Iron center, substrate recognition and mechanism of peptide deformylase

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

doi:10.1038/4162

Cited by 144 publications

(225 citation statements)

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“…S3), as previously demonstrated in solution (32 and His 136 in EcPDF), with a water molecule as the fourth ligand (corresponding to the water molecule W1 described in Ref. 18). This coordination shell is identical to those of other known PDFs and therefore does not account for differences in enzymatic activity with respect to iron PDFs.…”

Section: Resultsmentioning

confidence: 94%

“…However, these differences do not affect folding of the active site. We and others have reported the three-dimensional structures of PDFs from various bacteria, in complex with the catalytic metal cation and/or with a ligand, such as an inhibitor or a product of the deformylation reaction (17)(18)(19). No significant differences in overall or active site structure were observed between the two forms.…”

mentioning

confidence: 99%

“…No significant differences in overall or active site structure were observed between the two forms. The determination of these structures led to identification of the metal and peptide binding modes and elucidation of a catalytic mechanism for the deformylation reaction (13,18,19). For 3 decades, it has been widely accepted that eukaryotes have no peptide deformylase (20,21).…”

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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: Resultsmentioning

confidence: 94%

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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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“…It has been previously suggested that the Zn II ion in PDF exhibits a preference for a 4-coordinate environment, destabilizing the 5-coordinate intermediate in Scheme 2b and causing the lower reactivity of bacterial Zn II -PDF. 3,9 We propose that it is an inherent geometric preference of Fe II for a higher coordination number, which accounts for the much higher reactivity of Fe II -PDF as compared to Zn II -PDF. This proposal assumes that the release of the formate ligand does not enter into the rate-determining-step, or that the bonding mode does not affect the rate of release, as previously suggested.…”

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confidence: 97%

Geometric Preferences in Iron(II) and Zinc(II) Model Complexes of Peptide Deformylase

et al. 2006

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A combination of experimental and theoretical studies on (N,S(thiolate))M II -formate complexes (M = Fe, Zn) suggests a rationale for the metal ion dependence of peptide deformylase.Based on active site structure (tetrahedral (His 2 Cys)M II (OH n )), conserved sequence motifs, and function (hydrolysis), peptide deformylase (PDF) belongs to the mononuclear zinc(II) enzyme family. 1 However, recent evidence shows bacterial PDF to be the first example of an iron(II) metallopeptidase, which hydrolyzes the formyl bond of the N-terminus of newly synthesized polypeptides. [2][3][4] Intriguingly, the Zn II form of bacterial PDF is dramatically less active than the Fe II form, although their native structures are identical. [4][5][6] The mechanism of this enzyme and an explanation of the metal-ion dependence are under investigation. PDF is also a target for new antibiotic agents, and therefore knowledge regarding its mechanism is of practical significance. 7 We are involved in the synthesis of Zn II and Fe II model complexes of PDF to gain a better understanding of the mechanism and unusual metal dependence of this enzyme.Previously we reported the synthesis of (PATH)Zn II (O 2 CH), a model complex of the putative (formate)Zn II -PDF intermediate. 8 Analysis of the bonding mode in this complex showed that the formate was coordinated in an anisobidentate fashion. It was suggested that this bonding mode, as opposed to a purely monodentate interaction, might slow down the displacement of formate by water in the final step of the catalytic cycle, and account for the low reactivity of Zn-PDF. Following this argument, it was expected that the analogous (formate)Fe II -PDF would exhibit a monodentate bonding mode.Recently, high-resolution X-ray structures of (formate)M II -PDF (M = Zn, Fe) from Chan and coworkers have revealed bonding motifs in contrast to our prediction; monodentate coordination was observed in the case of Zn II and bidentate coordination was seen for Fe II The synthesis of 1 is shown in Scheme 1. Addition of (Py 2 S − )Na + to ferrous formate in MeOH gives a cloudy, yellow solution which turns clear over 18 h. Removal of the solvent under vacuum gives an orange solid which can be partly redissolved in toluene. Crystals of 1 were grown from Et 2 O/toluene, and an ORTEP diagram of 1 is shown in Figure 1. The iron center is in a five-coordinate geometry with the formate ligand occupying the axial position opposite the N(amine) donor. The N(pyridyl)-Fe II and S-Fe II distances (Table 1) are in the normal range. The N(amine)-Fe II distance of 2.366(4) Å is long, but is quite close to the related complexes (Py 2 S)Fe II X (X = Br, N(amine)-Fe II = 2.387(1) Å; X = Cl (2.352(2) Å). 10 There is no obvious reason for the elongation of this bond in these complexes, and theoretical calculations show that another isomer of 1 with a more conventional Fe II -N(amine) distance should be accessible (vide infra). Interestingly, the formate ligand is clearly monodentate with Fe-O(2) = 4.12 Å, and is in fact bound in ...

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“…A similar observation was made in a study of the substrate-free peptide deformylase. It contained a PEG molecule in the substrate-binding pocket mimicking a natural substrate (28), which was confirmed later by solving the peptide deformylase structure in complex with its product, a Met-Ala-Ser tripeptide (29). However, trials to overlay the PEG molecule with the vancomycin aglycone were not successful.…”

Section: Resultsmentioning

confidence: 92%

Crystal Structure of OxyC, a Cytochrome P450 Implicated in an Oxidative C–C Coupling Reaction during Vancomycin Biosynthesis

Pylypenko

Vitali

Zerbe

et al. 2003

Journal of Biological Chemistry

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Gene inactivation studies point to the involvement of OxyC in catalyzing the last oxidative phenol coupling reaction during glycopeptide antibiotic biosynthesis. Presently, the substrate and exact timing of the OxyC reaction are unknown. The substrate might be the bicyclic heptapeptide or a thioester derivative bound to a protein carrier domain. OxyC from the vancomycin producer Amycolatopsis orientalis was produced in Escherichia coli and crystallized, and its structure was determined to 1.9 Å resolution. OxyC gave UV-visible spectra characteristic of a P450-like hemoprotein in the low spin ferric state. After reduction to the ferrous state by dithionite the CO-ligated form gave a 450-nm peak in a UV-difference spectrum. The addition of vancomycin aglycone to OxyC produced type I changes to the UV spectrum. OxyC exhibits the typical P450-fold, with the Cys ligand loop containing the signature sequence FGHGX-HXCLG and Cys-356 being the proximal axial thiolate ligand of the heme iron. The observation of a water molecule bound to the heme iron is consistent with the UV-visible spectra of OxyC indicating a low spin heme. A polyethylene glycol molecule occupying the active site might mimic the bicyclic heptapeptide substrate. Analysis of the structure of Oxy-proteins and other P450s indicates regions that might be involved in binding of the redox partner and possibly the protein carrier domain.Vancomycin and related glycopeptides are clinically important antibiotics that act as inhibitors of bacterial peptidoglycan biosynthesis (1, 2). These antibiotics typically possess a heptapeptide aglycone that is rigidified by side chain cross-linking involving several of its constituent aromatic amino acids (Fig. 1). As a result of this cross-linking, a molecular cavity is created within the glycopeptide core, the surface of which is complementary to that of the terminal D-Ala-D-Ala dipeptide unit present in intermediates of peptidoglycan biosynthesis (2). The glycopeptides are thus able to bind this dipeptide with high affinity. The aromatic cross-links arise formally through oxidative phenol coupling reactions. Although phenol coupling reactions are widespread in natural product biosynthesis as a whole, knowledge about the enzymes catalyzing such processes is sparse. It is clear, however, that members of the cytochrome P450 family have evolved that are able to promote specific phenol coupling reactions, both in glycopeptide antibiotic biosynthesis and in other areas of secondary metabolism, particularly alkaloid biosynthesis (3).Biosynthetic gene clusters for several glycopeptide antibiotics have been cloned and sequenced recently, including those for chloroeremomycin (4), balhimycin (5), and teicoplanin (6) production. The organization of the biosynthetic genes in each cluster is very similar. This includes in the chloroeremomycin cluster three large nonribosomal peptide synthetase (NRPS) 1 genes and three P450 genes (oxyA, oxyB, and oxyC), as well as other genes involved in the biosynthesis of the constituent amino acids...

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Iron center, substrate recognition and mechanism of peptide deformylase

Cited by 144 publications

References 25 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

Geometric Preferences in Iron(II) and Zinc(II) Model Complexes of Peptide Deformylase

Crystal Structure of OxyC, a Cytochrome P450 Implicated in an Oxidative C–C Coupling Reaction during Vancomycin Biosynthesis

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