Arrangement and symmetry of the fungal E3BP-containing core of the pyruvate dehydrogenase complex

B O Forsberg,N Mortezaei,E Lindahl,R J Howard,S Aibara

doi:10.1038/s41467-020-18401-z

Abstract

The pyruvate dehydrogenase complex (PDC) is a multienzyme complex central to aerobic respiration, connecting glycolysis to mitochondrial oxidation of pyruvate. Similar to the E3-binding protein (E3BP) of mammalian PDC, PX selectively recruits E3 to the fungal PDC, but its divergent sequence suggests a distinct structural mechanism. Here, we report reconstructions of PDC from the filamentous fungus Neurospora crassa by cryo-electron microscopy, where we find protein X (PX) interior to the PDC core as opposed to substituting E2 core subunits as in mammals. Steric occlusion limits PX binding, resulting in predominantly tetrahedral symmetry, explaining previous observations in Saccharomyces cerevisiae. The PX-binding site is conserved in (and specific to) fungi, and complements possible C-terminal binding motifs in PX that are absent in mammalian E3BP. Consideration of multiple symmetries thus reveals a differential structural basis for E3BP-like function in fungal PDC.

Highlights

The pyruvate dehydrogenase complex (PDC) is a multienzyme complex central to aerobic respiration, connecting glycolysis to mitochondrial oxidation of pyruvate
Interior to the core assembly, we found an apparently ordered, non-icosahedral PDC component (Fig. 1a), which appears consistent with a mixture of states, incorrectly averaged under icosahedral symmetry
All icosahedral symmetries were attempted. While this alone did not aid the interpretation of the interior density for any such subsymmetry, 3D classification coupled with the application of tetrahedral symmetry yielded a correctly averaged reconstruction symmetry, evidenced by a protein-like density (Fig. 1d) and consistent background in the complementary interior volume

Summary

Introduction

The pyruvate dehydrogenase complex (PDC) is a multienzyme complex central to aerobic respiration, connecting glycolysis to mitochondrial oxidation of pyruvate. Similar to the E3binding protein (E3BP) of mammalian PDC, PX selectively recruits E3 to the fungal PDC, but its divergent sequence suggests a distinct structural mechanism. The pyruvate dehydrogenase complex (PDC) catalyzes the further formation of acetyl-coenzyme A (acetyl-CoA) from pyruvate, enabling the tricarboxylic acid cycle that sustains oxidative phosphorylation. The PDC attracts attention because aerobic fermentation is upregulated in many cancers, while inhibition of the PDC results in decreased mitochondrial glucose oxidation, known as the Warburg effect[3,4]. E1 catalyzes the decarboxylation of pyruvate and transfers the resultant acetyl group to an E2 carrier domain. E2 covalently links this acetyl group to CoA through its catalytic domain. The co-localization of the participating enzymes and substrates increases the overall rate by minimizing substrate diffusion, and tightly couples the chain of reactions[9]

Methods

Results

Conclusion