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

Research output: Contribution to journalArticlepeer-review

Abstract

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.
Original languageEnglish
Article number108727
JournalCell Reports
Volume34
Issue number6
DOIs
Publication statusPublished - 9 Feb 2021

Keywords

  • native cell extracts
  • cellular homogenates
  • keto acid dehydrogenase complexes
  • negative staining
  • cryo-EM
  • image processing
  • integrative structural biology
  • pyruvate dehydrogenase factory model

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