The multihued palette of dye-decolorizing peroxidases

Singh, Rahul; Eltis, Lindsay D.

doi:10.1016/j.abb.2015.01.014

Cited by 90 publications

(105 citation statements)

References 63 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The structure of a monomer unit is depicted in Figure 1A, for which the dimensions are roughly 49 Å × 46 Å × 39 Å. Tc DyP adopts a ferredoxin-like fold consisting of antiparallel β-sheets and peripheral α-helices, which is characteristic of the DyP-type family but distinct from the classical heme peroxidases primarily made of helical proteins. 1,14,30 Similar to other heme peroxidases, 31 Tc DyP has a histidine coordinating to the heme iron as the fifth ligand at a distance of 2.1 Å. However, unlike classical heme peroxidases such as horseradish peroxidase (HRP), 30–32 which use the distal histidine to catalyze oxidation, DyPs employ an aspartate in place of the distal histidine to perform the same function.…”

Section: Resultsmentioning

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

View full text Add to dashboard Cite

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.

show abstract

Section: Resultsmentioning

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

View full text Add to dashboard Cite

show abstract

“…(DyP, EC 1.11.1.19) The DyP enzyme is also a heme-based peroxidase that can cause lignin breakdown through a radical-mediated oxidation process. The DyPs are phylogenetically distinct [97] from other peroxidases as they possess an α + β ferredoxin-like fold [98]. However, their oxidation mechanism is similar to VP and MnP [99].…”

Section: Laccase (mentioning

confidence: 99%

Enzymatic Degradation of Lignin in Soil: A Review

et al. 2017

View full text Add to dashboard Cite

Lignin is a major component of soil organic matter and also a rich source of carbon dioxide in soils. However, because of its complex structure and recalcitrant nature, lignin degradation is a major challenge. Efforts have been made from time to time to understand the lignin polymeric structure better and develop simpler, economical, and bio-friendly methods of degradation. Certain enzymes from specialized bacteria and fungi have been identified by researchers that can metabolize lignin and enable utilization of lignin-derived carbon sources. In this review, we attempt to provide an overview of the complexity of lignin's polymeric structure, its distribution in forest soils, and its chemical nature. Herein, we focus on lignin biodegradation by various microorganism, fungi and bacteria present in plant biomass and soils that are capable of producing ligninolytic enzymes such as lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), and dye-decolorizing peroxidase (DyP). The relevant and recent reports have been included in this review.

show abstract

“…DyP-type peroxidases (DyPs) are haem b-containing enzymes that like classical peroxidases catalyse the reduction of hydrogen peroxide to water with concomitant oxidation of structurally diverse substrates. DyPs possess a number of unique properties: [1][2][3][4] (i) an amino acid sequence that shows no homology to classical haem peroxidases; (ii) a broad substrate specicity, which includes anthraquinone-based and azo dyes, complex phenolic and non-phenolic molecules like kra lignin, as well as carotenoids, phenols, aromatic sulphides and metal ions; (iii) an unusually low value of optimal pH for the catalytic activity (pH opt ); (iv) distinct catalytic residues and tertiary structure and (v) still largely unexplored physiological role. While plant and mammalian peroxidases are primarily a-helical proteins, DyPs encompass two domains that contain a-helices and anti-parallel b-sheets, which adopt a ferredoxin-like fold and form a crevice that sandwiches the haem cofactor.…”

Section: Introductionmentioning

confidence: 99%