2AI7

S.pneumoniae Polypeptide Deformylase complexed with SB-485345

Summary for 2AI7

• Entry DOI: 10.2210/pdb2ai7/pdb
• Related: 2AI8 2AI9 2AIA 2AIE
• Descriptor: Peptide deformylase, NICKEL (II) ION, SULFATE ION, ... (5 entities in total)
• Functional Keywords: hydrolase
• Biological source: Streptococcus pneumoniae
• Total number of polymer chains: 1
• Total formula weight: 23018.02

Authors

Smith, K.J.,Petit, C.M.,Aubart, K.,Smyth, M.,McManus, E.,Jones, J.,Fosberry, A.,Lewis, C.,Lonetto, M.,Christensen, S.B. (deposition date: 2005-07-29, release date: 2005-09-06, Last modification date: 2024-02-14)

Primary citation

Smith, K.J.,Petit, C.M.,Aubart, K.,Smyth, M.,McManus, E.,Jones, J.,Fosberry, A.,Lewis, C.,Lonetto, M.,Christensen, S.B.
Structural Variation and inhibitor binding in polypeptide deformylase from four different bacterial species
Protein Sci., 12:349-360, 2003

PubMed Abstract: 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.

PubMed: 12538898
DOI: 10.1110/ps.0229303

Experimental method

X-RAY DIFFRACTION (2 Å)