A structural and functional perspective of DyP-type peroxidase family

Yoshida, Toru; Sugano, Yasushi

doi:10.1016/j.abb.2015.01.022

Cited by 117 publications

(141 citation statements)

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“…Hence, BLAST (Basic Local Alignment Search Tool) searches [49] were performed using well characterized DyP-type peroxidases [50, 51] and laccases [52] against the genome of P. fluorescens , P. putida KT2440 and R. opacus to discover if there are any putative enzymes responsible for lignin breakdown (Additional file 1: Table S1 and S2). Two enzymes from the subfamily of DyPA and three from DyPB were selected from R. jostii RHA1 and P. fluorescens Pf-5 [16, 53, 54].…”

Section: Discussionmentioning

confidence: 99%

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RETRACTED ARTICLE: Bacterial conversion of depolymerized Kraft lignin

Ravi

Abdelaziz

Nöbel

et al. 2018

Biotechnol Biofuels

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BackgroundLignin is a potential feedstock for microbial conversion into various chemicals. However, the degradation rate of native or technical lignin is low, and depolymerization is needed to obtain reasonable conversion rates. In the current study, base-catalyzed depolymerization—using NaOH (5 wt%)—of softwood Kraft lignin was conducted in a continuous-flow reactor system at temperatures in the range 190–240 °C and residence times of 1 or 2 min. The ability of growth of nine bacterial strains belonging to the genera Pseudomonas and Rhodococcus was tested using the alkaline-treated lignin as a sole carbon source.ResultsPseudomonas fluorescens and Rhodococcus opacus showed the best growth of the tested species on plates with lignin. Further evaluation of P. fluorescens and R. opacus was made in liquid cultivations with depolymerized lignin (DL) at a concentration of 1 g/L. Size exclusion chromatography (SEC) showed that R. opacus consumed most of the available lower molecular weight compounds (approximately 0.1–0.4 kDa) in the DL, but the weight distribution of larger fractions was almost unaffected. Importantly, the consumed compounds included guaiacol—one of the main monomers in the DL. SEC analysis of P. fluorescens culture broth, in contrast, did not show a large conversion of low molecular weight compounds, and guaiacol remained unconsumed. However, a significant shift in molecular weight distribution towards lower average weights was seen.ConclusionsRhodococcus opacus and P. fluorescens were identified as two potential microbial candidates for the conversion/consumption of base-catalyzed depolymerized lignin, acting on low and high molecular weight lignin fragments, respectively. These findings will be of relevance for designing bioconversion of softwood Kraft lignin.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1240-7) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

“…As the enzymes from subfamily DyPC and DyPD were not found/annotated either in Pseudomonas or Rhodococcus group of organisms, those were selected from the well-studied Amycolatopsis sp. 75iv2 and Bjerkandera adusta , respectively [50, 55]. Additionally, two laccases were selected, one from P. fluorescens and another from R. opacus PD630.…”

Section: Discussionmentioning

confidence: 99%

RETRACTED ARTICLE: Bacterial conversion of depolymerized Kraft lignin

Ravi

Abdelaziz

Nöbel

et al. 2018

Biotechnol Biofuels

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“…The DyPs, discovered nearly a decade ago, form a distinct superfamily of peroxidases, due to their specific primary and tertiary structures and unique reaction characteristics [21]. Phylogenetic analyses have led to the classification of DyPs into four subfamilies (A-D), DyPs from bacteria belong to the A, B and C subfamilies (see Figure 2b), whereas fungal enzymes are found in the D subfamily [22].…”

Section: Enzymes For Lignin Breakdownmentioning

confidence: 99%

Enzymatic conversion of lignin into renewable chemicals

Bugg

Rahmanpour

2015

Current Opinion in Chemical Biology

227

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“…13 It has to be noted that sequence identity between classes is very low (< 15%), especially between fungal and bacterial DyPs. 14 Several fungal lignin-degrading enzymes such as lignin peroxidase (LiP) and versatile peroxidase (VP) have been found to oxidize substrates via surface-exposed tryptophanyl and tyrosyl radicals. 15–17 Similar mode of action was also suggested for the fungal Aau DyP from Auricularia auricula-judae .…”

Section: Introductionmentioning

confidence: 99%

Identification of Surface-Exposed Protein Radicals and A Substrate Oxidation Site in A-Class Dye-Decolorizing Peroxidase from Thermomonospora curvata

et al. 2016

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Dye-decolorizing peroxidases (DyPs) are a family of heme peroxidases, in which a catalytic distal aspartate is involved in H2O2 activation to catalyze oxidations in acidic conditions. They have received much attention due to their potential applications in lignin compound degradation and biofuel production from biomass. However, the mode of oxidation in bacterial DyPs remains unknown. We have recently reported that the bacterial TcDyP from Thermomonospora curvata is among the most active DyPs and shows activity toward phenolic lignin model compounds (J. Biol. Chem. 2015, 290, 23447). Based on the X-ray crystal structure solved at 1.75 Å, sigmoidal steady-state kinetics with Reactive Blue 19 (RB19), and formation of compound II-like product in the absence of reducing substrates observed with stopped-flow spectroscopy and electron paramagnetic resonance (EPR), we hypothesized that the TcDyP catalyzes oxidation of large-size substrates via multiple surface-exposed protein radicals. Among 7 tryptophans and 3 tyrosines in TcDyP consisting of 376 residues for the matured protein, W263, W376, and Y332 were identified as surface-exposed protein radicals. Only the W263 was also characterized as one of surface-exposed oxidation sites. SDS-PAGE and size-exclusion chromatography demonstrated that W376 represents an off-pathway destination for electron transfer, resulting in the crosslinking of proteins in the absence of substrates. Mutation of W376 improved compound I stability and overall catalytic efficiency toward RB19. While Y332 is highly conserved across all four classes of DyPs, its catalytic function in A-class TcDyP is minimal possibly due to its extremely small solvent accessible areas. Identification of surface-exposed protein radicals and substrate oxidation sites is important for understanding DyP mechanism and modulating its catalytic functions for improved activity on phenolic lignin.

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A structural and functional perspective of DyP-type peroxidase family

Cited by 117 publications

References 45 publications

RETRACTED ARTICLE: Bacterial conversion of depolymerized Kraft lignin

RETRACTED ARTICLE: Bacterial conversion of depolymerized Kraft lignin

Enzymatic conversion of lignin into renewable chemicals

Identification of Surface-Exposed Protein Radicals and A Substrate Oxidation Site in A-Class Dye-Decolorizing Peroxidase from Thermomonospora curvata

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