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Identification of key residues for activities of atypical glutathione S-transferase of Ceriporiopsis subvermispora, a selective degrader of lignin in woody biomass, by crystallography and functional mutagenesis.

Identifieur interne : 000134 ( Main/Exploration ); précédent : 000133; suivant : 000135

Identification of key residues for activities of atypical glutathione S-transferase of Ceriporiopsis subvermispora, a selective degrader of lignin in woody biomass, by crystallography and functional mutagenesis.

Auteurs : Wan Hasnidah Wan Osman [Japon] ; Bunzo Mikami [Japon] ; Naoki Saka [Japon] ; Keiko Kondo [Japon] ; Meng-I Lin [Japon] ; Takashi Nagata [Japon] ; Masato Katahira [Japon]

Source :

RBID : pubmed:30928378

Descripteurs français

English descriptors

Abstract

Ceriporiopsis subvermispora (C. subvermispora) is a selective degrader of lignin in the woody biomass. Glutathione S-transferases (GSTs) are multifunctional enzymes that play important roles in cellular detoxification and metabolism. The crystal structures of a GST of C. subvermispora, CsGST83044, in GSH-free and -bound forms were solved at 1.95 and 2.19 Å resolution, respectively. The structure of the GSH-bound form revealed that CsGST83044 can be categorized as an atypical-type of GST. In the GSH-bound form of CsGST83044, Asn22, Asn24, and Tyr46 are located closest to the sulfur atom and form hydrogen bonds with the thiol group. The functional mutagenesis indicated that they are critical for the enzymatic activities of CsGST83044. The critical residues of an atypical-type GST belonging to the GSTFuA class were revealed for the first time. A previous study indicated that CsGST83044 and another GST, CsGST63524, differ in substrate preference; CsGST83044 prefers smaller substrates than CsGST63524 for its esterase activity. The GSH-bound pocket of CsGST83044 turns out to be small, which may explain the preference for smaller substrates. Protein engineering of GSTs of C. subvermispora in the light of the obtained insight may pave a path in the future for utilization of the woody biomass.

DOI: 10.1016/j.ijbiomac.2019.03.199
PubMed: 30928378


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<term>Amino Acid Sequence (MeSH)</term>
<term>Binding Sites (MeSH)</term>
<term>Biomass (MeSH)</term>
<term>Coriolaceae (enzymology)</term>
<term>Crystallography, X-Ray (MeSH)</term>
<term>Glutathione Transferase (chemistry)</term>
<term>Glutathione Transferase (genetics)</term>
<term>Glutathione Transferase (metabolism)</term>
<term>Lignin (metabolism)</term>
<term>Models, Molecular (MeSH)</term>
<term>Mutagenesis (MeSH)</term>
<term>Protein Conformation (MeSH)</term>
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<term>Biomasse (MeSH)</term>
<term>Bois (composition chimique)</term>
<term>Conformation des protéines (MeSH)</term>
<term>Coriolaceae (enzymologie)</term>
<term>Cristallographie aux rayons X (MeSH)</term>
<term>Glutathione transferase (composition chimique)</term>
<term>Glutathione transferase (génétique)</term>
<term>Glutathione transferase (métabolisme)</term>
<term>Lignine (métabolisme)</term>
<term>Modèles moléculaires (MeSH)</term>
<term>Mutagenèse (MeSH)</term>
<term>Sites de fixation (MeSH)</term>
<term>Séquence d'acides aminés (MeSH)</term>
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<term>Glutathione transferase</term>
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<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en">
<term>Glutathione Transferase</term>
<term>Lignin</term>
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<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr">
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<term>Lignine</term>
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<term>Cristallographie aux rayons X</term>
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<div type="abstract" xml:lang="en">Ceriporiopsis subvermispora (C. subvermispora) is a selective degrader of lignin in the woody biomass. Glutathione S-transferases (GSTs) are multifunctional enzymes that play important roles in cellular detoxification and metabolism. The crystal structures of a GST of C. subvermispora, CsGST83044, in GSH-free and -bound forms were solved at 1.95 and 2.19 Å resolution, respectively. The structure of the GSH-bound form revealed that CsGST83044 can be categorized as an atypical-type of GST. In the GSH-bound form of CsGST83044, Asn22, Asn24, and Tyr46 are located closest to the sulfur atom and form hydrogen bonds with the thiol group. The functional mutagenesis indicated that they are critical for the enzymatic activities of CsGST83044. The critical residues of an atypical-type GST belonging to the GSTFuA class were revealed for the first time. A previous study indicated that CsGST83044 and another GST, CsGST63524, differ in substrate preference; CsGST83044 prefers smaller substrates than CsGST63524 for its esterase activity. The GSH-bound pocket of CsGST83044 turns out to be small, which may explain the preference for smaller substrates. Protein engineering of GSTs of C. subvermispora in the light of the obtained insight may pave a path in the future for utilization of the woody biomass.</div>
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<AbstractText>Ceriporiopsis subvermispora (C. subvermispora) is a selective degrader of lignin in the woody biomass. Glutathione S-transferases (GSTs) are multifunctional enzymes that play important roles in cellular detoxification and metabolism. The crystal structures of a GST of C. subvermispora, CsGST83044, in GSH-free and -bound forms were solved at 1.95 and 2.19 Å resolution, respectively. The structure of the GSH-bound form revealed that CsGST83044 can be categorized as an atypical-type of GST. In the GSH-bound form of CsGST83044, Asn22, Asn24, and Tyr46 are located closest to the sulfur atom and form hydrogen bonds with the thiol group. The functional mutagenesis indicated that they are critical for the enzymatic activities of CsGST83044. The critical residues of an atypical-type GST belonging to the GSTFuA class were revealed for the first time. A previous study indicated that CsGST83044 and another GST, CsGST63524, differ in substrate preference; CsGST83044 prefers smaller substrates than CsGST63524 for its esterase activity. The GSH-bound pocket of CsGST83044 turns out to be small, which may explain the preference for smaller substrates. Protein engineering of GSTs of C. subvermispora in the light of the obtained insight may pave a path in the future for utilization of the woody biomass.</AbstractText>
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<ChemicalList>
<Chemical>
<RegistryNumber>9005-53-2</RegistryNumber>
<NameOfSubstance UI="D008031">Lignin</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>EC 2.5.1.18</RegistryNumber>
<NameOfSubstance UI="D005982">Glutathione Transferase</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList>
<MeshHeading>
<DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D018533" MajorTopicYN="Y">Biomass</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D055453" MajorTopicYN="N">Coriolaceae</DescriptorName>
<QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D018360" MajorTopicYN="N">Crystallography, X-Ray</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D005982" MajorTopicYN="N">Glutathione Transferase</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D008031" MajorTopicYN="N">Lignin</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D008958" MajorTopicYN="N">Models, Molecular</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D016296" MajorTopicYN="Y">Mutagenesis</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D011487" MajorTopicYN="N">Protein Conformation</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D014934" MajorTopicYN="N">Wood</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName>
</MeshHeading>
</MeshHeadingList>
<KeywordList Owner="NOTNLM">
<Keyword MajorTopicYN="N">Ceriporiopsis subvermispora</Keyword>
<Keyword MajorTopicYN="N">Crystal structure</Keyword>
<Keyword MajorTopicYN="N">Glutathione S-transferase</Keyword>
</KeywordList>
</MedlineCitation>
<PubmedData>
<History>
<PubMedPubDate PubStatus="received">
<Year>2019</Year>
<Month>03</Month>
<Day>08</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted">
<Year>2019</Year>
<Month>03</Month>
<Day>26</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed">
<Year>2019</Year>
<Month>4</Month>
<Day>1</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline">
<Year>2019</Year>
<Month>11</Month>
<Day>7</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez">
<Year>2019</Year>
<Month>4</Month>
<Day>1</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList>
<ArticleId IdType="pubmed">30928378</ArticleId>
<ArticleId IdType="pii">S0141-8130(19)31760-X</ArticleId>
<ArticleId IdType="doi">10.1016/j.ijbiomac.2019.03.199</ArticleId>
</ArticleIdList>
</PubmedData>
</pubmed>
<affiliations>
<list>
<country>
<li>Japon</li>
</country>
<region>
<li>Région du Kansai</li>
</region>
<settlement>
<li>Kyoto</li>
</settlement>
<orgName>
<li>Université de Kyoto</li>
</orgName>
</list>
<tree>
<country name="Japon">
<region name="Région du Kansai">
<name sortKey="Osman, Wan Hasnidah Wan" sort="Osman, Wan Hasnidah Wan" uniqKey="Osman W" first="Wan Hasnidah Wan" last="Osman">Wan Hasnidah Wan Osman</name>
</region>
<name sortKey="Katahira, Masato" sort="Katahira, Masato" uniqKey="Katahira M" first="Masato" last="Katahira">Masato Katahira</name>
<name sortKey="Kondo, Keiko" sort="Kondo, Keiko" uniqKey="Kondo K" first="Keiko" last="Kondo">Keiko Kondo</name>
<name sortKey="Lin, Meng I" sort="Lin, Meng I" uniqKey="Lin M" first="Meng-I" last="Lin">Meng-I Lin</name>
<name sortKey="Mikami, Bunzo" sort="Mikami, Bunzo" uniqKey="Mikami B" first="Bunzo" last="Mikami">Bunzo Mikami</name>
<name sortKey="Nagata, Takashi" sort="Nagata, Takashi" uniqKey="Nagata T" first="Takashi" last="Nagata">Takashi Nagata</name>
<name sortKey="Saka, Naoki" sort="Saka, Naoki" uniqKey="Saka N" first="Naoki" last="Saka">Naoki Saka</name>
</country>
</tree>
</affiliations>
</record>

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