Structure of the dihydrolipoamide succinyltransferase (E2) component of the human alpha-ketoglutarate dehydrogenase complex (hKGDHc) revealed by cryo-EM and cross-linking mass spectrometry

https://m2.mtmt.hu/ hun 2026-09-22 07:55 JournalArticle 31917407 VALIDATED true Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary Central European Institute of Technology, Masaryk University, Brno, Czech Republic Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ, United States Export Date: 18 March 2021 CODEN: BBGSB Correspondence Address: Ambrus, A.; Department of Biochemistry, Budapest, 37-47 Tuzolto St., Hungary; email: ambrus.attila@med.semmelweis-univ.hu Funding details: National Institutes of Health, NIH, GM050380, LM2018127, R15-GM116077 Funding details: Magyar Tudományos Akadémia, MTA, 02001 Funding details: Semmelweis Egyetem Funding details: Ministerstvo Školství, Mládeže a Tělovýchovy, MŠMT Funding details: Hungarian Scientific Research Fund, OTKA Funding details: Magyar Tudományos Akadémia, MTA Funding details: Hungarian Scientific Research Fund, OTKA, 112230 Funding details: 61826 690289, 61830Z0100 EATV Funding details: 2017-1.2.1-NKP-2017-00002, KTIA_13_NAP-A-III/6 Funding text 1: Financial support was secured from the Hungarian Academy of Sciences (MTA grant 02001 to V.A-V.), Hungarian Scientific Research Fund (OTKA grant 112230 to V.A-V.), Hungarian Brain Research Program (grants KTIA_13_NAP-A-III/6 and 2017-1.2.1-NKP-2017-00002 to V.A-V.), Young Investigator Research Grants of Semmelweis University and Chemical Works of Gedeon Richter Plc. (to A.A.), Hungarian Higher Education Institution Excellence Program (FIKP grants 61826 690289 EATV and 61830Z0100 EATV to A.A.) and National Institutes of Health (grants GM050380 and R15-GM116077 to F. J.). CIISB research infrastructure project LM2018127 funded by MEYS CR is gratefully acknowledged for the financial support of the measurements at the CF Cryo-electron Microscopy and Tomography. Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary Central European Institute of Technology, Masaryk University, Brno, Czech Republic Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ, United States Export Date: 29 March 2021 CODEN: BBGSB Correspondence Address: Ambrus, A.; Department of Biochemistry, Budapest, 37-47 Tuzolto St., Hungary; email: ambrus.attila@med.semmelweis-univ.hu Funding details: National Institutes of Health, NIH, GM050380, LM2018127, R15-GM116077 Funding details: Magyar Tudományos Akadémia, MTA, 02001 Funding details: Ministerstvo Školství, Mládeže a Tělovýchovy, MŠMT Funding details: Hungarian Scientific Research Fund, OTKA Funding details: Magyar Tudományos Akadémia, MTA Funding details: Hungarian Scientific Research Fund, OTKA, 112230 Funding details: 61826 690289, 61830Z0100 EATV Funding text 1: Financial support was secured from the Hungarian Academy of Sciences (MTA grant 02001 to V.A-V.), Hungarian Scientific Research Fund (OTKA grant 112230 to V.A-V.), Hungarian Brain Research Program (grants KTIA_13_NAP-A-III/6 and 2017-1.2.1-NKP-2017-00002 to V.A-V.), Young Investigator Research Grants of Semmelweis University and Chemical Works of Gedeon Richter Plc . (to A.A.), Hungarian Higher Education Institution Excellence Program (FIKP grants 61826 690289 EATV and 61830Z0100 EATV to A.A.) and National Institutes of Health (grants GM050380 and R15-GM116077 to F. J.). CIISB research infrastructure project LM2018127 funded by MEYS CR is gratefully acknowledged for the financial support of the measurements at the CF Cryo-electron Microscopy and Tomography. Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary Central European Institute of Technology, Masaryk University, Brno, Czech Republic Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ, United States Export Date: 30 March 2021 CODEN: BBGSB Correspondence Address: Ambrus, A.; Department of Biochemistry, Budapest, 37-47 Tuzolto St., Hungary; email: ambrus.attila@med.semmelweis-univ.hu Funding details: National Institutes of Health, NIH, GM050380, LM2018127, R15-GM116077 Funding details: Magyar Tudományos Akadémia, MTA, 02001 Funding details: Ministerstvo Školství, Mládeže a Tělovýchovy, MŠMT Funding details: Hungarian Scientific Research Fund, OTKA Funding details: Magyar Tudományos Akadémia, MTA Funding details: Hungarian Scientific Research Fund, OTKA, 112230 Funding details: 61826 690289, 61830Z0100 EATV Funding text 1: Financial support was secured from the Hungarian Academy of Sciences (MTA grant 02001 to V.A-V.), Hungarian Scientific Research Fund (OTKA grant 112230 to V.A-V.), Hungarian Brain Research Program (grants KTIA_13_NAP-A-III/6 and 2017-1.2.1-NKP-2017-00002 to V.A-V.), Young Investigator Research Grants of Semmelweis University and Chemical Works of Gedeon Richter Plc . (to A.A.), Hungarian Higher Education Institution Excellence Program (FIKP grants 61826 690289 EATV and 61830Z0100 EATV to A.A.) and National Institutes of Health (grants GM050380 and R15-GM116077 to F. J.). CIISB research infrastructure project LM2018127 funded by MEYS CR is gratefully acknowledged for the financial support of the measurements at the CF Cryo-electron Microscopy and Tomography. 0 false 2026-05-27T12:26:03.424+0000 2022-11-16T13:22:05.965+0000 2021-03-16T08:56:51.441+0000 true 10054198 xBökönyi Zita /api/admin/10054198 Admin xBökönyi Zita (INAKTÍV_SE_AOK_OBI_Admin5_BZ, admin) true 10054198 2026-05-27T12:22:12.784+0000 2026-05-27T12:22:12.784+0000 2021-04-08T16:59:27.096+0000 true 10003134 Wolf György /api/admin/10003134 Admin Wolf György (MTMT Központi admin) true 10003134 2021-10-06T07:36:23.924+0000 true 10067876 Ladányi Gusztáv /api/admin/10067876 Admin Ladányi Gusztáv (MTMT API user, admin) true Admin 10003134 /api/admin/10003134 Wolf György (MTMT Központi admin) Wolf György true 10003134 true 2021-04-07T11:25:08.372+0000 true false true 24 24 /api/publicationtype/24 PublicationType Folyóiratcikk 1 true 24 JournalArticle true 10000059 Article true 24 24 /api/publicationtype/24 PublicationType Folyóiratcikk 1 true 24 JournalArticle /api/subtype/10000059 Szakcikk SubType Szakcikk (Folyóiratcikk) 101 true 10000059 true 1 /api/category/1 Category Tudományos true 1 Nagy, Balint Structure of the dihydrolipoamide succinyltransferase (E2) component of the human alpha-ketoglutarate dehydrogenase complex (hKGDHc) revealed by cryo-EM and cross-linking mass spectrometry Implications for the overall hKGDHc structure. true true /api/journal/27243 REVIEWED BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS 0304-4165 1872-8006 true false 27243 false 27243 true 0304-4165 1872-8006 Journal FOREIGN 1865 6 129889 129889 17 2021 The human mitochondrial alpha-ketoglutarate dehydrogenase complex (hKGDHc) converts KG to succinyl-CoA and NADH. Malfunction of and reactive oxygen species generation by the hKGDHc as well as its E1-E2 subcomplex are implicated in neurodegenerative disorders, ischemia-reperfusion injury, E3-deficiency and cancers.We performed cryo-EM, cross-linking mass spectrometry (CL-MS) and molecular modeling analyses to determine the structure of the E2 component of the hKGDHc (hE2k); hE2k transfers a succinyl group to CoA and forms the structural core of hKGDHc. We also assessed the overall structure of the hKGDHc by negative-stain EM and modeling.We report the 2.9 Å resolution cryo-EM structure of the hE2k component. The cryo-EM map comprises density for hE2k residues 151-386 - the entire (inner) core catalytic domain plus a few additional residues -, while residues 1-150 are not observed due to the inherent flexibility of the N-terminal region. The structure of the latter segment was also determined by CL-MS and homology modeling. Negative-stain EM on in vitro assembled hKGDHc and previous data were used to build a putative overall structural model of the hKGDHc.The E2 core of the hKGDHc is composed of 24 hE2k chains organized in octahedral (8 × 3 type) assembly. Each lipoyl domain is oriented towards the core domain of an adjacent chain in the hE2k homotrimer. hE1k and hE3 are most likely tethered at the edges and faces, respectively, of the cubic hE2k assembly.The revealed structural information will support the future pharmacologically targeting of the hKGDHc. 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Biokémiai és Molekuláris Biológiai Intézet (SE / AOK / I); Orvosi Biokémiai Intézet (SE / AOK / I) 7 24 3 10 0 true 10003134 Language 10002 /api/language/10002 Angol Angol English true 2 true PersonAuthorship 95701054 /api/authorship/95701054 Nagy, Balint [Csuka Nagy, Bálint (szerkezeti biokémia), szerző] Biokémiai és Molekuláris Biológiai Intézet (SE / AOK / I); Biokémiai Tanszék (SE / AOK / I / BMBI) 1 0.1 true false false Author 10059307 /api/author/10059307 Csuka Nagy Bálint (szerkezeti biokémia) Csuka Nagy Bálint true 10059307 true Nagy Balint true false false AuthorshipType 1 /api/authorshiptype/1 Szerző 0 true 0 true false true PersonAuthorship 95701055 /api/authorship/95701055 Polak, Martin 2 0.1 false false false Polak Martin true false false AuthorshipType 1 /api/authorshiptype/1 Szerző 0 true 0 true false true PersonAuthorship 95701056 /api/authorship/95701056 Ozohanics, Oliver [Ozohanics, Olivér (Tömegspektrometria), szerző] Biokémiai és Molekuláris Biológiai Intézet (SE / AOK / I); Biokémiai Tanszék (SE / AOK / I / BMBI) 3 0.1 false false false Author 10014144 /api/author/10014144 Ozohanics Olivér (Tömegspektrometria) Ozohanics Olivér true 10014144 true Ozohanics Oliver true false false AuthorshipType 1 /api/authorshiptype/1 Szerző 0 true 0 true false true PersonAuthorship 95701057 /api/authorship/95701057 Zambo, Zsofia [Zámbó, Zsófia Melinda (biokémia), szerző] Biokémiai és Molekuláris Biológiai Intézet (SE / AOK / I); Biokémiai Tanszék (SE / AOK / I / BMBI) 4 0.1 false false false Author 10060538 /api/author/10060538 Zámbó Zsófia Melinda (biokémia) Zámbó Zsófia Melinda true 10060538 true Zambo Zsofia true false false AuthorshipType 1 /api/authorshiptype/1 Szerző 0 true 0 true false true PersonAuthorship 95701058 /api/authorship/95701058 Szabo, Eszter [Szabó, Eszter (biokémia), szerző] Biokémiai és Molekuláris Biológiai Intézet (SE / AOK / I); Biokémiai Tanszék (SE / AOK / I / BMBI) 5 0.1 false false false Author 10060658 /api/author/10060658 Szabó Eszter (biokémia) Szabó Eszter true 10060658 true Szabo Eszter true false false AuthorshipType 1 /api/authorshiptype/1 Szerző 0 true 0 true false true PersonAuthorship 95701059 /api/authorship/95701059 Hubert, Agnes [Hubert, Ágnes (biokémia), szerző] Orvosi Biokémiai Intézet (SE / AOK / I) 6 0.1 false false false Author 10050261 /api/author/10050261 Hubert Ágnes (biokémia) Hubert Ágnes true 10050261 true Hubert Agnes true false false AuthorshipType 1 /api/authorshiptype/1 Szerző 0 true 0 true false true PersonAuthorship 95701060 /api/authorship/95701060 Jordan, Frank 7 0.1 false false false Jordan Frank true false false AuthorshipType 1 /api/authorshiptype/1 Szerző 0 true 0 true false true PersonAuthorship 95701061 /api/authorship/95701061 Novaček, Jiří 8 0.1 false false false Novaček Jiří true false false AuthorshipType 1 /api/authorshiptype/1 Szerző 0 true 0 true false true PersonAuthorship 95701062 /api/authorship/95701062 Adam-Vizi, Vera [Ádám, Veronika (idegtudomány, bio...), szerző] Biokémiai és Molekuláris Biológiai Intézet (SE / AOK / I); 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Structure of the dihydrolipoamide succinyltransferase (E2) component of the human alpha-ketoglutarate dehydrogenase complex (hKGDHc) revealed by cryo-EM and cross-linking mass spectrometry: Implications for the overall hKGDHc structure.. (2021) BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS 0304-4165 1872-8006 1865 6<div class="JournalArticle Publication long-list"> <div class="authors"> <img title="Forrásközlemény" style="float: left" src="/frontend/resources/grid/publication-core-icon.png"> <img title="Idézőközlemény" style="float: left" src="/frontend/resources/grid/publication-citation-icon.png"> <div class="autype autype0"> <a href="/gui2/?type=authors&mode=browse&sel=10059307" target="_blank">Nagy Balint (Csuka Nagy Bálint szerkezeti biokémia) </a> SE/AOK/I/Biokémiai és Molekuláris Biológiai Intézet; SE/AOK/I/BMBI/Biokémiai Tanszék ;    Polak Martin ;    <a href="/gui2/?type=authors&mode=browse&sel=10014144" target="_blank">Ozohanics Oliver (Ozohanics Olivér Tömegspektrometria) </a> SE/AOK/I/Biokémiai és Molekuláris Biológiai Intézet; SE/AOK/I/BMBI/Biokémiai Tanszék ;    <a href="/gui2/?type=authors&mode=browse&sel=10060538" target="_blank">Zambo Zsofia (Zámbó Zsófia Melinda biokémia) </a> SE/AOK/I/Biokémiai és Molekuláris Biológiai Intézet; SE/AOK/I/BMBI/Biokémiai Tanszék ;    <a href="/gui2/?type=authors&mode=browse&sel=10060658" target="_blank">Szabo Eszter (Szabó Eszter biokémia) </a> SE/AOK/I/Biokémiai és Molekuláris Biológiai Intézet; SE/AOK/I/BMBI/Biokémiai Tanszék ;    <a href="/gui2/?type=authors&mode=browse&sel=10050261" target="_blank">Hubert Agnes (Hubert Ágnes biokémia) </a> SE/AOK/I/Orvosi Biokémiai Intézet ;    Jordan Frank ;    Novaček Jiří ;    <a href="/gui2/?type=authors&mode=browse&sel=10000397" target="_blank">Adam-Vizi Vera (Ádám Veronika idegtudomány, biokémia) </a> SE/AOK/I/Biokémiai és Molekuláris Biológiai Intézet; SE/AOK/I/BMBI/Biokémiai Tanszék ;    <a href="/gui2/?type=authors&mode=browse&sel=10000177" target="_blank">Ambrus Attila ✉ (Ambrus Attila Biokémia) </a> SE/AOK/I/Biokémiai és Molekuláris Biológiai Intézet; SE/AOK/I/BMBI/Biokémiai Tanszék </div> </div> <div class="title"><a href="/gui2/?mode=browse&params=publication;31917407" target="_blank">Structure of the dihydrolipoamide succinyltransferase (E2) component of the human alpha-ketoglutarate dehydrogenase complex (hKGDHc) revealed by cryo-EM and cross-linking mass spectrometry : Implications for the overall hKGDHc structure..</a></div> <div> BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (<a target="_blank" href="https://portal.issn.org/resource/ISSN/0304-4165">0304-4165</a> <a target="_blank" href="https://portal.issn.org/resource/ISSN/1872-8006">1872-8006</a>): 1865 6 Paper 129889. 17 p. (2021) </div> <div class="pub-footer"> Nyelv: Angol | <a style="color:blue" title="10.1016/j.bbagen.2021.129889" target="_blank" href="https://doi.org/10.1016/j.bbagen.2021.129889"> DOI </a> <a style="color:blue" title="000640021000013" target="_blank" href="https://www.webofscience.com/wos/woscc/full-record/000640021000013"> WoS </a> <a style="color:blue" title="85102280127" target="_blank" href="http://www.scopus.com/record/display.url?origin=inward&eid=2-s2.0-85102280127"> Scopus </a> <a style="color:blue" title="33684457" target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=33684457&dopt=Abstract"> PubMed </a> <a style="color:blue" title="https://www.scopus.com/inward/record.uri?eid=2-s2.0-85102280127&doi=10.1016%2Fj.bbagen.2021.129889&partnerID=40&md5=8691a113f1e16ee12609d0527cb56018" target="_blank" href="https://www.scopus.com/inward/record.uri?eid=2-s2.0-85102280127&doi=10.1016%2Fj.bbagen.2021.129889&partnerID=40&md5=8691a113f1e16ee12609d0527cb56018"> Egyéb URL </a> <a style="color:blue" title="https://www.scopus.com/pages/publications/85102280127?origin=resultslist" target="_blank" href="https://www.scopus.com/pages/publications/85102280127?origin=resultslist"> Egyéb URL </a> <OnlyViewableByAuthor><div class="ratings"> <div class="journal-subject">Folyóirat szakterülete: Scopus - Biophysics   SJR indikátor: Q1</div> <div class="journal-subject">Folyóirat szakterülete: Scopus - Biochemistry   SJR indikátor: Q2</div> <div class="journal-subject">Folyóirat szakterülete: Scopus - Molecular Biology   SJR indikátor: Q2</div> </div></OnlyViewableByAuthor> <div class="publication-citation" style="margin-left: 0.5cm;"> Nyilvános idéző összesen: 28 | Független: 24 | Függő: 4 | Nem jelölt: 0 | WoS jelölt: 27 | Scopus jelölt: 27 | WoS/Scopus jelölt: 28 | DOI jelölt: 28 </div> <div class="publication-citation"> <a target="_blank" href="/api/publication?cond=citations.related;eq;31917407&sort=publishedYear,desc&sort=title"> Idézett közlemények száma: 17 </a> </div> <div class="mtid">Közlemény: 31917407 | Egyeztetett Forrás Idéző | Folyóiratcikk ( Szakcikk ) | Tudományos | kézi felvitel </div> <div class="funder"> (MTA TKI 02001), (112230) Támogató: OTKA, (KTIA_13_NAP-A-III/6), Hungarian National Brain Research Program(2017-1.2.1-NKP-2017-00002), (61826 690289 EATV), (61830Z0100 EATV) </div> <div class="lastModified">Utolsó módosítás: 2022.11.16. 14:22 Kovács Marcell (MTMT Közp., admin) </div> <div class="lockedBy">Központi kezelésű 2021.04.07. 13:25 Wolf György (MTMT Központi admin) </div> <pre class="comment" style="margin-top: 0; margin-bottom: 0;">Megjegyzés: Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary Central European Institute of Technology, Masaryk University, Brno, Czech Republic Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ, United States Export Date: 18 March 2021 ...</pre> </div></div>