DyP-type peroxidases comprise a novel heme peroxidase family

Sugano, Yasushi

doi:10.1007/s00018-008-8651-8

Cited by 226 publications

(280 citation statements)

References 106 publications

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“…DyP structures of procaryotic origin differ significantly from fungal enzymes because they lack the heme. In addition, their polypeptides are considerably (by one-third) smaller and form oligomers (dimers to hexamers) (37).…”

Section: Resultsmentioning

confidence: 99%

First Crystal Structure of a Fungal High-redox Potential Dye-decolorizing Peroxidase

Strittmatter

Liers

Ullrich

et al. 2013

Journal of Biological Chemistry

116

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Background: DyP-type peroxidases catalyze biotechnologically important reactions. Results: Based on the crystal structure of a fungal DyP, the conformational flexibility of Asp-168 is elucidated. Tyr-337 is identified as a surface-exposed substrate interaction site. Conclusion: Asp-168 and Tyr-337 are key residues directly involved in AauDyPI-catalysis. Significance: Peroxidases are biocatalysts, much sought after and ubiquitous enzymes in nature.

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Section: Resultsmentioning

confidence: 99%

First Crystal Structure of a Fungal High-redox Potential Dye-decolorizing Peroxidase

Strittmatter

Liers

Ullrich

et al. 2013

Journal of Biological Chemistry

116

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“…DyP peroxidase structural and sequence comparisons have revealed the conservation of the residues surrounding heme, including the histidine axial iron ligand (13). Structure modeling of YfeX identified H215 as the corresponding iron binding histidine residue (Fig.…”

Section: Yfex or Efeb Is Protoporphyrin IX (Ppix)mentioning

confidence: 99%

“…Out of the 100,000 clones screened, one recombinant plasmid, carrying the yfeX gene, was responsible for a bright red fluorescent colony phenotype. YfeX is a protein of unknown function belonging to the family of dye-decolorizing peroxidases (Dyp-peroxidase) identified in fungi (13). E. coli has another protein belonging to the Dyp family, EfeB (14).…”

mentioning

confidence: 99%

Bacteria capture iron from heme by keeping tetrapyrrol skeleton intact

Létoffé

Heuck

Delepelaire

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

134

126

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Because heme is a major iron-containing molecule in vertebrates, the ability to use heme-bound iron is a determining factor in successful infection by bacterial pathogens. Until today, all known enzymes performing iron extraction from heme did so through the rupture of the tetrapyrrol skeleton. Here, we identified 2 Escherichia coli paralogs, YfeX and EfeB, without any previously known physiological functions. YfeX and EfeB promote iron extraction from heme preserving the tetrapyrrol ring intact. This novel enzymatic reaction corresponds to the deferrochelation of the heme. YfeX and EfeB are the sole proteins able to provide iron from exogenous heme sources to E. coli. YfeX is located in the cytoplasm. EfeB is periplasmic and enables iron extraction from heme in the periplasm and iron uptake in the absence of any heme permease. YfeX and EfeB are widespread and highly conserved in bacteria. We propose that their physiological function is to retrieve iron from heme

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“…[1][2][3][4][5][6][7][8][9][10] They lack the distal histidine that is highly conserved in classical peroxidases and which acts as an acid/base catalyst in the reduction of hydrogen peroxide to water. DyPs are classified into four phylogenetically distinct classes (A-D); their physiological role is not fully established yet and it appears to be subfamilydependent.…”

mentioning

confidence: 99%

“…9 Thus, SERR in particular represents a promising approach for a more detailed mechanistic analysis of DyPs from different subfamilies, stabilizing either Cpd I or Cpd II. [1][2][3][4][5][6][7][8] We have recently observed Cpd I with t 1/2 4 60 h in distal PpDyP variants D132N and N136L, in which aspartate 132 was replaced by asparagine and asparagine 136 by leucine, respectively. 24 Future studies of these systems will contribute to a better understanding of both, molecular determinants of catalytic activity in DyP-type peroxidases, and of their mechanistic properties in the immobilised state, which is a prerequisite for application of these catalytically versatile and efficient enzymes in the construction of bioelectronic devices.…”

mentioning

confidence: 99%

Surface enhanced resonance Raman detection of a catalytic intermediate of DyP-type peroxidase

Todorović

Hildebrandt

Martins

2015

Phys. Chem. Chem. Phys.

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We report herein the vibrational spectroscopic characterisation of a catalytic intermediate formed by the reaction of H 2 O 2 with DyP-type peroxidase immobilised on a biocompatible coated metal support.The SERR spectroscopic approach is of general applicability to other peroxidases which form relatively stable catalytic intermediates.Dye-decolourising peroxidases (DyPs) are novel heme peroxidases, the primary sequence, structural and mechanistic properties of which are unrelated to those of other known peroxidases. [1][2][3][4][5][6][7][8][9][10] They lack the distal histidine that is highly conserved in classical peroxidases and which acts as an acid/base catalyst in the reduction of hydrogen peroxide to water. DyPs are classified into four phylogenetically distinct classes (A-D); their physiological role is not fully established yet and it appears to be subfamilydependent. 1-10 DyP from Pseudomonas putida MET94 (PpDyP) is an extremely versatile B-type DyP, capable of efficient oxidation of a wide range of anthraquinonic and azo dyes, phenolic substrates, the non-phenolic veratryl alcohol and even manganese and ferrous ions. 8 In the reaction with H 2 O 2 , PpDyP forms a stable Compound I (Cpd I) at a rate of 1.4 AE 0.3 Â 10 6 M À1 s À1 , comparable to those of classical peroxidases and other DyPs. 8 The intermediate is, like in other DyPs, surprisingly long-living, with a half-life of B60 min, as demonstrated by electronic absorption spectroscopy. 9 Upon immobilisation on biocompatible metal supports, PpDyP is capable of efficient electrocatalytic activity in the presence of hydrogen peroxide. The enzyme is therefore a promising candidate for the design of bio-electronic devices with unique DyP-type peroxidase substrate specificity. 9,10 Resonance Raman (RR) spectroscopy has been extensively used in the detection and characterisation of peroxidase and catalase-peroxidase catalytic intermediates, and RR spectroscopic fingerprints of Cpd I (two equivalent oxidised resting ferric state) and Cpd II (one equivalent oxidised resting ferric state) are well established. [11][12][13][14][15][16] However, a strong fluorescence impeded the RR studies of PpDyP intermediates. Here, we have probed catalytic intermediate species of immobilised PpDyP by surface enhanced RR (SERR) spectroscopy. The SERR spectra of heme proteins immobilised on nanostructured Ag surfaces exclusively display the cofactor signals of the adsorbed molecules. In addition, close proximity of the molecule to the metal surface can efficiently quench fluorescence. 17 Like in RR spectroscopy, SERR signals include, inter alia, the core-size marker bands (e.g. n 4 , n 3 , n 2 , n 10 ) which are specifically enhanced upon excitation in resonance with the Soret absorption band of the porphyrin. The frequencies of these modes are indicative of the redox and spin states and the coordination pattern of the heme iron.We have previously shown that the high frequency region of RR spectra of the resting PpDyP in solution displays broad marker bands, indicative of t...

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DyP-type peroxidases comprise a novel heme peroxidase family

Cited by 226 publications

References 106 publications

First Crystal Structure of a Fungal High-redox Potential Dye-decolorizing Peroxidase

First Crystal Structure of a Fungal High-redox Potential Dye-decolorizing Peroxidase

Bacteria capture iron from heme by keeping tetrapyrrol skeleton intact

Surface enhanced resonance Raman detection of a catalytic intermediate of DyP-type peroxidase

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