1LM6

Crystal Structure of Peptide Deformylase from Streptococcus pneumoniae

Summary for 1LM6

• Entry DOI: 10.2210/pdb1lm6/pdb
• Related: 1LM4 1LME
• Descriptor: peptide deformylase DEFB, FE (III) ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: pdf, metalloenzyme, peptide deformylase, hydrolase
• Biological source: Streptococcus pneumoniae
• Total number of polymer chains: 1
• Total formula weight: 24378.62

Authors

Kreusch, A.,Spraggon, G.,Lee, C.C.,Klock, H.,McMullan, D.,Ng, K.,Shin, T.,Vincent, J.,Warner, I.,Ericson, C.,Lesley, S.A. (deposition date: 2002-04-30, release date: 2003-06-24, Last modification date: 2023-11-15)

Primary citation

Kreusch, A.,Spraggon, G.,Lee, C.C.,Klock, H.,McMullan, D.,Ng, K.,Shin, T.,Vincent, J.,Warner, I.,Ericson, C.,Lesley, S.A.
Structure analysis of peptide deformylases from streptococcus pneumoniae,staphylococcus aureus, thermotoga maritima, and pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase
J.MOL.BIOL., 330:309-321, 2003

PubMed Abstract: Peptide deformylase (PDF) has received considerable attention during the last few years as a potential target for a new type of antibiotics. It is an essential enzyme in eubacteria for the removal of the formyl group from the N terminus of the nascent polypeptide chain. We have solved the X-ray structures of four members of this enzyme family, two from the Gram-positive pathogens Streptococcus pneumoniae and Staphylococcus aureus, and two from the Gram-negative bacteria Thermotoga maritima and Pseudomonas aeruginosa. Combined with the known structures from the Escherichia coli enzyme and the recently solved structure of the eukaryotic deformylase from Plasmodium falciparum, a complete picture of the peptide deformylase structure and function relationship is emerging. This understanding could help guide a more rational design of inhibitors. A structure-based comparison between PDFs reveals some conserved differences between type I and type II enzymes. Moreover, our structures provide insights into the known instability of PDF caused by oxidation of the metal-ligating cysteine residue.

PubMed: 12823970
DOI: 10.1016/S0022-2836(03)00596-5

Experimental method

X-RAY DIFFRACTION (1.75 Å)