Integrative structure of a 10-megadalton eukaryotic pyruvate dehydrogenase complex from native cell extracts.

Fotis L Kyrilis, Dmitry A Semchonok, Ioannis Skalidis, Christian Tüting, Farzad Hamdi, Francis J O'Reilly, Juri Rappsilber, Panagiotis L Kastritis

Cell reports 2021 Feb 09

filter terms:

The pyruvate dehydrogenase complex (PDHc) is a giant enzymatic assembly involved in pyruvate oxidation. PDHc components have been characterized in isolation, but the complex's quaternary structure has remained elusive due to sheer size, heterogeneity, and plasticity. Here, we identify fully assembled Chaetomium thermophilum α-keto acid dehydrogenase complexes in native cell extracts and characterize their domain arrangements utilizing mass spectrometry, activity assays, crosslinking, electron microscopy (EM), and computational modeling. We report the cryo-EM structure of the PDHc core and observe unique features of the previously unknown native state. The asymmetric reconstruction of the 10-MDa PDHc resolves spatial proximity of its components, agrees with stoichiometric data (60 E2p:12 E3BP:∼20 E1p: ≤ 12 E3), and proposes a minimum reaction path among component enzymes. The PDHc shows the presence of a dynamic pyruvate oxidation compartment, organized by core and peripheral protein species. Our data provide a framework for further understanding PDHc and α-keto acid dehydrogenase complex structure and function. Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved.

Citation

Fotis L Kyrilis, Dmitry A Semchonok, Ioannis Skalidis, Christian Tüting, Farzad Hamdi, Francis J O'Reilly, Juri Rappsilber, Panagiotis L Kastritis. Integrative structure of a 10-megadalton eukaryotic pyruvate dehydrogenase complex from native cell extracts. Cell reports. 2021 Feb 09;34(6):108727