Unique active site and subsite features in the arabinogalactan-degrading GH43 exo-β-1,3-galactanase from Phanerochaete chrysosporium.
Identifieur interne : 000002 ( Main/Exploration ); précédent : 000001; suivant : 000003Unique active site and subsite features in the arabinogalactan-degrading GH43 exo-β-1,3-galactanase from Phanerochaete chrysosporium.
Auteurs : Kaori Matsuyama [Japon] ; Naomi Kishine [Japon] ; Zui Fujimoto [Japon] ; Naoki Sunagawa [Japon] ; Toshihisa Kotake [Japon] ; Yoichi Tsumuraya ; Masahiro Samejima [Japon] ; Kiyohiko Igarashi [Japon] ; Satoshi Kaneko [Japon]Source :
- The Journal of biological chemistry [ 1083-351X ] ; 2020.
Abstract
Arabinogalactan proteins (AGPs) are plant proteoglycans with functions in growth and development. However, these functions are largely unexplored, mainly because of the complexity of the sugar moieties. These carbohydrate sequences are generally analyzed with the aid of glycoside hydrolases. The exo-β-1,3-galactanase is a glycoside hydrolase from the basidiomycete Phanerochaete chrysosporium (Pc1,3Gal43A), which specifically cleaves AGPs. However, its structure is not known in relation to its mechanism bypassing side chains. In this study, we solved the apo and liganded structures of Pc1,3Gal43A, which reveal a glycoside hydrolase family 43 subfamily 24 (GH43_sub24) catalytic domain together with a carbohydrate-binding module family (CBM) 35 binding domain. GH43_sub24 is known to lack the catalytic base Asp conserved among other GH43 subfamilies. Our structure in combination with kinetic analyses reveal that the tautomerized imidic acid group of Gln263 serves as the catalytic base residue instead. Pc1,3Gal43A has three subsites that continue from the bottom of the catalytic pocket to the solvent. Subsite -1 contains a space that can accommodate the C-6 methylol of Gal, enabling the enzyme to bypass the β-1,6-linked galactan side chains of AGPs. Furthermore, the galactan-binding domain in CBM35 has a different ligand interaction mechanism from other sugar-binding CBM35s, including those that bind galactomannan. Specifically, we noted a Gly->Trp substitution, which affects pyranose stacking, and an Asp->Asn substitution in the binding pocket, which recognizes β-linked rather than α-linked Gal residues. These findings should facilitate further structural analysis of AGPs and may also be helpful in engineering designer enzymes for efficient biomass utilization.
DOI: 10.1074/jbc.RA120.016149
PubMed: 33093171
Affiliations:
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chrysosporium</i>.</title><author><name sortKey="Matsuyama, Kaori" sort="Matsuyama, Kaori" uniqKey="Matsuyama K" first="Kaori" last="Matsuyama">Kaori Matsuyama</name><affiliation wicri:level="4"><nlm:affiliation>Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Agricultural and Life Sciences, The University of Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName></affiliation></author><author><name sortKey="Kishine, Naomi" sort="Kishine, Naomi" uniqKey="Kishine N" first="Naomi" last="Kishine">Naomi Kishine</name><affiliation wicri:level="1"><nlm:affiliation>Advanced Analysis Center, National Agriculture and Food Research Organization, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Advanced Analysis Center, National Agriculture and Food Research Organization</wicri:regionArea><wicri:noRegion>National Agriculture and Food Research Organization</wicri:noRegion></affiliation></author><author><name sortKey="Fujimoto, Zui" sort="Fujimoto, Zui" uniqKey="Fujimoto Z" first="Zui" last="Fujimoto">Zui Fujimoto</name><affiliation wicri:level="1"><nlm:affiliation>Advanced Analysis Center, National Agriculture and Food Research Organization, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Advanced Analysis Center, National Agriculture and Food Research Organization</wicri:regionArea><wicri:noRegion>National Agriculture and Food Research Organization</wicri:noRegion></affiliation></author><author><name sortKey="Sunagawa, Naoki" sort="Sunagawa, Naoki" uniqKey="Sunagawa N" first="Naoki" last="Sunagawa">Naoki Sunagawa</name><affiliation wicri:level="4"><nlm:affiliation>Graduate School of Agricultural and Life Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Agricultural and Life Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName></affiliation></author><author><name sortKey="Kotake, Toshihisa" sort="Kotake, Toshihisa" uniqKey="Kotake T" first="Toshihisa" last="Kotake">Toshihisa Kotake</name><affiliation wicri:level="1"><nlm:affiliation>Graduate School of Science and Engineering, Saitama University, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Science and Engineering, Saitama University</wicri:regionArea><wicri:noRegion>Saitama University</wicri:noRegion></affiliation></author><author><name sortKey="Tsumuraya, Yoichi" sort="Tsumuraya, Yoichi" uniqKey="Tsumuraya Y" first="Yoichi" last="Tsumuraya">Yoichi Tsumuraya</name><affiliation><nlm:affiliation>Saitama University.</nlm:affiliation><wicri:noCountry code="no comma">Saitama University.</wicri:noCountry></affiliation></author><author><name sortKey="Samejima, Masahiro" sort="Samejima, Masahiro" uniqKey="Samejima M" first="Masahiro" last="Samejima">Masahiro Samejima</name><affiliation wicri:level="4"><nlm:affiliation>Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Agricultural and Life Sciences, The University of Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName></affiliation></author><author><name sortKey="Igarashi, Kiyohiko" sort="Igarashi, Kiyohiko" uniqKey="Igarashi K" first="Kiyohiko" last="Igarashi">Kiyohiko Igarashi</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName></affiliation></author><author><name sortKey="Kaneko, Satoshi" sort="Kaneko, Satoshi" uniqKey="Kaneko S" first="Satoshi" last="Kaneko">Satoshi Kaneko</name><affiliation wicri:level="1"><nlm:affiliation>University of the Ryukyus, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>University of the Ryukyus</wicri:regionArea></affiliation></author></analytic><series><title level="j">The Journal of biological chemistry</title><idno type="eISSN">1083-351X</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Arabinogalactan proteins (AGPs) are plant proteoglycans with functions in growth and development. However, these functions are largely unexplored, mainly because of the complexity of the sugar moieties. These carbohydrate sequences are generally analyzed with the aid of glycoside hydrolases. The exo-β-1,3-galactanase is a glycoside hydrolase from the basidiomycete <i>Phanerochaete chrysosporium</i> (<i>Pc</i>1,3Gal43A), which specifically cleaves AGPs. However, its structure is not known in relation to its mechanism bypassing side chains. In this study, we solved the apo and liganded structures of <i>Pc</i>1,3Gal43A, which reveal a glycoside hydrolase family 43 subfamily 24 (GH43_sub24) catalytic domain together with a carbohydrate-binding module family (CBM) 35 binding domain. GH43_sub24 is known to lack the catalytic base Asp conserved among other GH43 subfamilies. Our structure in combination with kinetic analyses reveal that the tautomerized imidic acid group of Gln263 serves as the catalytic base residue instead. <i>Pc</i>1,3Gal43A has three subsites that continue from the bottom of the catalytic pocket to the solvent. Subsite -1 contains a space that can accommodate the C-6 methylol of Gal, enabling the enzyme to bypass the β-1,6-linked galactan side chains of AGPs. Furthermore, the galactan-binding domain in CBM35 has a different ligand interaction mechanism from other sugar-binding CBM35s, including those that bind galactomannan. Specifically, we noted a Gly->Trp substitution, which affects pyranose stacking, and an Asp->Asn substitution in the binding pocket, which recognizes β-linked rather than α-linked Gal residues. These findings should facilitate further structural analysis of AGPs and may also be helpful in engineering designer enzymes for efficient biomass utilization.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">33093171</PMID><DateRevised><Year>2020</Year><Month>10</Month><Day>23</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1083-351X</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Oct</Month><Day>22</Day></PubDate></JournalIssue><Title>The Journal of biological chemistry</Title><ISOAbbreviation>J Biol Chem</ISOAbbreviation></Journal><ArticleTitle>Unique active site and subsite features in the arabinogalactan-degrading GH43 exo-β-1,3-galactanase from <i>Phanerochaete chrysosporium</i>.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">jbc.RA120.016149</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1074/jbc.RA120.016149</ELocationID><Abstract><AbstractText>Arabinogalactan proteins (AGPs) are plant proteoglycans with functions in growth and development. However, these functions are largely unexplored, mainly because of the complexity of the sugar moieties. These carbohydrate sequences are generally analyzed with the aid of glycoside hydrolases. The exo-β-1,3-galactanase is a glycoside hydrolase from the basidiomycete <i>Phanerochaete chrysosporium</i> (<i>Pc</i>1,3Gal43A), which specifically cleaves AGPs. However, its structure is not known in relation to its mechanism bypassing side chains. In this study, we solved the apo and liganded structures of <i>Pc</i>1,3Gal43A, which reveal a glycoside hydrolase family 43 subfamily 24 (GH43_sub24) catalytic domain together with a carbohydrate-binding module family (CBM) 35 binding domain. GH43_sub24 is known to lack the catalytic base Asp conserved among other GH43 subfamilies. Our structure in combination with kinetic analyses reveal that the tautomerized imidic acid group of Gln263 serves as the catalytic base residue instead. <i>Pc</i>1,3Gal43A has three subsites that continue from the bottom of the catalytic pocket to the solvent. Subsite -1 contains a space that can accommodate the C-6 methylol of Gal, enabling the enzyme to bypass the β-1,6-linked galactan side chains of AGPs. Furthermore, the galactan-binding domain in CBM35 has a different ligand interaction mechanism from other sugar-binding CBM35s, including those that bind galactomannan. Specifically, we noted a Gly->Trp substitution, which affects pyranose stacking, and an Asp->Asn substitution in the binding pocket, which recognizes β-linked rather than α-linked Gal residues. These findings should facilitate further structural analysis of AGPs and may also be helpful in engineering designer enzymes for efficient biomass utilization.</AbstractText><CopyrightInformation>Published under license by The American Society for Biochemistry and Molecular Biology, Inc.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Matsuyama</LastName><ForeName>Kaori</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kishine</LastName><ForeName>Naomi</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Advanced Analysis Center, National Agriculture and Food Research Organization, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fujimoto</LastName><ForeName>Zui</ForeName><Initials>Z</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-3551-6854</Identifier><AffiliationInfo><Affiliation>Advanced Analysis Center, National Agriculture and Food Research Organization, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sunagawa</LastName><ForeName>Naoki</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Graduate School of Agricultural and Life Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kotake</LastName><ForeName>Toshihisa</ForeName><Initials>T</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-1110-5006</Identifier><AffiliationInfo><Affiliation>Graduate School of Science and Engineering, Saitama University, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tsumuraya</LastName><ForeName>Yoichi</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Saitama University.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Samejima</LastName><ForeName>Masahiro</ForeName><Initials>M</Initials><Identifier Source="ORCID">https://orcid.org/0000-0001-8034-2454</Identifier><AffiliationInfo><Affiliation>Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Igarashi</LastName><ForeName>Kiyohiko</ForeName><Initials>K</Initials><Identifier Source="ORCID">https://orcid.org/0000-0001-5152-7177</Identifier><AffiliationInfo><Affiliation>Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kaneko</LastName><ForeName>Satoshi</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>University of the Ryukyus, Japan.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>10</Month><Day>22</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Biol Chem</MedlineTA><NlmUniqueID>2985121R</NlmUniqueID><ISSNLinking>0021-9258</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Phanerochaete chrysosporium</Keyword><Keyword MajorTopicYN="N">arabinogalactan-protein</Keyword><Keyword MajorTopicYN="N">biodegradation</Keyword><Keyword MajorTopicYN="N">carbohydrate metabolism</Keyword><Keyword MajorTopicYN="N">carbohydrate-binding module family 35</Keyword><Keyword MajorTopicYN="N">carbohydrate-binding protein</Keyword><Keyword MajorTopicYN="N">enzyme structure</Keyword><Keyword MajorTopicYN="N">exo-β-1,3-galactanase</Keyword><Keyword MajorTopicYN="N">glycoside hydrolase family 43</Keyword><Keyword MajorTopicYN="N">plant cell wall</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>10</Month><Day>22</Day></PubMedPubDate><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>09</Month><Day>22</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>10</Month><Day>23</Day><Hour>5</Hour><Minute>50</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>10</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>10</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">33093171</ArticleId><ArticleId IdType="pii">RA120.016149</ArticleId><ArticleId IdType="doi">10.1074/jbc.RA120.016149</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Japon</li></country><region><li>Région de Kantō</li></region><settlement><li>Tokyo</li></settlement><orgName><li>Université de Tokyo</li></orgName></list><tree><noCountry><name sortKey="Tsumuraya, Yoichi" sort="Tsumuraya, Yoichi" uniqKey="Tsumuraya Y" first="Yoichi" last="Tsumuraya">Yoichi Tsumuraya</name></noCountry><country name="Japon"><region name="Région de Kantō"><name sortKey="Matsuyama, Kaori" sort="Matsuyama, Kaori" uniqKey="Matsuyama K" first="Kaori" last="Matsuyama">Kaori Matsuyama</name></region><name sortKey="Fujimoto, Zui" sort="Fujimoto, Zui" uniqKey="Fujimoto Z" first="Zui" last="Fujimoto">Zui Fujimoto</name><name sortKey="Igarashi, Kiyohiko" sort="Igarashi, Kiyohiko" uniqKey="Igarashi K" first="Kiyohiko" last="Igarashi">Kiyohiko Igarashi</name><name sortKey="Kaneko, Satoshi" sort="Kaneko, Satoshi" uniqKey="Kaneko S" first="Satoshi" last="Kaneko">Satoshi Kaneko</name><name sortKey="Kishine, Naomi" sort="Kishine, Naomi" uniqKey="Kishine N" first="Naomi" last="Kishine">Naomi Kishine</name><name sortKey="Kotake, Toshihisa" sort="Kotake, Toshihisa" uniqKey="Kotake T" first="Toshihisa" last="Kotake">Toshihisa Kotake</name><name sortKey="Samejima, Masahiro" sort="Samejima, Masahiro" uniqKey="Samejima M" first="Masahiro" last="Samejima">Masahiro Samejima</name><name sortKey="Sunagawa, Naoki" sort="Sunagawa, Naoki" uniqKey="Sunagawa N" first="Naoki" last="Sunagawa">Naoki Sunagawa</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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