X-ray structure of the direct electron transfer-type FAD glucose dehydrogenase catalytic subunit complexed with a hitchhiker protein.
Identifieur interne : 000191 ( Main/Exploration ); précédent : 000190; suivant : 000192X-ray structure of the direct electron transfer-type FAD glucose dehydrogenase catalytic subunit complexed with a hitchhiker protein.
Auteurs : Hiromi Yoshida [Japon] ; Katsuhiro Kojima [Japon] ; Masaki Shiota [Japon] ; Keiichi Yoshimatsu [États-Unis] ; Tomohiko Yamazaki [Japon] ; Stefano Ferri [Japon] ; Wakako Tsugawa [Japon] ; Shigehiro Kamitori [Japon] ; Koji Sode [Japon]Source :
- Acta crystallographica. Section D, Structural biology [ 2059-7983 ] ; 2019.
Descripteurs français
- KwdFr :
- Burkholderia cepacia (enzymologie), Cristallographie aux rayons X (méthodes), Domaine catalytique (MeSH), Flavine adénine dinucléotide (composition chimique), Glucose dehydrogenases (composition chimique), Modèles moléculaires (MeSH), Protéines recombinantes (composition chimique), Transport d'électrons (MeSH).
- MESH :
- composition chimique : Flavine adénine dinucléotide, Glucose dehydrogenases, Protéines recombinantes.
- enzymologie : Burkholderia cepacia.
- méthodes : Cristallographie aux rayons X.
- Domaine catalytique, Modèles moléculaires, Transport d'électrons.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Flavin-Adenine Dinucleotide, Glucose Dehydrogenases, Recombinant Proteins.
- enzymology : Burkholderia cepacia.
- methods : Crystallography, X-Ray.
- Catalytic Domain, Electron Transport, Models, Molecular.
Abstract
The bacterial flavin adenine dinucleotide (FAD)-dependent glucose dehydrogenase complex derived from Burkholderia cepacia (BcGDH) is a representative molecule of direct electron transfer-type FAD-dependent dehydrogenase complexes. In this study, the X-ray structure of BcGDHγα, the catalytic subunit (α-subunit) of BcGDH complexed with a hitchhiker protein (γ-subunit), was determined. The most prominent feature of this enzyme is the presence of the 3Fe-4S cluster, which is located at the surface of the catalytic subunit and functions in intramolecular and intermolecular electron transfer from FAD to the electron-transfer subunit. The structure of the complex revealed that these two molecules are connected through disulfide bonds and hydrophobic interactions, and that the formation of disulfide bonds is required to stabilize the catalytic subunit. The structure of the complex revealed the putative position of the electron-transfer subunit. A comparison of the structures of BcGDHγα and membrane-bound fumarate reductases suggested that the whole BcGDH complex, which also includes the membrane-bound β-subunit containing three heme c moieties, may form a similar overall structure to fumarate reductases, thus accomplishing effective electron transfer.
DOI: 10.1107/S2059798319010878
PubMed: 31478907
PubMed Central: PMC6719666
Affiliations:
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dehydrogenase catalytic subunit complexed with a hitchhiker protein.</title><author><name sortKey="Yoshida, Hiromi" sort="Yoshida, Hiromi" uniqKey="Yoshida H" first="Hiromi" last="Yoshida">Hiromi Yoshida</name><affiliation wicri:level="1"><nlm:affiliation>Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793</wicri:regionArea><wicri:noRegion>Kagawa 761-0793</wicri:noRegion></affiliation></author><author><name sortKey="Kojima, Katsuhiro" sort="Kojima, Katsuhiro" uniqKey="Kojima K" first="Katsuhiro" last="Kojima">Katsuhiro Kojima</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Shiota, Masaki" sort="Shiota, Masaki" uniqKey="Shiota M" first="Masaki" last="Shiota">Masaki Shiota</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Yoshimatsu, Keiichi" sort="Yoshimatsu, Keiichi" uniqKey="Yoshimatsu K" first="Keiichi" last="Yoshimatsu">Keiichi Yoshimatsu</name><affiliation wicri:level="2"><nlm:affiliation>Department of Chemistry, Missouri State University, Springfield, MO 65897, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry, Missouri State University, Springfield, MO 65897</wicri:regionArea><placeName><region type="state">Missouri (État)</region></placeName></affiliation></author><author><name sortKey="Yamazaki, Tomohiko" sort="Yamazaki, Tomohiko" uniqKey="Yamazaki T" first="Tomohiko" last="Yamazaki">Tomohiko Yamazaki</name><affiliation wicri:level="1"><nlm:affiliation>Research Center for Functional Materials, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Research Center for Functional Materials, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047</wicri:regionArea><wicri:noRegion>Ibaraki 305-0047</wicri:noRegion></affiliation></author><author><name sortKey="Ferri, Stefano" sort="Ferri, Stefano" uniqKey="Ferri S" first="Stefano" last="Ferri">Stefano Ferri</name><affiliation wicri:level="1"><nlm:affiliation>Department of Applied Chemistry and Biochemical Engineering, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8561, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Applied Chemistry and Biochemical Engineering, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8561</wicri:regionArea><wicri:noRegion>Shizuoka 432-8561</wicri:noRegion></affiliation></author><author><name sortKey="Tsugawa, Wakako" sort="Tsugawa, Wakako" uniqKey="Tsugawa W" first="Wakako" last="Tsugawa">Wakako Tsugawa</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Kamitori, Shigehiro" sort="Kamitori, Shigehiro" uniqKey="Kamitori S" first="Shigehiro" last="Kamitori">Shigehiro Kamitori</name><affiliation wicri:level="1"><nlm:affiliation>Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793</wicri:regionArea><wicri:noRegion>Kagawa 761-0793</wicri:noRegion></affiliation></author><author><name sortKey="Sode, Koji" sort="Sode, Koji" uniqKey="Sode K" first="Koji" last="Sode">Koji Sode</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author></analytic><series><title level="j">Acta crystallographica. Section D, Structural biology</title><idno type="eISSN">2059-7983</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Burkholderia cepacia (enzymology)</term><term>Catalytic Domain (MeSH)</term><term>Crystallography, X-Ray (methods)</term><term>Electron Transport (MeSH)</term><term>Flavin-Adenine Dinucleotide (chemistry)</term><term>Glucose Dehydrogenases (chemistry)</term><term>Models, Molecular (MeSH)</term><term>Recombinant Proteins (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Burkholderia cepacia (enzymologie)</term><term>Cristallographie aux rayons X (méthodes)</term><term>Domaine catalytique (MeSH)</term><term>Flavine adénine dinucléotide (composition chimique)</term><term>Glucose dehydrogenases (composition chimique)</term><term>Modèles moléculaires (MeSH)</term><term>Protéines recombinantes (composition chimique)</term><term>Transport d'électrons (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Flavin-Adenine Dinucleotide</term><term>Glucose Dehydrogenases</term><term>Recombinant Proteins</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Flavine adénine dinucléotide</term><term>Glucose dehydrogenases</term><term>Protéines recombinantes</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Burkholderia cepacia</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Burkholderia cepacia</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Crystallography, X-Ray</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Cristallographie aux rayons X</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Catalytic Domain</term><term>Electron Transport</term><term>Models, Molecular</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Domaine catalytique</term><term>Modèles moléculaires</term><term>Transport d'électrons</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The bacterial flavin adenine dinucleotide (FAD)-dependent glucose dehydrogenase complex derived from Burkholderia cepacia (BcGDH) is a representative molecule of direct electron transfer-type FAD-dependent dehydrogenase complexes. In this study, the X-ray structure of BcGDHγα, the catalytic subunit (α-subunit) of BcGDH complexed with a hitchhiker protein (γ-subunit), was determined. The most prominent feature of this enzyme is the presence of the 3Fe-4S cluster, which is located at the surface of the catalytic subunit and functions in intramolecular and intermolecular electron transfer from FAD to the electron-transfer subunit. The structure of the complex revealed that these two molecules are connected through disulfide bonds and hydrophobic interactions, and that the formation of disulfide bonds is required to stabilize the catalytic subunit. The structure of the complex revealed the putative position of the electron-transfer subunit. A comparison of the structures of BcGDHγα and membrane-bound fumarate reductases suggested that the whole BcGDH complex, which also includes the membrane-bound β-subunit containing three heme c moieties, may form a similar overall structure to fumarate reductases, thus accomplishing effective electron transfer.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31478907</PMID><DateCompleted><Year>2019</Year><Month>12</Month><Day>30</Day></DateCompleted><DateRevised><Year>2020</Year><Month>02</Month><Day>25</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">2059-7983</ISSN><JournalIssue CitedMedium="Internet"><Volume>75</Volume><Issue>Pt 9</Issue><PubDate><Year>2019</Year><Month>Sep</Month><Day>01</Day></PubDate></JournalIssue><Title>Acta crystallographica. Section D, Structural biology</Title><ISOAbbreviation>Acta Crystallogr D Struct Biol</ISOAbbreviation></Journal><ArticleTitle>X-ray structure of the direct electron transfer-type FAD glucose dehydrogenase catalytic subunit complexed with a hitchhiker protein.</ArticleTitle><Pagination><MedlinePgn>841-851</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1107/S2059798319010878</ELocationID><Abstract><AbstractText>The bacterial flavin adenine dinucleotide (FAD)-dependent glucose dehydrogenase complex derived from Burkholderia cepacia (BcGDH) is a representative molecule of direct electron transfer-type FAD-dependent dehydrogenase complexes. In this study, the X-ray structure of BcGDHγα, the catalytic subunit (α-subunit) of BcGDH complexed with a hitchhiker protein (γ-subunit), was determined. The most prominent feature of this enzyme is the presence of the 3Fe-4S cluster, which is located at the surface of the catalytic subunit and functions in intramolecular and intermolecular electron transfer from FAD to the electron-transfer subunit. The structure of the complex revealed that these two molecules are connected through disulfide bonds and hydrophobic interactions, and that the formation of disulfide bonds is required to stabilize the catalytic subunit. The structure of the complex revealed the putative position of the electron-transfer subunit. A comparison of the structures of BcGDHγα and membrane-bound fumarate reductases suggested that the whole BcGDH complex, which also includes the membrane-bound β-subunit containing three heme c moieties, may form a similar overall structure to fumarate reductases, thus accomplishing effective electron transfer.</AbstractText><CopyrightInformation>open access.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yoshida</LastName><ForeName>Hiromi</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kojima</LastName><ForeName>Katsuhiro</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shiota</LastName><ForeName>Masaki</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yoshimatsu</LastName><ForeName>Keiichi</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Missouri State University, Springfield, MO 65897, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yamazaki</LastName><ForeName>Tomohiko</ForeName><Initials>T</Initials><Identifier Source="ORCID">0000-0003-2136-8042</Identifier><AffiliationInfo><Affiliation>Research Center for Functional Materials, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ferri</LastName><ForeName>Stefano</ForeName><Initials>S</Initials><Identifier Source="ORCID">0000-0003-1424-4367</Identifier><AffiliationInfo><Affiliation>Department of Applied Chemistry and Biochemical Engineering, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8561, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tsugawa</LastName><ForeName>Wakako</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kamitori</LastName><ForeName>Shigehiro</ForeName><Initials>S</Initials><Identifier Source="ORCID">0000-0002-3950-3372</Identifier><AffiliationInfo><Affiliation>Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sode</LastName><ForeName>Koji</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>JP16H04175</GrantID><Agency>Japan Society for the Promotion of Science</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>08</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Acta Crystallogr D Struct Biol</MedlineTA><NlmUniqueID>101676043</NlmUniqueID><ISSNLinking>2059-7983</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D011994">Recombinant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>146-14-5</RegistryNumber><NameOfSubstance UI="D005182">Flavin-Adenine Dinucleotide</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 1.1.1.-</RegistryNumber><NameOfSubstance UI="D005948">Glucose Dehydrogenases</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D016956" MajorTopicYN="N">Burkholderia cepacia</DescriptorName><QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020134" MajorTopicYN="N">Catalytic Domain</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018360" MajorTopicYN="N">Crystallography, X-Ray</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004579" MajorTopicYN="N">Electron Transport</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005182" MajorTopicYN="N">Flavin-Adenine Dinucleotide</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005948" MajorTopicYN="N">Glucose Dehydrogenases</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008958" MajorTopicYN="N">Models, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011994" MajorTopicYN="N">Recombinant Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Burkholderia cepacia</Keyword><Keyword MajorTopicYN="N">direct electron transfer</Keyword><Keyword MajorTopicYN="N">flavin adenine dinucleotide-dependent dehydrogenase complex</Keyword><Keyword MajorTopicYN="N">glucose dehydrogenase</Keyword><Keyword MajorTopicYN="N">glucose sensors</Keyword><Keyword MajorTopicYN="N">hitchhiker protein</Keyword><Keyword MajorTopicYN="N">iron–sulfur cluster</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>05</Month><Day>01</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>08</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>9</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>9</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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Kojima</name><name sortKey="Shiota, Masaki" sort="Shiota, Masaki" uniqKey="Shiota M" first="Masaki" last="Shiota">Masaki Shiota</name><name sortKey="Sode, Koji" sort="Sode, Koji" uniqKey="Sode K" first="Koji" last="Sode">Koji Sode</name><name sortKey="Tsugawa, Wakako" sort="Tsugawa, Wakako" uniqKey="Tsugawa W" first="Wakako" last="Tsugawa">Wakako Tsugawa</name><name sortKey="Yamazaki, Tomohiko" sort="Yamazaki, Tomohiko" uniqKey="Yamazaki T" first="Tomohiko" last="Yamazaki">Tomohiko Yamazaki</name></country><country name="États-Unis"><region name="Missouri (État)"><name sortKey="Yoshimatsu, Keiichi" sort="Yoshimatsu, Keiichi" uniqKey="Yoshimatsu K" first="Keiichi" last="Yoshimatsu">Keiichi Yoshimatsu</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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