Distinctive features of the two classes of eukaryotic peptide deformylases

J Mol Biol. 2001 Dec 7;314(4):695-708. doi: 10.1006/jmbi.2001.5175.

Abstract

Peptide deformylases (PDFs) are essential enzymes of the N-terminal protein processing pathway of eubacteria. The recent discovery of two types of PDFs in higher plants, PDF1A and PDF1B, and the detection of PDF1A in humans, have raised questions concerning the importance of deformylation in eukaryotes. Here, we have characterized fully in vitro and compared the properties of the two classes of eukaryotic PDFs, PDF1A and PDF1B, using the PDFs from Arabidopsis thaliana and Lycopersicon esculentum. We have shown that the PDFs of a given class (1A or 1B) all display similar features, independently of their origin. We also observed similar specificity of all plant PDFs for natural substrate peptides, but identified a number of biochemical differences between the two classes (1A or 1B). The main difference lies at the level of the bound cofactor, iron for PDF1B-like bacterial PDFs, and zinc for PDF1A. The nature of the metal cation has important consequences concerning the relative sensitivity to oxygen of the two plant PDFs. Investigation of the specificity of these enzymes with unusual substrates revealed additional differences between the two types of PDFs, enabling us to identify specific inhibitors with a lower affinity against PDF1As. However, the two plant PDFs were inhibited equally strongly in vitro by actinonin, an antibiotic that specifically acts on bacterial PDFs. Uptake of actinonin by A. thaliana seedlings was used to investigate the function of PDFs in the plant. Because it induces an albino phenotype, we conclude that deformylation is likely to play an essential role in the chloroplast.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amidohydrolases*
  • Aminopeptidases / antagonists & inhibitors
  • Aminopeptidases / chemistry*
  • Aminopeptidases / classification*
  • Aminopeptidases / isolation & purification
  • Arabidopsis / drug effects
  • Arabidopsis / enzymology*
  • Arabidopsis / metabolism
  • Binding Sites
  • Catalytic Domain
  • Chloroplasts / drug effects
  • Chloroplasts / enzymology
  • Chloroplasts / metabolism
  • Coenzymes / metabolism
  • Enzyme Inhibitors / pharmacology
  • Enzyme Stability
  • Eukaryotic Cells / drug effects
  • Eukaryotic Cells / enzymology*
  • Eukaryotic Cells / metabolism
  • Half-Life
  • Hydroxamic Acids / pharmacology
  • Iron / metabolism
  • Lycopersicon esculentum / enzymology*
  • Oxygen / metabolism
  • Plant Proteins / antagonists & inhibitors
  • Plant Proteins / chemistry
  • Plant Proteins / classification
  • Plant Proteins / isolation & purification
  • Spectrophotometry, Atomic
  • Substrate Specificity
  • Zinc / metabolism

Substances

  • Coenzymes
  • Enzyme Inhibitors
  • Hydroxamic Acids
  • Plant Proteins
  • Iron
  • Aminopeptidases
  • Amidohydrolases
  • peptide deformylase
  • Zinc
  • actinonin
  • Oxygen