2AI8 image
Deposition Date 2005-07-29
Release Date 2005-09-06
Last Version Date 2024-02-14
Entry Detail
PDB ID:
2AI8
Keywords:
Title:
E.coli Polypeptide Deformylase complexed with SB-485343
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.70 Å
R-Value Free:
0.22
R-Value Work:
0.21
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Peptide deformylase
Gene (Uniprot):def
Chain IDs:A, B, C
Chain Length:168
Number of Molecules:3
Biological Source:Escherichia coli
Primary Citation
Structural Variation and inhibitor binding in polypeptide deformylase from four different bacterial species.
Protein Sci. 12 349 360 (2003)
PMID: 12538898 DOI: 10.1110/ps.0229303

Abstact

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.

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