1LM6 image
Deposition Date 2002-04-30
Release Date 2003-06-24
Last Version Date 2023-11-15
Entry Detail
PDB ID:
1LM6
Keywords:
Title:
Crystal Structure of Peptide Deformylase from Streptococcus pneumoniae
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.75 Å
R-Value Free:
0.25
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 43
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:peptide deformylase DEFB
Gene (Uniprot):def
Chain IDs:A
Chain Length:215
Number of Molecules:1
Biological Source:Streptococcus pneumoniae
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
OCS A CYS CYSTEINESULFONIC ACID
Primary Citation
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)
PMID: 12823970 DOI: 10.1016/S0022-2836(03)00596-5

Abstact

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.

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