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Structure — human E1 (shown in 3D)
Human pyruvate dehydrogenase E1 (α₂β₂ holoenzyme, mature form) bound to its thiamin pyrophosphate (TPP) cofactor and Mg²⁺ — 1NI4 (Ciszak EM, Korotchkina LG, Dominiak PM, Sidhu S & Patel MS, J Biol Chem 2003, PMID:12651851). The 3D protein backbone is chain A (α) + chain B (β); the TPP cofactor and its pocket residues (His263, Val138, Tyr89, Asp167/Asn196 Mg²⁺-anchor, Arg90 pyrophosphate) come straight from this structure.
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Mechanism review — E1/E2/E3 catalysis & regulation
Comprehensive account of the PDH-complex reaction (five transfer steps), cofactors (TPP, lipoamide on the Lys "swinging arm", CoA, FAD, NAD⁺), and regulation by PDK phosphorylation / PDP dephosphorylation — Patel MS, Nemeria NS, Furey W & Jordan F, "The pyruvate dehydrogenase complexes: structure-based function and regulation", J Biol Chem 2014, PMID:24798336.
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Native complex cryo-EM — where E1/E2/E3 sit together
The intact ~9.5 MDa PDH complex (multiple E1/E2/E3 copies around an icosahedral E2 core), showing that E2 is the scaffold whose lipoyl domains rotate to ferry the acetyl group between the E1, E2-catalytic, and E3 active sites — 7B9K (Škerlová J et al., Nat Commun 2021, PMID:34489474). The E1 α/β interface seen in 1NI4 is the same catalytic unit; E2's transacetylase and E3's dehydrogenase active sites are drawn schematically on this frame, each clearly labeled [schematic].
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① E1 — decarboxylation (pyruvate → CO₂ + hydroxyethyl-TPP)
TPP thiazolium C2 (the reactive ylide carbon) attacks the pyruvate carbonyl, and the bound pyruvate loses CO₂ to give hydroxyethylidene-TPP — the reactive two-carbon adduct. This is the rate-limiting, irreversible step; it also dictates substrate specificity for pyruvate. [schematic substrate; the TPP scaffold itself is the real 1NI4 cofactor.]
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② E1 — reductive acetylation (HE-TPP + lipoamide)
The reactive C2 unit is transferred to the oxidized lipoamide disulfide (the S–S "swinging arm"), reducing it and giving S-acetyldihydrolipoamide while regenerating TPP. [schematic lipoyl arm.]
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③ E2 — transacetylation (→ acetyl-CoA)
At the E2 (dihydrolipoyl transacetylase) active site, CoA-SH attacks the S-acetyl thioester, yielding acetyl-CoA (the TCA fuel) and dihydrolipoamide (the reduced arm). Active-site thioester chemistry; [schematic].
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④ E3 — reoxidation (NAD⁺ → NADH)
At the E3 (dihydrolipoyl dehydrogenase) active site, the reduced dihydrolipoamide is reoxidized to lipoamide (disulfide) via the enzyme's FAD, and the electrons pass to NAD⁺ to give NADH + H⁺ — the arm's electron sink that harvests reducing equivalents. [schematic.]
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Overall reaction & regulation
Pyruvate + CoA + NAD⁺ → Acetyl-CoA + CO₂ + NADH + H⁺ (ΔG°′ ≈ −8 kcal/mol; essentially irreversible). Regulated by covalent modification: pyruvate dehydrogenase kinase (PDK) phosphorylates/inactivates E1; PDH phosphatase (PDP) reactivates. Dichloroacetate inhibits PDK and thereby holds PDH on. Single-letter cofactor note: the lipoyl group is covalently bound to a conserved Lys ε-amino group on each E2 lipoyl domain (the "swinging arm"). — see Patel et al. 2014 review (PMID:24798336).
› The 3D protein is the real E1 holoenzyme (PDB 1NI4) with its genuine TPP / Mg²⁺. Substrates, products and the E2/E3 arm chemistry are drawn as compact schematic molecules posed at the active-site pocket and are labeled [schematic].