Crystallographic and kinetic analyses of the FdsBG subcomplex of the cytosolic formate dehydrogenase FdsABG from Cupriavidus necator.
Identifieur interne : 000150 ( Main/Exploration ); précédent : 000149; suivant : 000151Crystallographic and kinetic analyses of the FdsBG subcomplex of the cytosolic formate dehydrogenase FdsABG from Cupriavidus necator.
Auteurs : Tynan Young [États-Unis] ; Dimitri Niks [États-Unis] ; Sheron Hakopian [États-Unis] ; Timothy K. Tam [États-Unis] ; Xuejun Yu [États-Unis] ; Russ Hille [États-Unis] ; Gregor M. Blaha [États-Unis]Source :
- The Journal of biological chemistry [ 1083-351X ] ; 2020.
Abstract
Formate oxidation to carbon dioxide is a key reaction in one-carbon compound metabolism, and its reverse reaction represents the first step in carbon assimilation in the acetogenic and methanogenic branches of many anaerobic organisms. The molybdenum-containing dehydrogenase FdsABG is a soluble NAD+-dependent formate dehydrogenase and a member of the NADH dehydrogenase superfamily. Here, we present the first structure of the FdsBG subcomplex of the cytosolic FdsABG formate dehydrogenase from the hydrogen-oxidizing bacterium Cupriavidus necator H16 both with and without bound NADH. The structures revealed that the two iron-sulfur clusters, Fe4S4 in FdsB and Fe2S2 in FdsG, are closer to the FMN than they are in other NADH dehydrogenases. Rapid kinetic studies and EPR measurements of rapid freeze-quenched samples of the NADH reduction of FdsBG identified a neutral flavin semiquinone, FMNH•, not previously observed to participate in NADH-mediated reduction of the FdsABG holoenzyme. We found that this semiquinone forms through the transfer of one electron from the fully reduced FMNH-, initially formed via NADH-mediated reduction, to the Fe2S2 cluster. This Fe2S2 cluster is not part of the on-path chain of iron-sulfur clusters connecting the FMN of FdsB with the active-site molybdenum center of FdsA. According to the NADH-bound structure, the nicotinamide ring stacks onto the re-face of the FMN. However, NADH binding significantly reduced the electron density for the isoalloxazine ring of FMN and induced a conformational change in residues of the FMN-binding pocket that display peptide-bond flipping upon NAD+ binding in proper NADH dehydrogenases.
DOI: 10.1074/jbc.RA120.013264
PubMed: 32249211
PubMed Central: PMC7212643
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Tam</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biochemistry, University of California, Riverside, California 92521.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Department of Biochemistry, University of California, Riverside</wicri:cityArea></affiliation></author><author><name sortKey="Yu, Xuejun" sort="Yu, Xuejun" uniqKey="Yu X" first="Xuejun" last="Yu">Xuejun Yu</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biochemistry, University of California, Riverside, California 92521.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Department of Biochemistry, University of California, Riverside</wicri:cityArea></affiliation></author><author><name sortKey="Hille, Russ" sort="Hille, Russ" uniqKey="Hille R" first="Russ" last="Hille">Russ Hille</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, University of California, Riverside, California 92521 russ.hille@ucr.edu.</nlm:affiliation><country wicri:rule="url">États-Unis</country><wicri:regionArea>Department of Biochemistry, University of California, Riverside</wicri:regionArea><wicri:noRegion>Riverside</wicri:noRegion></affiliation></author><author><name sortKey="Blaha, Gregor M" sort="Blaha, Gregor M" uniqKey="Blaha G" first="Gregor M" last="Blaha">Gregor M. Blaha</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, University of California, Riverside, California 92521 gregor.blaha@ucr.edu.</nlm:affiliation><country wicri:rule="url">États-Unis</country><wicri:regionArea>Department of Biochemistry, University of California, Riverside</wicri:regionArea><wicri:noRegion>Riverside</wicri:noRegion></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">Formate oxidation to carbon dioxide is a key reaction in one-carbon compound metabolism, and its reverse reaction represents the first step in carbon assimilation in the acetogenic and methanogenic branches of many anaerobic organisms. The molybdenum-containing dehydrogenase FdsABG is a soluble NAD<sup>+</sup>-dependent formate dehydrogenase and a member of the NADH dehydrogenase superfamily. Here, we present the first structure of the FdsBG subcomplex of the cytosolic FdsABG formate dehydrogenase from the hydrogen-oxidizing bacterium <i>Cupriavidus necator</i> H16 both with and without bound NADH. The structures revealed that the two iron-sulfur clusters, Fe<sub>4</sub>S<sub>4</sub> in FdsB and Fe<sub>2</sub>S<sub>2</sub> in FdsG, are closer to the FMN than they are in other NADH dehydrogenases. Rapid kinetic studies and EPR measurements of rapid freeze-quenched samples of the NADH reduction of FdsBG identified a neutral flavin semiquinone, FMNH<sup>•</sup>, not previously observed to participate in NADH-mediated reduction of the FdsABG holoenzyme. We found that this semiquinone forms through the transfer of one electron from the fully reduced FMNH<sup>-</sup>, initially formed via NADH-mediated reduction, to the Fe<sub>2</sub>S<sub>2</sub> cluster. This Fe<sub>2</sub>S<sub>2</sub> cluster is not part of the on-path chain of iron-sulfur clusters connecting the FMN of FdsB with the active-site molybdenum center of FdsA. According to the NADH-bound structure, the nicotinamide ring stacks onto the <i>re</i>-face of the FMN. However, NADH binding significantly reduced the electron density for the isoalloxazine ring of FMN and induced a conformational change in residues of the FMN-binding pocket that display peptide-bond flipping upon NAD<sup>+</sup> binding in proper NADH dehydrogenases.</div></front></TEI><pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">32249211</PMID><DateRevised><Year>2020</Year><Month>05</Month><Day>19</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1083-351X</ISSN><JournalIssue CitedMedium="Internet"><Volume>295</Volume><Issue>19</Issue><PubDate><Year>2020</Year><Month>May</Month><Day>08</Day></PubDate></JournalIssue><Title>The Journal of biological chemistry</Title><ISOAbbreviation>J Biol Chem</ISOAbbreviation></Journal><ArticleTitle>Crystallographic and kinetic analyses of the FdsBG subcomplex of the cytosolic formate dehydrogenase FdsABG from <i>Cupriavidus necator</i>.</ArticleTitle><Pagination><MedlinePgn>6570-6585</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1074/jbc.RA120.013264</ELocationID><Abstract><AbstractText>Formate oxidation to carbon dioxide is a key reaction in one-carbon compound metabolism, and its reverse reaction represents the first step in carbon assimilation in the acetogenic and methanogenic branches of many anaerobic organisms. The molybdenum-containing dehydrogenase FdsABG is a soluble NAD<sup>+</sup>-dependent formate dehydrogenase and a member of the NADH dehydrogenase superfamily. Here, we present the first structure of the FdsBG subcomplex of the cytosolic FdsABG formate dehydrogenase from the hydrogen-oxidizing bacterium <i>Cupriavidus necator</i> H16 both with and without bound NADH. The structures revealed that the two iron-sulfur clusters, Fe<sub>4</sub>S<sub>4</sub> in FdsB and Fe<sub>2</sub>S<sub>2</sub> in FdsG, are closer to the FMN than they are in other NADH dehydrogenases. Rapid kinetic studies and EPR measurements of rapid freeze-quenched samples of the NADH reduction of FdsBG identified a neutral flavin semiquinone, FMNH<sup>•</sup>, not previously observed to participate in NADH-mediated reduction of the FdsABG holoenzyme. We found that this semiquinone forms through the transfer of one electron from the fully reduced FMNH<sup>-</sup>, initially formed via NADH-mediated reduction, to the Fe<sub>2</sub>S<sub>2</sub> cluster. This Fe<sub>2</sub>S<sub>2</sub> cluster is not part of the on-path chain of iron-sulfur clusters connecting the FMN of FdsB with the active-site molybdenum center of FdsA. According to the NADH-bound structure, the nicotinamide ring stacks onto the <i>re</i>-face of the FMN. However, NADH binding significantly reduced the electron density for the isoalloxazine ring of FMN and induced a conformational change in residues of the FMN-binding pocket that display peptide-bond flipping upon NAD<sup>+</sup> binding in proper NADH dehydrogenases.</AbstractText><CopyrightInformation>© 2020 Young et al.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Young</LastName><ForeName>Tynan</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, University of California, Riverside, California 92521.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Niks</LastName><ForeName>Dimitri</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, University of California, Riverside, California 92521.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hakopian</LastName><ForeName>Sheron</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, University of California, Riverside, California 92521.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tam</LastName><ForeName>Timothy K</ForeName><Initials>TK</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, University of California, Riverside, California 92521.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yu</LastName><ForeName>Xuejun</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, University of California, Riverside, California 92521.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hille</LastName><ForeName>Russ</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, University of California, Riverside, California 92521 russ.hille@ucr.edu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Blaha</LastName><ForeName>Gregor M</ForeName><Initials>GM</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, University of California, Riverside, California 92521 gregor.blaha@ucr.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>PDB</DataBankName><AccessionNumberList><AccessionNumber>6HLI</AccessionNumber><AccessionNumber>6HL2</AccessionNumber><AccessionNumber>6HL3</AccessionNumber><AccessionNumber>5XFA</AccessionNumber><AccessionNumber>5XF9</AccessionNumber><AccessionNumber>2FUG</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>04</Month><Day>05</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">FdsABG</Keyword><Keyword MajorTopicYN="N">carbon assimilation</Keyword><Keyword MajorTopicYN="N">electron transfer</Keyword><Keyword MajorTopicYN="N">enzyme kinetics</Keyword><Keyword MajorTopicYN="N">enzyme structure</Keyword><Keyword MajorTopicYN="N">flavin mononucleotide (FMN)</Keyword><Keyword MajorTopicYN="N">formate dehydrogenase</Keyword><Keyword MajorTopicYN="N">nicotinamide adenine dinucleotide (NADH)</Keyword><Keyword MajorTopicYN="N">protein crystallization</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>03</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>03</Month><Day>30</Day></PubMedPubDate><PubMedPubDate 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sortKey="Young, Tynan" sort="Young, Tynan" uniqKey="Young T" first="Tynan" last="Young">Tynan Young</name></region><name sortKey="Blaha, Gregor M" sort="Blaha, Gregor M" uniqKey="Blaha G" first="Gregor M" last="Blaha">Gregor M. Blaha</name><name sortKey="Hakopian, Sheron" sort="Hakopian, Sheron" uniqKey="Hakopian S" first="Sheron" last="Hakopian">Sheron Hakopian</name><name sortKey="Hille, Russ" sort="Hille, Russ" uniqKey="Hille R" first="Russ" last="Hille">Russ Hille</name><name sortKey="Niks, Dimitri" sort="Niks, Dimitri" uniqKey="Niks D" first="Dimitri" last="Niks">Dimitri Niks</name><name sortKey="Tam, Timothy K" sort="Tam, Timothy K" uniqKey="Tam T" first="Timothy K" last="Tam">Timothy K. Tam</name><name sortKey="Yu, Xuejun" sort="Yu, Xuejun" uniqKey="Yu X" first="Xuejun" last="Yu">Xuejun Yu</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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