the four enzymes studied. We also describe the binding of nonpeptidic inhibitor molecules SB-485345, SB-543668, and SB-505684 to both S. pneumoniae and E. coli PDF. Comparison of these structures shows similar binding interactions with both Gram-negative and Gram-positive species. Understanding the similarities and subtle differences in active site structure between species will help to design broad-spectrum polypeptide deformylase inhibitor molecules.
  Selected figure(s)  
Figure 2.
Figure 2. Crystal structures of E. coli, H. influenzae, S. aureus, and S. pneumoniae PDF. Comparison of the crystal structure of PDF from E. coli (cyan), H. influenzae (dark blue), S. pneumoniae (green), and S. aureus (yellow). (A) S. pneumoniae and S. aureus PDF. (B) E. coli and H. influenzae PDF. (C) All four species of PDF. The bound nickel is in red, and His 132, His 136, and Cys 90 are shown as a ball-and-stick representation. S. pneumoniae PDF is 13 residues longer at the N terminus than S. aureus PDF. The major difference between PDF from E. coli and from H. influenzae is the angle of the C-terminal -helix. This is mainly due to the presence of bulky Phe 96 in H. influenzae PDF (Q in E. coli PDF), which packs against the C-terminal -helix. The figure was made using RIBBONS (Carson 1991).
Figure 5.
Figure 5. Binding of SB-543668 and SB-505684 to E. coli and S. pneumoniae PDF. SB-505684 binding to E. coli PDF (A) and S. pneumoniae PDF (B); SB-543668 binding to E. coli PDF (C) and S. pneumoniae PDF (D). Inhibitor molecules are colored in red, hydrogen bonds are marked as dashed lines, and water molecules are shown as red spheres. The figure was prepared with XTALVIEW (McRee 1993).
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2003, 12, 349-360) copyright 2003.  
  Figures were selected by the author.  

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.  
19627112 C.D.Amero, D.W.Byerly, C.A.McElroy, A.Simmons, and M.P.Foster (2009).
Ligand-induced changes in the structure and dynamics of Escherichia coli peptide deformylase.
  Biochemistry, 48, 7595-7607.  
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
16816197 J.Huang, G.S.Van Aller, A.N.Taylor, J.J.Kerrigan, W.S.Liu, J.M.Trulli, Z.Lai, D.Holmes, K.M.Aubart, J.R.Brown, and M.Zalacain (2006).
Phylogenomic and biochemical characterization of three Legionella pneumophila polypeptide deformylases.
  J Bacteriol, 188, 5249-5257.  
16913833 T.Meinnel, A.Serero, and C.Giglione (2006).
Impact of the N-terminal amino acid on targeted protein degradation.
  Biol Chem, 387, 839-851.  
16113286 I.T.Kudva, R.W.Griffin, J.M.Garren, S.B.Calderwood, and M.John (2005).
Identification of a protein subset of the anthrax spore immunome in humans immunized with the anthrax vaccine adsorbed preparation.
  Infect Immun, 73, 5685-5696.  
16049914 J.H.Moon, J.K.Park, and E.E.Kim (2005).
Structure analysis of peptide deformylase from Bacillus cereus.
  Proteins, 61, 217-220.
PDB codes: 1ws0 1ws1
  16508119 J.K.Park, J.H.Moon, J.H.Kim, and E.E.Kim (2005).
Crystallization and preliminary X-ray crystallographic analysis of peptide deformylase (PDF) from Bacillus cereus in ligand-free and actinonin-bound forms.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 150-152.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.