Engineering of a Manganese-Binding Site in Lignin Peroxidase Isozyme H8 from Phanerochaete chrysosporium

2001 ◽  
Vol 284 (3) ◽  
pp. 723-728 ◽  
Author(s):  
Tünde Mester ◽  
Ming Tien
Keyword(s):  
Binding Site ◽  
Phanerochaete Chrysosporium ◽  
Lignin Peroxidase ◽  
Peroxidase Isozyme ◽  
Manganese Binding Site

Molecular cloning and sequences of lignin peroxidase genes of Phanerochaete chrysosporium

1989 ◽  
Vol 9 (6) ◽  
pp. 2743-2747
Author(s):  
H Schalch ◽  
J Gaskell ◽  
T L Smith ◽  
D Cullen
Keyword(s):  
Molecular Cloning ◽  
Phanerochaete Chrysosporium ◽  
Lignin Peroxidase ◽  
Nucleotide Sequences ◽  
Peroxidase Isozyme ◽  
Genomic Clones

The genomic clones encoding lignin peroxidase isozyme H8 and two closely related genes were isolated from Phanerochaete chrysosporium BKM-1767, and their nucleotide sequences were determined. The positions and approximate lengths of introns were found to be highly conserved in all three clones. Analysis of homokaryotic derivatives indicated that the three clones are not alleles of the same gene(s).

scholarly journals Experimental and theoretical insights into the effects of pH on catalysis of bond-cleavage by the lignin peroxidase isozyme H8 from Phanerochaete chrysosporium

2021 ◽  
Author(s):  
Le Thanh Mai Pham ◽  
Kai Deng ◽  
Trent R Northen ◽  
Steven W Singer ◽  
Paul D Adams ◽  
...  
Keyword(s):  
Phanerochaete Chrysosporium ◽  
Lignin Peroxidase ◽  
Bond Cleavage ◽  
Product Distribution ◽  
Bond Breaking ◽  
Hydroxyl Groups ◽  
Elastic Band ◽  
Theoretical Understanding ◽  
Peroxidase Isozyme ◽  
Lignin Peroxidases

Abstract Background:Lignin peroxidases catalyze a variety of reactions, resulting in cleavage of both β-O-4’ ether bonds and C–C bonds in lignin, both of which are essential for depolymerizing lignin into fragments amendable to biological or chemical upgrading to valuable products. Studies of the specificity of lignin peroxidases to catalyze these various reactions and the role reaction conditions such as pH play have been limited by the lack of assays that allow quantification of specific bond-breaking events. The subsequent theoretical understanding of the underlying mechanisms by which pH modulates the activity of lignin peroxidases remains nascent. Here, we report on combined experimental and theoretical studies of the effect of pH on the enzyme-catalyzed cleavage of β-O-4’ ether bonds and of C–C bonds by a lignin peroxidase isozyme H8 from Phanerochaete chrysosporium and an acid stabilized variant of the same enzyme.Results: Using a nanostructure initiator mass spectrometry assay that provides quantification of bond breaking in a phenolic model lignin dimer we found that catalysis of degradation of the dimer to products by an acid-stabilized variant of lignin peroxidase isozyme H8 increased from 38.4 % at pH 5 to 92.5% at pH 2.6. At pH 2.6, the observed product distribution resulted from 65.5% b-O-4’ ether bond cleavage, 27.0% Ca-C1 carbon bond cleavage and 3.6% Ca-oxidation as by-product. Using ab initio molecular dynamic simulations and climbing-image Nudge Elastic Band based transition state searches, we suggest the effect of lower pH is via protonation of aliphatic hydroxyl groups under which extremely acidic conditions resulted in lower energetic barriers for bond-cleavages, particularly β-O-4’ bonds. Conclusion: These coupled experimental results and theoretical explanations suggest pH is a key driving force for selective and efficient lignin peroxidase isozyme H8 catalyzed depolymerization of the phenolic lignin dimer and further suggest that engineering of lignin peroxidase isozyme H8 and other enzymes involved lignin depolymerization should include targeting stability at low pH.

scholarly journals Experimental and theoretical insights into the effects of pH on catalysis of bond-cleavage by the lignin peroxidase isozyme H8 from Phanerochaete chrysosporium

2020 ◽  
Author(s):  
Le Thanh Mai Pham ◽  
Kai Deng ◽  
Trent R Northen ◽  
Steven W Singer ◽  
Paul D Adams ◽  
...  
Keyword(s):  
Phanerochaete Chrysosporium ◽  
Lignin Peroxidase ◽  
Bond Cleavage ◽  
Product Distribution ◽  
Hydroxyl Groups ◽  
Aryl Ether ◽  
Elastic Band ◽  
Theoretical Understanding ◽  
Peroxidase Isozyme ◽  
Lignin Peroxidases

Abstract Background: Lignin peroxidases catalyze a variety of reactions, including cleavage of both β-aryl ether bonds and C–C bonds in lignin, both of which are essential for depolymerizing lignin into fragments amendable to biological or chemical upgrading to valuable products. Studies of the specificity of lignin peroxidases to catalyze these various reactions and the role reaction conditions such as pH play have been limited by the lack of assays that allow quantification of specific bond-breaking events. The subsequent theoretical understanding of the underlying mechanisms by which pH modulates the activity of lignin peroxidases remains nascent. Here, we report on combined experimental and theoretical studies of the effect of pH on the enzyme-catalyzed cleavage of β-aryl ether bonds and of C–C bonds by a lignin peroxidase isozyme H8 from Phanerochaete chrysosporium and an acid stabilized variant of the same enzyme. Results: Using a nanostructure initiator mass spectrometry assay that provides quantification of bond cleavages in a phenolic model lignin dimer we found that degradation of the lignin dimer was greatly enhanced at lower pH, and the acid-stable lignin peroxidase isozyme H8 increased the degradation of the lignin dimer to products from 38.4 % at pH 5 to 92.5% at pH 2.6. At pH 2.6, the observed product distribution resulted from 65.5% b -aryl ether bond cleavage, 27.0% C a -aryl carbon bond cleavage and 3.6% C a -oxidation as by-product . Using ab initio molecular dynamic simulations and climbing-image Nudge Elastic Band based transition state searches, we suggest the effect of lower pH is via hydration of hydronium cation on aliphatic and phenolic hydroxyl groups under, which extremely acidic conditions resulted in lower energetic barriers for bond-cleavages, especially β-ether bonds. Conclusion: These coupled experimental results and theoretical explanations suggest pH is a key driving force for selective and efficient lignin peroxidase isozyme H8 catalyzed depolymerization of lignin and further suggest that lignin peroxidase isozyme H8 engineering efforts include targeting stability at low pH.

scholarly journals Experimental and theoretical insights into the effects of pH on catalysis of bond-cleavage by the lignin peroxidase isozyme H8 from Phanerochaete chrysosporium

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Le Thanh Mai Pham ◽  
Kai Deng ◽  
Trent R. Northen ◽  
Steven W. Singer ◽  
Paul D. Adams ◽  
...  
Keyword(s):  
Phanerochaete Chrysosporium ◽  
Lignin Peroxidase ◽  
Bond Cleavage ◽  
Product Distribution ◽  
Bond Breaking ◽  
Hydroxyl Groups ◽  
Elastic Band ◽  
Theoretical Understanding ◽  
Peroxidase Isozyme ◽  
Lignin Peroxidases

Abstract Background Lignin peroxidases catalyze a variety of reactions, resulting in cleavage of both β-O-4′ ether bonds and C–C bonds in lignin, both of which are essential for depolymerizing lignin into fragments amendable to biological or chemical upgrading to valuable products. Studies of the specificity of lignin peroxidases to catalyze these various reactions and the role reaction conditions such as pH play have been limited by the lack of assays that allow quantification of specific bond-breaking events. The subsequent theoretical understanding of the underlying mechanisms by which pH modulates the activity of lignin peroxidases remains nascent. Here, we report on combined experimental and theoretical studies of the effect of pH on the enzyme-catalyzed cleavage of β-O-4′ ether bonds and of C–C bonds by a lignin peroxidase isozyme H8 from Phanerochaete chrysosporium and an acid stabilized variant of the same enzyme. Results Using a nanostructure initiator mass spectrometry assay that provides quantification of bond breaking in a phenolic model lignin dimer we found that catalysis of degradation of the dimer to products by an acid-stabilized variant of lignin peroxidase isozyme H8 increased from 38.4% at pH 5 to 92.5% at pH 2.6. At pH 2.6, the observed product distribution resulted from 65.5% β-O-4′ ether bond cleavage, 27.0% Cα-C1 carbon bond cleavage, and 3.6% Cα-oxidation as by-product. Using ab initio molecular dynamic simulations and climbing-image Nudge Elastic Band based transition state searches, we suggest the effect of lower pH is via protonation of aliphatic hydroxyl groups under which extremely acidic conditions resulted in lower energetic barriers for bond-cleavages, particularly β-O-4′ bonds. Conclusion These coupled experimental results and theoretical explanations suggest pH is a key driving force for selective and efficient lignin peroxidase isozyme H8 catalyzed depolymerization of the phenolic lignin dimer and further suggest that engineering of lignin peroxidase isozyme H8 and other enzymes involved in lignin depolymerization should include targeting stability at low pH.

scholarly journals Molecular cloning and sequences of lignin peroxidase genes of Phanerochaete chrysosporium.

1989 ◽  
Vol 9 (6) ◽  
pp. 2743-2747 ◽  
Author(s):  
H Schalch ◽  
J Gaskell ◽  
T L Smith ◽  
D Cullen
Keyword(s):  
Molecular Cloning ◽  
Phanerochaete Chrysosporium ◽  
Lignin Peroxidase ◽  
Nucleotide Sequences ◽  
Peroxidase Isozyme ◽  
Genomic Clones

The genomic clones encoding lignin peroxidase isozyme H8 and two closely related genes were isolated from Phanerochaete chrysosporium BKM-1767, and their nucleotide sequences were determined. The positions and approximate lengths of introns were found to be highly conserved in all three clones. Analysis of homokaryotic derivatives indicated that the three clones are not alleles of the same gene(s).

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