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==Crystal structure of the lignin peroxidase (ApeLiP) from Agrocybe pediades== | ==Crystal structure of the lignin peroxidase (ApeLiP) from Agrocybe pediades== | ||
<StructureSection load='7oo5' size='340' side='right'caption='[[7oo5]]' scene=''> | <StructureSection load='7oo5' size='340' side='right'caption='[[7oo5]], [[Resolution|resolution]] 1.85Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OO5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OO5 FirstGlance]. <br> | <table><tr><td colspan='2'>[[7oo5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrocybe_pediades Agrocybe pediades]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OO5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OO5 FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7oo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7oo5 OCA], [https://pdbe.org/7oo5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7oo5 RCSB], [https://www.ebi.ac.uk/pdbsum/7oo5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7oo5 ProSAT]</span></td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7oo5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7oo5 OCA], [https://pdbe.org/7oo5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7oo5 RCSB], [https://www.ebi.ac.uk/pdbsum/7oo5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7oo5 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Lignin biodegradation has been extensively studied in white-rot fungi, which largely belong to order Polyporales. Among the enzymes that wood-rotting polypores secrete, lignin peroxidases (LiPs) have been labeled as the most efficient. Here, we characterize a similar enzyme (ApeLiP) from a fungus of the order Agaricales (with ~13,000 described species), the soil-inhabiting mushroom Agrocybe pediades. X-ray crystallography revealed that ApeLiP is structurally related to Polyporales LiPs, with a conserved heme-pocket and a solvent-exposed tryptophan. Its biochemical characterization shows that ApeLiP can oxidize both phenolic and non-phenolic lignin model-compounds, as well as different dyes. Moreover, using stopped-flow rapid spectrophotometry and 2D-NMR, we demonstrate that ApeLiP can also act on real lignin. Characterization of a variant lacking the above tryptophan residue shows that this is the oxidation site for lignin and other high redox-potential substrates, and also plays a role in phenolic substrate oxidation. The reduction potentials of the catalytic-cycle intermediates were estimated by stopped-flow in equilibrium reactions, showing similar activation by H2O2, but a lower potential for the rate-limiting step (compound-II reduction) compared to other LiPs. Unexpectedly, ApeLiP was stable from acidic to basic pH, a relevant feature for application considering its different optima for oxidation of phenolic and nonphenolic compounds. | |||
Agaricales Mushroom Lignin Peroxidase: From Structure-Function to Degradative Capabilities.,Sanchez-Ruiz MI, Ayuso-Fernandez I, Rencoret J, Gonzalez-Ramirez AM, Linde D, Davo-Siguero I, Romero A, Gutierrez A, Martinez AT, Ruiz-Duenas FJ Antioxidants (Basel). 2021 Sep 12;10(9). pii: antiox10091446. doi:, 10.3390/antiox10091446. PMID:34573078<ref>PMID:34573078</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7oo5" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Lignin peroxidase|Lignin peroxidase]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Agrocybe pediades]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Romero A]] | [[Category: Romero A]] | ||
[[Category: Ruiz-Duenas FJ]] | [[Category: Ruiz-Duenas FJ]] | ||
Revision as of 15:53, 1 February 2024
Crystal structure of the lignin peroxidase (ApeLiP) from Agrocybe pediadesCrystal structure of the lignin peroxidase (ApeLiP) from Agrocybe pediades
Structural highlights
Publication Abstract from PubMedLignin biodegradation has been extensively studied in white-rot fungi, which largely belong to order Polyporales. Among the enzymes that wood-rotting polypores secrete, lignin peroxidases (LiPs) have been labeled as the most efficient. Here, we characterize a similar enzyme (ApeLiP) from a fungus of the order Agaricales (with ~13,000 described species), the soil-inhabiting mushroom Agrocybe pediades. X-ray crystallography revealed that ApeLiP is structurally related to Polyporales LiPs, with a conserved heme-pocket and a solvent-exposed tryptophan. Its biochemical characterization shows that ApeLiP can oxidize both phenolic and non-phenolic lignin model-compounds, as well as different dyes. Moreover, using stopped-flow rapid spectrophotometry and 2D-NMR, we demonstrate that ApeLiP can also act on real lignin. Characterization of a variant lacking the above tryptophan residue shows that this is the oxidation site for lignin and other high redox-potential substrates, and also plays a role in phenolic substrate oxidation. The reduction potentials of the catalytic-cycle intermediates were estimated by stopped-flow in equilibrium reactions, showing similar activation by H2O2, but a lower potential for the rate-limiting step (compound-II reduction) compared to other LiPs. Unexpectedly, ApeLiP was stable from acidic to basic pH, a relevant feature for application considering its different optima for oxidation of phenolic and nonphenolic compounds. Agaricales Mushroom Lignin Peroxidase: From Structure-Function to Degradative Capabilities.,Sanchez-Ruiz MI, Ayuso-Fernandez I, Rencoret J, Gonzalez-Ramirez AM, Linde D, Davo-Siguero I, Romero A, Gutierrez A, Martinez AT, Ruiz-Duenas FJ Antioxidants (Basel). 2021 Sep 12;10(9). pii: antiox10091446. doi:, 10.3390/antiox10091446. PMID:34573078[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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