Structures and comparison of endogenous 2-oxoglutarate and pyruvate dehydrogenase complexes from bovine kidney
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Abstract
The α-keto acid dehydrogenase complex family catalyzes the essential oxidative decarboxylation of α-keto acids to yield acyl-CoA and NADH. Despite performing the same overarching reaction, members of the family have different component structures and structural organization between each other and across phylogenetic species. While native structures of α-keto acid dehydrogenase complexes from bacteria and fungi became available recently, the atomic structure and organization of their mammalian counterparts in native states remain unknown. Here, we report the cryo-electron microscopy structures of the endogenous cubic 2-oxoglutarate dehydrogenase complex (OGDC) and icosahedral pyruvate dehydrogenase complex (PDC) cores from bovine kidney determined at resolutions of 3.5 Å and 3.8 Å, respectively. The structures of multiple proteins were reconstructed from a single lysate sample, allowing direct structural comparison without the concerns of differences arising from sample preparation and structure determination. Although native and recombinant E2 core scaffold structures are similar, the native structures are decorated with their peripheral E1 and E3 subunits. Asymmetric sub-particle reconstructions support heterogeneity in the arrangements of these peripheral subunits. In addition, despite sharing a similar monomeric fold, OGDC and PDC E2 cores have distinct interdomain and intertrimer interactions, which suggests a means of modulating self-assembly to mitigate heterologous binding between mismatched E2 species. The lipoyl moiety lies near a mobile gatekeeper within the interdomain active site of OGDC E2 and PDC E2. Analysis of the twofold related intertrimer interface identified secondary structural differences and chemical interactions between icosahedral and cubic geometries of the core. Taken together, our study provides a direct structural comparison of OGDC and PDC from the same source and offers new insights into determinants of interdomain interactions and of architecture diversity among α-keto acid dehydrogenase complexes.
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A nested shell structure coordinates enzyme communication in pyruvate oxidationPreprint
Träger, T. K., Maity, S., Kyrilis, F. L., Tüting, C., Hamdi, F., Kafetzopoulos, G., Brotzakis, Z. F., Neuhaus, A., Blanqué, A., Gatsogiannis, C., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.12.724543
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Higher-order structural organization of mitochondrial metabolism
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The Pyruvate Dehydrogenase Complex: A 90-Year-Old Enigma Shaping the Future of Structural Enzymology
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- Authors
- Liu, S., Xia, X., Zhen, J., Li, Z., & Zhou, Z. H.
- Affiliations
- California NanoSystems Institute (US)
- Corresponding author
- Zhou, Z. Hong
- Venue
- Cell Discovery
- Published
- 2022-11-22
- Volume
- 8
- Issue
- 1
- Pages
- 126-126
- ISSN
- 2056-5968 (ISSN-L)
- PMC
- PMC9681731
- OpenAlex
- W4309646950
- Cited by
- 29
- References
- 68
- Citations by year
- 2026: 7 · 2025: 5 · 2024: 9 · 2023: 7 · 2022: 1
- FWCI
- 2.33
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Cell Discovery (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- National Science Foundation (DMR-1548924)
- U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (R01GM071940)
- U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (5T32AI060567)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biochemistry › Biochemical Acid Research Studies
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Keywords
- 2-oxoglutarate dehydrogenase, pyruvate dehydrogenase complex, bovine kidney, cryo-EM structure, domain-domain interactions, self-assembly, oxidative decarboxylation
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