Structural analysis of an endogenous 4-megadalton succinyl-CoA-generating metabolon

• Published in: Communications biology Vol. 6; no. 1; p. 552
• Main Authors: Skalidis, Ioannis, Kyrilis, Fotis L., Tüting, Christian, Hamdi, Farzad, Träger, Toni K., Belapure, Jaydeep, Hause, Gerd, Fratini, Marta, O’Reilly, Francis J., Heilmann, Ingo, Rappsilber, Juri, Kastritis, Panagiotis L.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 22.05.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 101/1; 101/28; 101/58; 14/19; 14/63; 38; 38/77; 631/45/535/1258/1259; 631/45/607; 631/535/1258/1259; 631/553/2710; 82/16; 82/29; 82/83; Acyl Coenzyme A - metabolism; Biology; Biomedical and Life Sciences; Citric Acid Cycle; Cytoplasm; Dehydrogenases; Hydrogen bonding; Ketoglutarate Dehydrogenase Complex - chemistry; Ketoglutarate Dehydrogenase Complex - metabolism; Ketoglutaric acid; Life Sciences; Structure-function relationships; Succinyl-CoA; Tricarboxylic acid cycle
• ISSN: 2399-3642; 2399-3642
• DOI: 10.1038/s42003-023-04885-0

The oxoglutarate dehydrogenase complex (OGDHc) participates in the tricarboxylic acid cycle and, in a multi-step reaction, decarboxylates α-ketoglutarate, transfers succinyl to CoA, and reduces NAD+. Due to its pivotal role in metabolism, OGDHc enzymatic components have been studied in isolation; however, their interactions within the endogenous OGDHc remain elusive. Here, we discern the organization of a thermophilic, eukaryotic, native OGDHc in its active state. By combining biochemical, biophysical, and bioinformatic methods, we resolve its composition, 3D architecture, and molecular function at 3.35 Å resolution. We further report the high-resolution cryo-EM structure of the OGDHc core (E2o), which displays various structural adaptations. These include hydrogen bonding patterns confining interactions of OGDHc participating enzymes (E1o-E2o-E3), electrostatic tunneling that drives inter-subunit communication, and the presence of a flexible subunit (E3BPo), connecting E2o and E3. This multi-scale analysis of a succinyl-CoA-producing native cell extract provides a blueprint for structure-function studies of complex mixtures of medical and biotechnological value. Summary Multi-scale and integrative structural analyses provide insight into metabolic regulation by the higher-order architecture of the Chaetomium thermophilum oxoglutarate dehydrogenase complex (OGDHc) metabolon.