1LME

Crystal Structure of Peptide Deformylase from Thermotoga maritima

Summary for 1LME

• Entry DOI: 10.2210/pdb1lme/pdb
• Related: 1lm4 1lm6
• Descriptor: peptide deformylase (2 entities in total)
• Functional Keywords: thermophile, pdf, peptide deformylase, metalloenzyme, deformylation, structural genomics, psi, protein structure initiative, joint center for structural genomics, jcsg, hydrolase
• Biological source: Thermotoga maritima
• Total number of polymer chains: 2
• Total formula weight: 41127.54

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.,Joint Center for Structural Genomics (JCSG) (deposition date: 2002-05-01, 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 (2.2 Å)