Basidiomycete DyPs: Genomic diversity, structural–functional aspects, reaction mechanism and environmental significance

The first enzyme with dye-decolorizing peroxidase (DyP) activity was described in 1999 from an arthroconidial culture of the fungus Bjerkandera adusta. However, the first DyP sequence had been deposited three years before, as a peroxidase gene from a culture of an unidentified fungus of the family P...

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Autores: Linde, Dolores, Ruiz-Dueñas, Francisco J., Fernandez-Fueyo, Elena, Guallar, Víctor|||0000-0002-4580-1114, Hammel, Kenneth E., Pogni, Rebecca, Martínez, Angel T.
Formato: artículo
Fecha de publicación:2015
País:España
Recursos:Universitat Politècnica de Catalunya (UPC)
Repositorio:UPCommons. Portal del coneixement obert de la UPC
Idioma:inglés
OAI Identifier:oai:upcommons.upc.edu:2117/84145
Acesso em linha:https://hdl.handle.net/2117/84145
https://dx.doi.org/10.1016/j.abb.2015.01.018
Access Level:acceso abierto
Palavra-chave:Genetic code
Dye-decolorizing peroxidases
CDE superfamily
Molecular structure
Reaction mechanism
Catalytic tryptophan
Long-range electron transfer
Substituted anthraquinone breakdown
Ligninolysis
Genètica bioquímica
Àrees temàtiques de la UPC::Enginyeria mecànica::Impacte ambiental
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spelling Basidiomycete DyPs: Genomic diversity, structural–functional aspects, reaction mechanism and environmental significanceLinde, DoloresRuiz-Dueñas, Francisco J.Fernandez-Fueyo, ElenaGuallar, Víctor|||0000-0002-4580-1114Hammel, Kenneth E.Pogni, RebeccaMartínez, Angel T.Genetic codeDye-decolorizing peroxidasesCDE superfamilyMolecular structureReaction mechanismCatalytic tryptophanLong-range electron transferSubstituted anthraquinone breakdownLigninolysisGenètica bioquímicaÀrees temàtiques de la UPC::Enginyeria mecànica::Impacte ambientalThe first enzyme with dye-decolorizing peroxidase (DyP) activity was described in 1999 from an arthroconidial culture of the fungus Bjerkandera adusta. However, the first DyP sequence had been deposited three years before, as a peroxidase gene from a culture of an unidentified fungus of the family Polyporaceae (probably Irpex lacteus). Since the first description, fewer than ten basidiomycete DyPs have been purified and characterized, but a large number of sequences are available from genomes. DyPs share a general fold and heme location with chlorite dismutases and other DyP-type related proteins (such as Escherichia coli EfeB), forming the CDE superfamily. Taking into account the lack of an evolutionary relationship with the catalase-peroxidase superfamily, the observed heme pocket similarities must be considered as a convergent type of evolution to provide similar reactivity to the enzyme cofactor. Studies on the Auricularia auricula-judae DyP showed that high-turnover oxidation of anthraquinone type and other DyP substrates occurs via long-range electron transfer from an exposed tryptophan (Trp377, conserved in most basidiomycete DyPs), whose catalytic radical was identified in the H2O2-activated enzyme. The existence of accessory oxidation sites in DyP is suggested by the residual activity observed after site-directed mutagenesis of the above tryptophan. DyP degradation of substituted anthraquinone dyes (such as Reactive Blue 5) most probably proceeds via typical one-electron peroxidase oxidations and product breakdown without a DyP-catalyzed hydrolase reaction. Although various DyPs are able to break down phenolic lignin model dimers, and basidiomycete DyPs also present marginal activity on nonphenolic dimers, a significant contribution to lignin degradation is unlikely because of the low activity on high redox-potential substratesThis work was supported by the INDOX (KBBE-2013-7-613549; www.indoxproject.eu) European project, the BIO2011-26694 (HIPOP) and CTQ2013-48287 projects of the Spanish Ministry of Economy and Competitiveness (MINECO), and the PRIN 2009-STNWX3 project of the Italian Ministry of Education, University and Research (MIUR). FJR-D thanks a Ramón y Cajal contract of MINECO. The authors thank Verónica Sáez-Jiménez for data on Reactive Blue 5 decolorization by VP and its heme-channel variants.Peer ReviewedElsevier20152015-05-1520162016-03-10journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/2117/84145https://dx.doi.org/10.1016/j.abb.2015.01.018reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)InglésengMinisterio de Economía y Competitividad http://doi.org/10.13039/501100003329 CTQ2013-48287-R DISENYO COMPUTACIONAL RACIONAL DE OXIDOREDUCTASAS PARA APLICACIONES INDUSTRIALES Y TECNOLOGICASEuropean Commission http://dx.doi.org/10.13039/100011102 Seventh Framework Programme 613549 Optimized oxidoreductases for medium and large scale industrial biotransformationsopen accesshttp://purl.org/coar/access_right/c_abf2Attribution-NonCommercial-NoDerivs 4.0 International Licensehttps://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/841452026-05-27T15:37:01Z
dc.title.none.fl_str_mv Basidiomycete DyPs: Genomic diversity, structural–functional aspects, reaction mechanism and environmental significance
title Basidiomycete DyPs: Genomic diversity, structural–functional aspects, reaction mechanism and environmental significance
spellingShingle Basidiomycete DyPs: Genomic diversity, structural–functional aspects, reaction mechanism and environmental significance
Linde, Dolores
Genetic code
Dye-decolorizing peroxidases
CDE superfamily
Molecular structure
Reaction mechanism
Catalytic tryptophan
Long-range electron transfer
Substituted anthraquinone breakdown
Ligninolysis
Genètica bioquímica
Àrees temàtiques de la UPC::Enginyeria mecànica::Impacte ambiental
title_short Basidiomycete DyPs: Genomic diversity, structural–functional aspects, reaction mechanism and environmental significance
title_full Basidiomycete DyPs: Genomic diversity, structural–functional aspects, reaction mechanism and environmental significance
title_fullStr Basidiomycete DyPs: Genomic diversity, structural–functional aspects, reaction mechanism and environmental significance
title_full_unstemmed Basidiomycete DyPs: Genomic diversity, structural–functional aspects, reaction mechanism and environmental significance
title_sort Basidiomycete DyPs: Genomic diversity, structural–functional aspects, reaction mechanism and environmental significance
dc.creator.none.fl_str_mv Linde, Dolores
Ruiz-Dueñas, Francisco J.
Fernandez-Fueyo, Elena
Guallar, Víctor|||0000-0002-4580-1114
Hammel, Kenneth E.
Pogni, Rebecca
Martínez, Angel T.
author Linde, Dolores
author_facet Linde, Dolores
Ruiz-Dueñas, Francisco J.
Fernandez-Fueyo, Elena
Guallar, Víctor|||0000-0002-4580-1114
Hammel, Kenneth E.
Pogni, Rebecca
Martínez, Angel T.
author_role author
author2 Ruiz-Dueñas, Francisco J.
Fernandez-Fueyo, Elena
Guallar, Víctor|||0000-0002-4580-1114
Hammel, Kenneth E.
Pogni, Rebecca
Martínez, Angel T.
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv Genetic code
Dye-decolorizing peroxidases
CDE superfamily
Molecular structure
Reaction mechanism
Catalytic tryptophan
Long-range electron transfer
Substituted anthraquinone breakdown
Ligninolysis
Genètica bioquímica
Àrees temàtiques de la UPC::Enginyeria mecànica::Impacte ambiental
topic Genetic code
Dye-decolorizing peroxidases
CDE superfamily
Molecular structure
Reaction mechanism
Catalytic tryptophan
Long-range electron transfer
Substituted anthraquinone breakdown
Ligninolysis
Genètica bioquímica
Àrees temàtiques de la UPC::Enginyeria mecànica::Impacte ambiental
description The first enzyme with dye-decolorizing peroxidase (DyP) activity was described in 1999 from an arthroconidial culture of the fungus Bjerkandera adusta. However, the first DyP sequence had been deposited three years before, as a peroxidase gene from a culture of an unidentified fungus of the family Polyporaceae (probably Irpex lacteus). Since the first description, fewer than ten basidiomycete DyPs have been purified and characterized, but a large number of sequences are available from genomes. DyPs share a general fold and heme location with chlorite dismutases and other DyP-type related proteins (such as Escherichia coli EfeB), forming the CDE superfamily. Taking into account the lack of an evolutionary relationship with the catalase-peroxidase superfamily, the observed heme pocket similarities must be considered as a convergent type of evolution to provide similar reactivity to the enzyme cofactor. Studies on the Auricularia auricula-judae DyP showed that high-turnover oxidation of anthraquinone type and other DyP substrates occurs via long-range electron transfer from an exposed tryptophan (Trp377, conserved in most basidiomycete DyPs), whose catalytic radical was identified in the H2O2-activated enzyme. The existence of accessory oxidation sites in DyP is suggested by the residual activity observed after site-directed mutagenesis of the above tryptophan. DyP degradation of substituted anthraquinone dyes (such as Reactive Blue 5) most probably proceeds via typical one-electron peroxidase oxidations and product breakdown without a DyP-catalyzed hydrolase reaction. Although various DyPs are able to break down phenolic lignin model dimers, and basidiomycete DyPs also present marginal activity on nonphenolic dimers, a significant contribution to lignin degradation is unlikely because of the low activity on high redox-potential substrates
publishDate 2015
dc.date.none.fl_str_mv 2015
2015-05-15
2016
2016-03-10
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/2117/84145
https://dx.doi.org/10.1016/j.abb.2015.01.018
url https://hdl.handle.net/2117/84145
https://dx.doi.org/10.1016/j.abb.2015.01.018
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Ministerio de Economía y Competitividad http://doi.org/10.13039/501100003329 CTQ2013-48287-R DISENYO COMPUTACIONAL RACIONAL DE OXIDOREDUCTASAS PARA APLICACIONES INDUSTRIALES Y TECNOLOGICAS
European Commission http://dx.doi.org/10.13039/100011102 Seventh Framework Programme 613549 Optimized oxidoreductases for medium and large scale industrial biotransformations
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial-NoDerivs 4.0 International License
https://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial-NoDerivs 4.0 International License
https://creativecommons.org/licenses/by-nc-nd/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:UPCommons. Portal del coneixement obert de la UPC
instname:Universitat Politècnica de Catalunya (UPC)
instname_str Universitat Politècnica de Catalunya (UPC)
reponame_str UPCommons. Portal del coneixement obert de la UPC
collection UPCommons. Portal del coneixement obert de la UPC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.300724

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