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Mapping the Long-Range Electron Transfer Route in Ligninolytic Peroxidases.

Identifieur interne : 000164 ( Main/Exploration ); précédent : 000163; suivant : 000165

Mapping the Long-Range Electron Transfer Route in Ligninolytic Peroxidases.

Auteurs : Sandra Acebes [Espagne] ; Francisco J. Ruiz-Due As [Espagne] ; Mario Toubes [Espagne] ; Veronica Sáez-Jiménez [Espagne] ; Marta Pérez-Boada [Espagne] ; M Fátima Lucas [Espagne] ; Angel T. Martínez [Espagne] ; Victor Guallar [Espagne]

Source :

RBID : pubmed:28375014

Descripteurs français

English descriptors

Abstract

Combining a computational analysis with site-directed mutagenesis, we have studied the long-range electron transfer pathway in versatile and lignin peroxidases, two enzymes of biotechnological interest that play a key role for fungal degradation of the bulky lignin molecule in plant biomass. The in silico study established two possible electron transfer routes starting at the surface tryptophan residue previously identified as responsible for oxidation of the bulky lignin polymer. Moreover, in both enzymes, a second buried tryptophan residue appears as a top electron transfer carrier, indicating the prevalence of one pathway. Site-directed mutagenesis of versatile peroxidase (from Pleurotus eryngii) allowed us to corroborate the computational analysis and the role played by the buried tryptophan (Trp244) and a neighbor phenylalanine residue (Phe198), together with the surface tryptophan, in the electron transfer. These three aromatic residues are highly conserved in all the sequences analyzed (up to a total of 169). The importance of the surface (Trp171) and buried (Trp251) tryptophan residues in lignin peroxidase has been also confirmed by directed mutagenesis of the Phanerochaete chrysosporium enzyme. Overall, the combined procedure identifies analogous electron transfer pathways in the long-range oxidation mechanism for both ligninolytic peroxidases, constituting a good example of how computational analysis avoids making extensive trial-error mutagenic experiments.

DOI: 10.1021/acs.jpcb.7b00835
PubMed: 28375014


Affiliations:


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Le document en format XML

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<term>Amino Acid Sequence (MeSH)</term>
<term>Electron Transport (MeSH)</term>
<term>Lignin (metabolism)</term>
<term>Models, Molecular (MeSH)</term>
<term>Mutagenesis, Site-Directed (MeSH)</term>
<term>Oxidation-Reduction (MeSH)</term>
<term>Peroxidases (chemistry)</term>
<term>Peroxidases (genetics)</term>
<term>Peroxidases (metabolism)</term>
<term>Pleurotus (chemistry)</term>
<term>Pleurotus (enzymology)</term>
<term>Pleurotus (genetics)</term>
<term>Substrate Specificity (MeSH)</term>
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<term>Lignine (métabolisme)</term>
<term>Modèles moléculaires (MeSH)</term>
<term>Mutagenèse dirigée (MeSH)</term>
<term>Oxydoréduction (MeSH)</term>
<term>Peroxidases (composition chimique)</term>
<term>Peroxidases (génétique)</term>
<term>Peroxidases (métabolisme)</term>
<term>Pleurotus (composition chimique)</term>
<term>Pleurotus (enzymologie)</term>
<term>Pleurotus (génétique)</term>
<term>Spécificité du substrat (MeSH)</term>
<term>Séquence d'acides aminés (MeSH)</term>
<term>Transport d'électrons (MeSH)</term>
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<term>Peroxidases</term>
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<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en">
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<term>Lignin</term>
<term>Peroxidases</term>
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<term>Pleurotus</term>
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<keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr">
<term>Peroxidases</term>
<term>Pleurotus</term>
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<keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr">
<term>Pleurotus</term>
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<term>Peroxidases</term>
<term>Pleurotus</term>
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<term>Peroxidases</term>
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<term>Electron Transport</term>
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<term>Mutagenesis, Site-Directed</term>
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<term>Mutagenèse dirigée</term>
<term>Oxydoréduction</term>
<term>Spécificité du substrat</term>
<term>Séquence d'acides aminés</term>
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<div type="abstract" xml:lang="en">Combining a computational analysis with site-directed mutagenesis, we have studied the long-range electron transfer pathway in versatile and lignin peroxidases, two enzymes of biotechnological interest that play a key role for fungal degradation of the bulky lignin molecule in plant biomass. The in silico study established two possible electron transfer routes starting at the surface tryptophan residue previously identified as responsible for oxidation of the bulky lignin polymer. Moreover, in both enzymes, a second buried tryptophan residue appears as a top electron transfer carrier, indicating the prevalence of one pathway. Site-directed mutagenesis of versatile peroxidase (from Pleurotus eryngii) allowed us to corroborate the computational analysis and the role played by the buried tryptophan (Trp244) and a neighbor phenylalanine residue (Phe198), together with the surface tryptophan, in the electron transfer. These three aromatic residues are highly conserved in all the sequences analyzed (up to a total of 169). The importance of the surface (Trp171) and buried (Trp251) tryptophan residues in lignin peroxidase has been also confirmed by directed mutagenesis of the Phanerochaete chrysosporium enzyme. Overall, the combined procedure identifies analogous electron transfer pathways in the long-range oxidation mechanism for both ligninolytic peroxidases, constituting a good example of how computational analysis avoids making extensive trial-error mutagenic experiments.</div>
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<AbstractText>Combining a computational analysis with site-directed mutagenesis, we have studied the long-range electron transfer pathway in versatile and lignin peroxidases, two enzymes of biotechnological interest that play a key role for fungal degradation of the bulky lignin molecule in plant biomass. The in silico study established two possible electron transfer routes starting at the surface tryptophan residue previously identified as responsible for oxidation of the bulky lignin polymer. Moreover, in both enzymes, a second buried tryptophan residue appears as a top electron transfer carrier, indicating the prevalence of one pathway. Site-directed mutagenesis of versatile peroxidase (from Pleurotus eryngii) allowed us to corroborate the computational analysis and the role played by the buried tryptophan (Trp244) and a neighbor phenylalanine residue (Phe198), together with the surface tryptophan, in the electron transfer. These three aromatic residues are highly conserved in all the sequences analyzed (up to a total of 169). The importance of the surface (Trp171) and buried (Trp251) tryptophan residues in lignin peroxidase has been also confirmed by directed mutagenesis of the Phanerochaete chrysosporium enzyme. Overall, the combined procedure identifies analogous electron transfer pathways in the long-range oxidation mechanism for both ligninolytic peroxidases, constituting a good example of how computational analysis avoids making extensive trial-error mutagenic experiments.</AbstractText>
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<ForeName>Victor</ForeName>
<Initials>V</Initials>
<Identifier Source="ORCID">0000-0002-4580-1114</Identifier>
<AffiliationInfo>
<Affiliation>Barcelona Supercomputing Center, Joint BSC-CRG-IRB Research Program in Computational Biology , Jordi Girona 29, E-08034 Barcelona, Spain.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>ICREA , Passeig Lluís Companys 23, E-08010 Barcelona, Spain.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList>
<PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic">
<Year>2017</Year>
<Month>04</Month>
<Day>14</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo>
<Country>United States</Country>
<MedlineTA>J Phys Chem B</MedlineTA>
<NlmUniqueID>101157530</NlmUniqueID>
<ISSNLinking>1520-5207</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList>
<Chemical>
<RegistryNumber>9005-53-2</RegistryNumber>
<NameOfSubstance UI="D008031">Lignin</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>EC 1.11.1.-</RegistryNumber>
<NameOfSubstance UI="D010544">Peroxidases</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>EC 1.11.1.-</RegistryNumber>
<NameOfSubstance UI="C042858">lignin peroxidase</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList>
<MeshHeading>
<DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D004579" MajorTopicYN="N">Electron Transport</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D008031" MajorTopicYN="N">Lignin</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D008958" MajorTopicYN="N">Models, Molecular</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D016297" MajorTopicYN="N">Mutagenesis, Site-Directed</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D010084" MajorTopicYN="N">Oxidation-Reduction</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D010544" MajorTopicYN="N">Peroxidases</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D020076" MajorTopicYN="N">Pleurotus</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName>
<QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D013379" MajorTopicYN="N">Substrate Specificity</DescriptorName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
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<History>
<PubMedPubDate PubStatus="pubmed">
<Year>2017</Year>
<Month>4</Month>
<Day>5</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline">
<Year>2018</Year>
<Month>5</Month>
<Day>4</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez">
<Year>2017</Year>
<Month>4</Month>
<Day>5</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList>
<ArticleId IdType="pubmed">28375014</ArticleId>
<ArticleId IdType="doi">10.1021/acs.jpcb.7b00835</ArticleId>
</ArticleIdList>
</PubmedData>
</pubmed>
<affiliations>
<list>
<country>
<li>Espagne</li>
</country>
<region>
<li>Catalogne</li>
<li>Communauté de Madrid</li>
</region>
</list>
<tree>
<country name="Espagne">
<region name="Catalogne">
<name sortKey="Acebes, Sandra" sort="Acebes, Sandra" uniqKey="Acebes S" first="Sandra" last="Acebes">Sandra Acebes</name>
</region>
<name sortKey="Guallar, Victor" sort="Guallar, Victor" uniqKey="Guallar V" first="Victor" last="Guallar">Victor Guallar</name>
<name sortKey="Guallar, Victor" sort="Guallar, Victor" uniqKey="Guallar V" first="Victor" last="Guallar">Victor Guallar</name>
<name sortKey="Lucas, M Fatima" sort="Lucas, M Fatima" uniqKey="Lucas M" first="M Fátima" last="Lucas">M Fátima Lucas</name>
<name sortKey="Lucas, M Fatima" sort="Lucas, M Fatima" uniqKey="Lucas M" first="M Fátima" last="Lucas">M Fátima Lucas</name>
<name sortKey="Martinez, Angel T" sort="Martinez, Angel T" uniqKey="Martinez A" first="Angel T" last="Martínez">Angel T. Martínez</name>
<name sortKey="Perez Boada, Marta" sort="Perez Boada, Marta" uniqKey="Perez Boada M" first="Marta" last="Pérez-Boada">Marta Pérez-Boada</name>
<name sortKey="Ruiz Due As, Francisco J" sort="Ruiz Due As, Francisco J" uniqKey="Ruiz Due As F" first="Francisco J" last="Ruiz-Due As">Francisco J. Ruiz-Due As</name>
<name sortKey="Saez Jimenez, Veronica" sort="Saez Jimenez, Veronica" uniqKey="Saez Jimenez V" first="Veronica" last="Sáez-Jiménez">Veronica Sáez-Jiménez</name>
<name sortKey="Toubes, Mario" sort="Toubes, Mario" uniqKey="Toubes M" first="Mario" last="Toubes">Mario Toubes</name>
</country>
</tree>
</affiliations>
</record>

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