8OIU
Cryo-EM reconstruction of the native 24-mer E2o core of the 2-oxoglutarate dehydrogenase complex of C. thermophilum at 3.35 A resolution
Summary for 8OIU
| Entry DOI | 10.2210/pdb8oiu/pdb |
| EMDB information | 16900 |
| Descriptor | Dihydrolipoyllysine-residue succinyltransferase (1 entity in total) |
| Functional Keywords | dihydrolipoyl succinyltransferase, e2, oxoglutarate, a-ketoglutarate, transferase |
| Biological source | Thermochaetoides thermophila DSM 1495 |
| Total number of polymer chains | 1 |
| Total formula weight | 45987.00 |
| Authors | Skalidis, I.,Tueting, C.,Kyrilis, F.L.,Hamdi, F.,Kastritis, P.L. (deposition date: 2023-03-23, release date: 2023-05-31, Last modification date: 2024-07-24) |
| Primary citation | Skalidis, I.,Kyrilis, F.L.,Tuting, C.,Hamdi, F.,Trager, T.K.,Belapure, J.,Hause, G.,Fratini, M.,O'Reilly, F.J.,Heilmann, I.,Rappsilber, J.,Kastritis, P.L. Structural analysis of an endogenous 4-megadalton succinyl-CoA-generating metabolon. Commun Biol, 6:552-552, 2023 Cited by PubMed Abstract: 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. PubMed: 37217784DOI: 10.1038/s42003-023-04885-0 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.35 Å) |
Structure validation
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