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Mechanistic Insights into Dye-Decolorizing Peroxidase Revealed by Solvent Isotope and Viscosity Effects

Journal Article · · ACS Catalysis
 [1];  [1];  [1];  [2];  [1]
  1. Kansas State Univ., Manhattan, KS (United States). Dept. of Chemistry
  2. Kansas State Univ., Manhattan, KS (United States). Dept. of Biochemistry and Molecular Biophysics
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Dye-decolorizing peroxidases (DyPs) are a family of H2O2-dependent heme peroxidases that have shown potential applications in lignin degradation and valorization. However, the DyP kinetic mechanism remains underexplored. Using structural biology and solvent isotope (sKIE) and viscosity effects, many mechanistic characteristics have been determined for the B-class ElDyP from Enterobacter lignolyticus. Its structure revealed that a water molecule acts as the sixth axial ligand and two channels at diameters of ~3.0 and 8.0 Å lead to the heme center. A conformational change of ERS* to ERS, which have identical spectral characteristics, was proposed as the final step in DyPs’ bisubstrate Ping-Pong mechanism. This step is also the rate-determining step in ABTS oxidation. The normal KIE of wild-type ElDyP with D2O2 at pD 3.5 suggested that compound 0 deprotonation by the distal aspartate is rate-limiting in the formation of compound I, which is more reactive under acidic pH than under neutral or alkaline pH. The viscosity effects and other biochemical methods implied that the reducing substrate binds with compound I instead of the free enzyme. The significant inverse sKIEs of kcat/KM and kERS* suggested that the aquo release in ElDyP is mechanistically important and may explain the enzyme’s adoption of two-electron reduction for compound I. The distal aspartate is catalytically more important than the distal arginine and plays key roles in determining ElDyP’s optimum acidic pH. The kinetic mechanism of D143H-ElDyP was also briefly studied. The results obtained will pave the way for future protein engineering to improve DyPs’ lignolytic activity.
Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (US)
Sponsoring Organization:
USDOE
OSTI ID:
1408114
Journal Information:
ACS Catalysis, Journal Name: ACS Catalysis Journal Issue: 9 Vol. 7; ISSN 2155-5435
Publisher:
American Chemical Society (ACS)Copyright Statement
Country of Publication:
United States
Language:
ENGLISH

References (62)

Dye-Decolorizing Peroxidase (DyP) book January 2014
Determination of Rate Constants for Rapid Peroxidase Reactions journal November 1995
Crystal structures of pristine and oxidatively processed lignin peroxidase expressed in Escherichia coli and of the W171F variant that eliminates the redox active tryptophan 171. Implications for the reaction mechanism journal January 2001
DyP-type peroxidases comprise a novel heme peroxidase family journal December 2008
A robust and extracellular heme-containing peroxidase from Thermobifida fusca as prototype of a bacterial peroxidase superfamily journal December 2009
DyP-type peroxidases: a promising and versatile class of enzymes journal November 2013
Structure and Action Mechanism of Ligninolytic Enzymes journal June 2008
Measurement of protein using bicinchoninic acid journal October 1985
Simultaneous determination of hemes a, b, and c from pyridine hemochrome spectra journal February 1987
The toolbox of Auricularia auricula-judae dye-decolorizing peroxidase – Identification of three new potential substrate-interaction sites journal May 2015
The multihued palette of dye-decolorizing peroxidases journal May 2015
A structural and functional perspective of DyP-type peroxidase family journal May 2015
Crystal structure and biochemical features of dye-decolorizing peroxidase YfeX from Escherichia coli O157 Asp 143 and Arg 232 play divergent roles toward different substrates journal February 2017
Exploring bacterial lignin degradation journal April 2014
The emerging role for bacteria in lignin degradation and bio-product formation journal June 2011
Crystal structures of dye-decolorizing peroxidase with ascorbic acid and 2,6-dimethoxyphenol journal November 2012
Bacterial enzymes involved in lignin degradation journal October 2016
A formula for correlating p K a values determined in D 2 O and H 2 O journal January 2004
Ultrahigh (0.93Å) resolution structure of manganese peroxidase from Phanerochaete chrysosporium: Implications for the catalytic mechanism journal June 2010
A Dye-Decolorizing Peroxidase from Vibrio cholerae journal October 2015
Enantioselective Synthesis of Dilignol Model Compounds and Their Stereodiscrimination Study with a Dye-Decolorizing Peroxidase journal March 2017
Identification of Surface-Exposed Protein Radicals and A Substrate Oxidation Site in A-Class Dye-Decolorizing Peroxidase from Thermomonospora curvata journal October 2016
Isotope effect studies of chicken liver NADP malic enzyme: role of the metal ion and viscosity dependence journal April 1988
Identification of DypB from Rhodococcus jostii RHA1 as a Lignin Peroxidase journal June 2011
Characterization of Dye-Decolorizing Peroxidases from Rhodococcus jostii RHA1 journal June 2011
Inverse Solvent Isotope Effects Demonstrate Slow Aquo Release from Hypoxia Inducible Factor-Prolyl Hydroxylase (PHD2) journal August 2012
Inverse Solvent Isotope Effects Arising from Substrate Triggering in the Factor Inhibiting Hypoxia Inducible Factor journal February 2013
A Flexible Glutamine Regulates the Catalytic Activity of Toluene o -Xylene Monooxygenase journal May 2014
Mechanism of the Reaction Catalyzed by Acetoacetate Decarboxylase. Importance of Lysine 116 in Determining the p K a of Active-Site Lysine 115 † journal January 1996
Identification and Characterization of a Multifunctional Dye Peroxidase from a Lignin-Reactive Bacterium journal September 2012
Oxidative Mechanisms Involved in Lignin Degradation by White-Rot Fungi journal November 2001
Heme Enzyme Structure and Function journal January 2014
The Catalytic Valorization of Lignin for the Production of Renewable Chemicals journal June 2010
Heme Oxygenase His25Ala Mutant: Replacement of the Proximal Histidine Iron Ligand by Exogenous Bases Restores Catalytic Activity journal March 1995
Inverse Solvent Isotope Effects in the NAD-Malic Enzyme Reaction Are the Result of the Viscosity Difference between D2O and H2O: Implications for Solvent Isotope Effect Studies journal June 1995
The Poulos−Kraut Mechanism of Compound I Formation in Horseradish Peroxidase:  A QM/MM Study journal June 2006
Lignocellulose: A chewy problem journal June 2011
Formic-acid-induced depolymerization of oxidized lignin to aromatics journal November 2014
A dye-decolorizing peroxidase from Bacillus subtilis exhibiting substrate-dependent optimum temperature for dyes and β-ether lignin dimer journal February 2015
Pathways for degradation of lignin in bacteria and fungi journal January 2011
Unveiling the basis of alkaline stability of an evolved versatile peroxidase journal June 2016
Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study journal February 2015
The steady-state kinetics of peroxidase with 2,2′-azino-di-(3-ethyl-benzthiazoline-6-sulphonic acid) as chromogen journal January 1975
Kinetic evidence for the formation of a Michaelis–Menten-like complex between horseradish peroxidase compound II and di-(N-acetyl-l-tyrosine) journal May 1999
Deuterium isotope effect on the intramolecular electron transfer in Pseudomonas aeruginosa azurin journal April 2001
Bacteria capture iron from heme by keeping tetrapyrrol skeleton intact journal June 2009
Lignin valorization through integrated biological funneling and chemical catalysis journal August 2014
Crystal structure of the pristine peroxidase ferryl center and its relevance to proton-coupled electron transfer journal January 2016
Roles of Water in Heme Peroxidase and Catalase Mechanisms journal January 2001
Characterization of Dye-decolorizing Peroxidase (DyP) from Thermomonospora curvata Reveals Unique Catalytic Properties of A-type DyPs journal July 2015
Dissection of the Stepwise Mechanism to β-Lactam Formation and Elucidation of a Rate-determining Conformational Change in β-Lactam Synthetase journal January 2009
Protein Ionizable Groups: p K Values and Their Contribution to Protein Stability and Solubility journal January 2009
PHENIX: a comprehensive Python-based system for macromolecular structure solution journal January 2010
Features and development of Coot journal March 2010
Lignin-degrading enzymes journal February 2015
Lignin Valorization: Improving Lignin Processing in the Biorefinery journal May 2014
Characterization of Axial and Proximal Histidine Mutations of the Decaheme Cytochrome MtrA from Shewanella sp. Strain ANA-3 and Implications for the Electron Transport System journal November 2012
The Escherichia coli Protein YfeX Functions as a Porphyrinogen Oxidase, Not a Heme Dechelatase journal November 2011
Horseradish peroxidase. XXIX. Reactions in water and deuterium oxide: cyanide binding, compound I formation, and reactions of compounds I and II with ferrocyanide journal November 1978
Lignin Biosynthesis journal June 2003
Characterization of Fermentation Residues from the Production of Bio-Ethanol from Lignocellulosic Feedstocks journal December 2011
Complete genome sequence of “Enterobacter lignolyticus” SCF1 journal September 2011

Cited By (2)

A subtle structural change in the distal haem pocket has a remarkable effect on tuning hydrogen peroxide reactivity in dye decolourising peroxidases from Streptomyces lividans journal January 2020
Roles of distal aspartate and arginine of B-class dye-decolorizing peroxidase in heterolytic hydrogen peroxide cleavage journal August 2018

Figures / Tables (10)

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Table 1(p. 6)table Table 1
Table 2(p. 7)table Table 2
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Table 3(p. 9)table Table 3
Figure 5(p. 10)figure Figure 5
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Figure 7(p. 11)figure Figure 7

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