A nested shell structure coordinates enzyme communication in pyruvate oxidation

The pyruvate dehydrogenase complex (PDHc) ¹ links glycolysis to the Krebs cycle by catalyzing the oxidative decarboxylation of pyruvate to acetyl-CoA and CO₂, a process essential for life ^2,3 . PDHc is formed by structural proteins (E3-binding protein, E3BP) ^4–7 , enzymatic subunits (E1, E2, E3) ^4,6 , and mobile lipoyl domains (LDs), the latter shuttling intermediates across active sites ^6,8 . Although numerous details regarding pyruvate oxidation steps have been elucidated ⁹ , the precise organization of the entire PDHc remains unknown due to its large size and dynamic heterogeneity. Here, we employ in silico , in vitro , and in situ methods to propose a multi-scale model of PDHc that includes approximately one million atoms and to visualize multiple conformational states. This model reveals a ∼40-50 nm nested shell structure, formed by flexible linkers that spatially coordinate the E1 and E3 enzyme complexes around the E2-E3BP core scaffold. This structure acts as a molecular sieve, selectively guiding lipoyl arms while maintaining enzyme positioning with sub-nm precision. During catalysis, the nested shell structure expands and adopts a mechanically reinforced state comparable in magnitude to viral assemblies ¹⁰ . Our findings provide structural context for the textbook “link reaction” ¹¹ , building on decades of biochemical knowledge, are transferable to functional aspects of other α-ketoacid dehydrogenase complexes, and, ultimately, expand our understanding of primary metabolism as a whole.