Catalytic properties and crystal structure of UDP-galactose 4-epimerase-like l-threonine 3-dehydrogenase from Phytophthora infestans.
Identifieur interne : 000279 ( Main/Exploration ); précédent : 000278; suivant : 000280Catalytic properties and crystal structure of UDP-galactose 4-epimerase-like l-threonine 3-dehydrogenase from Phytophthora infestans.
Auteurs : Kazunari Yoneda [Japon] ; Rina Nagano [Japon] ; Takuya Mikami [Japon] ; Haruhiko Sakuraba [Japon] ; Kenji Fukui [Japon] ; Tomohiro Araki [Japon] ; Toshihisa Ohshima [Japon]Source :
- Enzyme and microbial technology [ 1879-0909 ] ; 2020.
Abstract
We report, for the first time, the three-dimensional structure and biochemical properties of a UDP-galactose 4-epimerase-like l-threonine 3-dehydrogenase (GalE-like L-ThrDH) from Phytophthora infestans, a plant disease-causing fungus. We identified GalE-like L-ThrDH using Kyoto Encyclopedia of Genes and Genomes (KEGG) database as a candidate target for the development of a new fungicide. The GalE-like L-ThrDH gene was expressed in Escherichia coli, and its product was purified and characterized. N-Acetylglycine was found to act as a competitive inhibitor of the enzyme (Ki =0.18 mM). The crystal structure of the unique hexameric GalE-like L-ThrDH was determined using the molecular replacement method at a resolution of 2.3 Å, in the presence of NAD+ and citrate, an analogue of the substrate. Based on the molecular docking simulation, N-acetylglycine molecule was modeled into the active site and the binding mode and inhibition mechanism of N-acetylglycine were elucidated.
DOI: 10.1016/j.enzmictec.2020.109627
PubMed: 32912687
Affiliations:
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Electronic address: kyoneda@agri.u-tokai.ac.jp.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, 862-8652</wicri:regionArea><wicri:noRegion>862-8652</wicri:noRegion></affiliation></author><author><name sortKey="Nagano, Rina" sort="Nagano, Rina" uniqKey="Nagano R" first="Rina" last="Nagano">Rina Nagano</name><affiliation wicri:level="1"><nlm:affiliation>Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, 862-8652, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, 862-8652</wicri:regionArea><wicri:noRegion>862-8652</wicri:noRegion></affiliation></author><author><name sortKey="Mikami, Takuya" sort="Mikami, Takuya" uniqKey="Mikami T" first="Takuya" last="Mikami">Takuya Mikami</name><affiliation wicri:level="1"><nlm:affiliation>Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, 862-8652, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, 862-8652</wicri:regionArea><wicri:noRegion>862-8652</wicri:noRegion></affiliation></author><author><name sortKey="Sakuraba, Haruhiko" sort="Sakuraba, Haruhiko" uniqKey="Sakuraba H" first="Haruhiko" last="Sakuraba">Haruhiko Sakuraba</name><affiliation wicri:level="1"><nlm:affiliation>Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0795, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0795</wicri:regionArea><wicri:noRegion>761-0795</wicri:noRegion></affiliation></author><author><name sortKey="Fukui, Kenji" sort="Fukui, Kenji" uniqKey="Fukui K" first="Kenji" last="Fukui">Kenji Fukui</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Osaka, 569-8686, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Biochemistry, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Osaka, 569-8686</wicri:regionArea><wicri:noRegion>569-8686</wicri:noRegion></affiliation></author><author><name sortKey="Araki, Tomohiro" sort="Araki, Tomohiro" uniqKey="Araki T" first="Tomohiro" last="Araki">Tomohiro Araki</name><affiliation wicri:level="1"><nlm:affiliation>Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, 862-8652, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, 862-8652</wicri:regionArea><wicri:noRegion>862-8652</wicri:noRegion></affiliation></author><author><name sortKey="Ohshima, Toshihisa" sort="Ohshima, Toshihisa" uniqKey="Ohshima T" first="Toshihisa" last="Ohshima">Toshihisa Ohshima</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1, Ohmiya, Asahi-ku, Osaka, 535-8585, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1, Ohmiya, Asahi-ku, Osaka, 535-8585</wicri:regionArea><wicri:noRegion>535-8585</wicri:noRegion></affiliation></author></analytic><series><title level="j">Enzyme and microbial technology</title><idno type="eISSN">1879-0909</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">We report, for the first time, the three-dimensional structure and biochemical properties of a UDP-galactose 4-epimerase-like l-threonine 3-dehydrogenase (GalE-like L-ThrDH) from Phytophthora infestans, a plant disease-causing fungus. We identified GalE-like L-ThrDH using Kyoto Encyclopedia of Genes and Genomes (KEGG) database as a candidate target for the development of a new fungicide. The GalE-like L-ThrDH gene was expressed in Escherichia coli, and its product was purified and characterized. N-Acetylglycine was found to act as a competitive inhibitor of the enzyme (Ki =0.18 mM). The crystal structure of the unique hexameric GalE-like L-ThrDH was determined using the molecular replacement method at a resolution of 2.3 Å, in the presence of NAD<sup>+</sup> and citrate, an analogue of the substrate. Based on the molecular docking simulation, N-acetylglycine molecule was modeled into the active site and the binding mode and inhibition mechanism of N-acetylglycine were elucidated.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">32912687</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>11</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1879-0909</ISSN><JournalIssue CitedMedium="Internet"><Volume>140</Volume><PubDate><Year>2020</Year><Month>Oct</Month></PubDate></JournalIssue><Title>Enzyme and microbial technology</Title><ISOAbbreviation>Enzyme Microb Technol</ISOAbbreviation></Journal><ArticleTitle>Catalytic properties and crystal structure of UDP-galactose 4-epimerase-like l-threonine 3-dehydrogenase from Phytophthora infestans.</ArticleTitle><Pagination><MedlinePgn>109627</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S0141-0229(20)30120-4</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.enzmictec.2020.109627</ELocationID><Abstract><AbstractText>We report, for the first time, the three-dimensional structure and biochemical properties of a UDP-galactose 4-epimerase-like l-threonine 3-dehydrogenase (GalE-like L-ThrDH) from Phytophthora infestans, a plant disease-causing fungus. We identified GalE-like L-ThrDH using Kyoto Encyclopedia of Genes and Genomes (KEGG) database as a candidate target for the development of a new fungicide. The GalE-like L-ThrDH gene was expressed in Escherichia coli, and its product was purified and characterized. N-Acetylglycine was found to act as a competitive inhibitor of the enzyme (Ki =0.18 mM). The crystal structure of the unique hexameric GalE-like L-ThrDH was determined using the molecular replacement method at a resolution of 2.3 Å, in the presence of NAD<sup>+</sup> and citrate, an analogue of the substrate. Based on the molecular docking simulation, N-acetylglycine molecule was modeled into the active site and the binding mode and inhibition mechanism of N-acetylglycine were elucidated.</AbstractText><CopyrightInformation>Copyright © 2020 Elsevier Inc. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yoneda</LastName><ForeName>Kazunari</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, 862-8652, Japan. Electronic address: kyoneda@agri.u-tokai.ac.jp.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nagano</LastName><ForeName>Rina</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, 862-8652, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mikami</LastName><ForeName>Takuya</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, 862-8652, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sakuraba</LastName><ForeName>Haruhiko</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0795, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fukui</LastName><ForeName>Kenji</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Osaka, 569-8686, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Araki</LastName><ForeName>Tomohiro</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto-shi, Kumamoto, 862-8652, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ohshima</LastName><ForeName>Toshihisa</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1, Ohmiya, Asahi-ku, Osaka, 535-8585, Japan.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>06</Month><Day>24</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Enzyme Microb Technol</MedlineTA><NlmUniqueID>8003761</NlmUniqueID><ISSNLinking>0141-0229</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">3-dehydrogenase</Keyword><Keyword MajorTopicYN="N">Crystal structure</Keyword><Keyword MajorTopicYN="N">Enzymological characterization</Keyword><Keyword MajorTopicYN="N">Phytophthora infestans</Keyword><Keyword MajorTopicYN="N">UDP-galactose 4-epimerase-like l-threonine</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>04</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>06</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>06</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>9</Month><Day>11</Day><Hour>5</Hour><Minute>37</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>9</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>9</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32912687</ArticleId><ArticleId IdType="pii">S0141-0229(20)30120-4</ArticleId><ArticleId IdType="doi">10.1016/j.enzmictec.2020.109627</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Japon</li></country></list><tree><country name="Japon"><noRegion><name sortKey="Yoneda, Kazunari" sort="Yoneda, Kazunari" uniqKey="Yoneda K" first="Kazunari" last="Yoneda">Kazunari Yoneda</name></noRegion><name sortKey="Araki, Tomohiro" sort="Araki, Tomohiro" uniqKey="Araki T" first="Tomohiro" last="Araki">Tomohiro Araki</name><name sortKey="Fukui, Kenji" sort="Fukui, Kenji" uniqKey="Fukui K" first="Kenji" last="Fukui">Kenji Fukui</name><name sortKey="Mikami, Takuya" sort="Mikami, Takuya" uniqKey="Mikami T" first="Takuya" last="Mikami">Takuya Mikami</name><name sortKey="Nagano, Rina" sort="Nagano, Rina" uniqKey="Nagano R" first="Rina" last="Nagano">Rina Nagano</name><name sortKey="Ohshima, Toshihisa" sort="Ohshima, Toshihisa" uniqKey="Ohshima T" first="Toshihisa" last="Ohshima">Toshihisa Ohshima</name><name sortKey="Sakuraba, Haruhiko" sort="Sakuraba, Haruhiko" uniqKey="Sakuraba H" first="Haruhiko" last="Sakuraba">Haruhiko Sakuraba</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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