1LRU

Crystal Structure of E.coli Peptide Deformylase Complexed with Antibiotic Actinonin

Summary for 1LRU

• Entry DOI: 10.2210/pdb1lru/pdb
• Related: 1LQW 1LQY 1LRY
• Descriptor: PEPTIDE DEFORMYLASE, ZINC ION, ACTINONIN, ... (5 entities in total)
• Functional Keywords: actinonin, inhibition, polypeptide deformylase, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 3
• Total formula weight: 59223.59

Authors

Guilloteau, J.-P.,Mathieu, M.,Giglione, C.,Blanc, V.,Dupuy, A.,Chevrier, M.,Gil, P.,Famechon, A.,Meinnel, T.,Mikol, V. (deposition date: 2002-05-16, release date: 2002-07-24, Last modification date: 2024-02-14)

Primary citation

Guilloteau, J.P.,Mathieu, M.,Giglione, C.,Blanc, V.,Dupuy, A.,Chevrier, M.,Gil, P.,Famechon, A.,Meinnel, T.,Mikol, V.
The crystal structures of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: a platform for the structure-based design of antibacterial agents.
J.Mol.Biol., 320:951-962, 2002

PubMed Abstract: Bacterial peptide deformylase (PDF) belongs to a sub-family of metalloproteases that catalyse the removal of the N-terminal formyl group from newly synthesised proteins. PDF is essential in prokaryotes and conserved throughout the eubacteria. It is therefore considered an attractive target for developing new antibacterial agents. Here, we report the crystal structures of four bacterial deformylases, free or bound to the naturally occurring antibiotic actinonin, including two from the major bacterial pathogens Pseudomonas aeruginosa and Staphylococcus aureus. The overall tertiary structure is essentially conserved but shows significant differences, namely at the C terminus, which are directly related to the deformylase type (i.e. I or II) they belong to. The geometry around the catalytic metal ion exhibits a high level of similarity within the different enzymes, as does the binding mode of actinonin to the various deformylases. However, some significant structural differences are found in the vicinity of the active site, highlighting the structural and molecular requirements for the design of a deformylase inhibitor active against a broad spectrum of bacterial strains.

PubMed: 12126617
DOI: 10.1016/S0022-2836(02)00549-1

Experimental method

X-RAY DIFFRACTION (2.1 Å)