Isolation and Crystallization of Functionally CompetentEscherichia coliPeptide Deformylase Forms Containing either Iron or Nickel in the Active Site

Groche, D.; Becker, Andreas; Schlichting, Ilme; Kabsch, Wolfgang; Schultz, Sabine; Wagner, A.

doi:10.1006/bbrc.1998.8616

Cited by 118 publications

(133 citation statements)

References 19 publications

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“…However, the metal coordination shell and the active site environment in the structure described here are strictly identical to those reported for iron PDFs. It therefore remains unclear why PDF1A from A. thaliana is active with zinc as the cofactor, whereas other PDFs are active with a bound ferrous ion and inactivated with zinc (9,10,55). Interestingly, LiPDF also contains a tightly bound zinc ion rather than the ferrous ion usually observed (52).…”

Section: Discussionmentioning

confidence: 99%

“…The fourth ligand of the tetrahedrally coordinated metal ion corresponds to a water molecule. Bacterial PDFs are mononuclear iron enzymes (9,10). It is noteworthy that this is in contrast to most metalloproteases with a conserved HEXXH motif (part of motif 3 in PDFs), which use zinc instead of iron as catalytic cation (for a review, see Ref.…”

mentioning

confidence: 99%

“…The ferrous cation of PDF is extremely sensitive to oxidation, making the enzyme unstable (9,12). This cation can be replaced by Ni 2ϩ (9,13) or Co 2ϩ (14) to give stable variants with little or no loss of catalytic activity. Zinc substitution results in inactive enzymes.…”

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confidence: 99%

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The Crystal Structure of Mitochondrial (Type 1A) Peptide Deformylase Provides Clear Guidelines for the Design of Inhibitors Specific for the Bacterial Forms

Fieulaine

Juillan-Binard

Serero

et al. 2005

Journal of Biological Chemistry

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Peptide deformylase (PDF) inhibitors have a strong potential to be used as a new class of antibiotics. However, recent studies have shown that the mitochondria of most eukaryotes, including humans, contain an essential PDF, PDF1A. The crystal structure of the Arabidopsis thaliana PDF1A (AtPDF1A), considered representative of PDF1As in general, has been determined. This structure displays several similarities to that of known bacterial PDFs. AtPDF1A behaves as a dimer, with the C-terminal residues responsible for linking the two subunits. This arrangement is similar to that of Leptospira interrogans PDF, the only other dimeric PDF identified to date. AtPDF1A is the first PDF for which zinc has been identified as the catalytic ion. However, the zinc binding pocket does not differ from the binding pockets of PDFs with iron rather than zinc. The crystal structure of AtPDF1A in complex with a substrate analog revealed that the substrate binding pocket of PDF1A displays strong modifications. The S1 binding pocket is significantly narrower, due to the creation of a floor from residues present in all PDF1As but not in bacterial PDFs. A true S3 pocket is created by the residues of a helical CD-loop, which is very long in PDF1As. Finally, these modified substrate binding pockets modify the position of the substrate in the active site. These differences provide guidelines for the design of bacterial PDF inhibitors that will not target mitochondrial PDFs.

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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The Crystal Structure of Mitochondrial (Type 1A) Peptide Deformylase Provides Clear Guidelines for the Design of Inhibitors Specific for the Bacterial Forms

Fieulaine

Juillan-Binard

Serero

et al. 2005

Journal of Biological Chemistry

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“…(Ni), NiCl 2 was added. The respective concentrations of each compound were described previously (11,21 of a number of N-terminal protein sequencing data (reviewed in Ref. 9).…”

Section: Discussionmentioning

confidence: 99%

“…1). In most PDFs, an Fe 2ϩ cation is bound by three residues of motifs 2 and 3 and plays a crucial role in hydrolytic activity (20,21). This ion is highly unstable, and several agents and procedures have been described that preserve deformylase activity (reviewed in Ref.…”

Section: The Nucleotide Sequence(s) Reported In This Paper Has Been Smentioning

confidence: 99%

An Unusual Peptide Deformylase Features in the Human Mitochondrial N-terminal Methionine Excision Pathway

Serero

Giglione

Sardini

et al. 2003

Journal of Biological Chemistry

126

137

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Dedicated machinery for N-terminal methionine excision (NME) was recently identified in plant organelles and shown to be essential in plastids. We report here the existence of mitochondrial NME in mammals, as shown by the identification of cDNAs encoding specific peptide deformylases (PDFs) and new methionine aminopeptidases (MAP1D). We cloned the two full-length human cDNAs and showed that the N-terminal domains of the encoded enzymes were specifically involved in targeting to mitochondria. In contrast to mitochondrial MAP1D, the human PDF sequence differed from that of known PDFs in several key features. We characterized the human PDF fully in vivo and in vitro. Comparison of the processed human enzyme with the plant mitochondrial PDF1A, to which it is phylogenetically related, showed that the human enzyme had an extra N-terminal domain involved in both mitochondrial targeting and enzyme stability. Mammalian PDFs also display non-random substitutions in the conserved motifs important for activity. Human PDF site-directed mutagenesis variants were studied and compared with the corresponding plant PDF1A variants. We found that amino acid substitutions in human PDF specifically altered its catalytic site, resulting in an enzyme intermediate between bacterial PDF1Bs and plant PDF1As. Because (i) human PDF was found to be active both in vitro and in vivo, (ii) the entire machinery is conserved and expressed in most animals, (iii) the mitochondrial genome expresses substrates for these enzymes, and (iv) mRNA synthesis is regulated, we conclude that animal mitochondria have a functional NME machinery that can be regulated.

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Peptide Deformylase

Becker¹,

Kabsch²

2004

Handbook of Metalloproteins

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Peptide deformylase (EC 3.5.1.31) is a mononuclear iron enzyme that cleaves the formyl group of the N ‐terminal formyl‐methionine residue of nascent polypeptide chains in eubacteria. It is strictly stereospecific for a L ‐amino acid as the first residue of formyl‐peptide substrates and strongly prefers substrates with at least two or more residues. The native enzyme from Escherichia coli is a monomeric protein of 168 amino acid residues that contains one tightly bound Fe 2+ ion. The metal ion is tetrahedrally coordinated by a water molecule and the side chains of residues Cys90, His132, and His136. Similar to thermolysin, the two histidines are part of the HEXXH motif and the glutamate residue is required for enzymatic activity. The native iron form of peptide deformylase is extremely sensitive to oxidative destruction. On substitution of the iron ion by Ni 2+ or Co 2+ the enzyme is insensitive to oxidation and maintains its activity, whereas the Zn 2+ form is nearly inactive.

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Isolation and Crystallization of Functionally CompetentEscherichia coliPeptide Deformylase Forms Containing either Iron or Nickel in the Active Site

Cited by 118 publications

References 19 publications

The Crystal Structure of Mitochondrial (Type 1A) Peptide Deformylase Provides Clear Guidelines for the Design of Inhibitors Specific for the Bacterial Forms

The Crystal Structure of Mitochondrial (Type 1A) Peptide Deformylase Provides Clear Guidelines for the Design of Inhibitors Specific for the Bacterial Forms

An Unusual Peptide Deformylase Features in the Human Mitochondrial N-terminal Methionine Excision Pathway

Peptide Deformylase

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