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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 a representative α/β pair — chain A (α) + chain B (β); residue numbers follow the 1NI4 (PDB-author) numbering. The TPP cofactor and its pocket residues come straight from this structure: His263/Val138/Tyr89 in the C2 pocket, Asp167/Asn196/Tyr198 coordinating the structural Mg²⁺, Arg90 in direct contact with the pyrophosphate (2.6 Å), and β-subunit Glu59 rowing up against the cofactor.
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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 E2 core alone — 7B9K is the E. coli E2p cubic core (24-mer, lipoyl domains included), not the intact complex — captured by cryo-EM to show the channeling mechanism by which lipoyl domains insert into the E2 catalytic domain (Škerlová J et al., Nat Commun 2021, PMID:34489474). It is cited here for the channeling principle only; the E2 transacetylase pocket on screen is drawn schematically. The E1 α/β interface seen in 1NI4 is the same catalytic unit.
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E1 ① — Pyruvate arrives
Pyruvate docks beside the TPP thiazolium C2 in the His263-lined pocket. The TPP scaffold and pocket residues are the real 1NI4 coordinates; the pyruvate pose is [schematic].Source: TPP scaffold & pocket residues — PDB 1NI4 (Ciszak 2003, PMID:12651851, measured); pyruvate pose [schematic] (Fidelity card, no E1·pyruvate co-crystal)
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E1 ② — Ylide attack → decarboxylation
The TPP C2-ylide attacks the pyruvate keto carbon; the transient lactyl-TPP (LThDP) loses CO₂ at once — the step that makes the direction effectively irreversible (a specific rate-limiting assignment is not re-verified this review) — leaving hydroxyethylidene-TPP (HE-TPP), cross-faded in place with CO₂ budding off beside it. The tautomer/proton path is (hypothetical, lit.-based); the arrow and traveling marker trace the drawn trajectory.Source: E1 TPP mechanism (ylide attack → LThDP → decarboxylation → HE-TPP) — Patel et al. 2014 review (PMID:24798336); tautomer/proton path is hypothetical, lit.-based — this card; LThDP transient & CO₂ departure = drawn schematic
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E1 ③ — Lipoamide arm swings in
The oxidized lipoamide disulfide (E2's tethered swinging arm) rotates to the E1 site to accept the two-carbon unit. [schematic].Source: lipoamide = covalently tethered "swinging arm" per Overall reaction card; arm rotation to E1 — Patel et al. 2014 (PMID:24798336); pose & rotation [schematic] (Fidelity card, mesh static)
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E1 ④ — Reductive acetylation → SLIPO
The two-carbon unit transfers onto the disulfide arm — S–S reduced, S-acetyldihydrolipoamide cross-fading in as the marker flies — with TPP regenerated behind it. His263★ lines the pocket (proposed role — not a general base).Source: reductive acetylation → S-acetyldihydrolipoamide, TPP regenerated — Patel et al. 2014 (PMID:24798336); His263 role = proposed pocket-lining, measured 4.07 Å off TPP C2 (1NI4, manifest geomClaim)
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E1 ⑤ — Acetylated arm departs
S-acetyldihydrolipoamide swings away toward the E2 site — a tethered swing, not free diffusion.Source: tethered arm is covalently bound to E2 Lys ε-amino (Overall reaction card); swing [schematic] — Fidelity card (mesh static, no co-crystal); direction toward E2 — Patel et al. 2014 (PMID:24798336)
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E2 ① — Acetylated arm arrives
The acetylated arm reaches the E2 pocket — a [schematic] pocket drawn on the E1 frame.Source: E2 pocket drawn schematically on the E1 frame (Fidelity card — no human E2 pocket co-crystallized); channeling principle only from 7B9K (Škerlová 2021, PMID:34489474)
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E2 ② — CoA-SH arrives
CoA-SH docks with its thiol poised at the arm's thioester. [schematic].Source: transacetylation step (CoA-SH ↔ acetylated arm thioester) — Patel et al. 2014 (PMID:24798336); CoA-SH pose [schematic] (Fidelity card, no E2·CoA co-crystal)
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E2 ③ — Transacetylation → acetyl-CoA
CoA sulfur attacks the thioester: acetyl-CoA (the TCA fuel) forms in place while the arm is left reduced as dihydrolipoamide. Magenta marker and blue arrow trace CoA-S → thioester-C.Source: transacetylation → acetyl-CoA + dihydrolipoamide — Patel et al. 2014 (PMID:24798336); acetyl-CoA as TCA fuel — Overall reaction card; chemistry drawn schematically
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E2 ④ — Products depart
Acetyl-CoA leaves for the TCA cycle; the dihydrolipoamide arm swings on to the E3 site.Source: acetyl-CoA → TCA, dihydrolipoamide → E3 — Overall reaction card / Patel et al. 2014 (PMID:24798336); departures are display poses, no measured exit geometry
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E3 ① — Reduced arm arrives
Dihydrolipoamide reaches the E3 site beside the genuine FAD (1ZY8). The arm pose is [schematic].Source: genuine FAD + E3 DLD homodimer — real crystal coordinates, PDB 1ZY8 (2.59 Å, X-ray; cited on this page, no link in whitelist); reduced-arm pose [schematic] (Fidelity card, no E3·arm co-crystal)
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E3 ② — NAD⁺ arrives
NAD⁺ docks as the electron acceptor. No nucleotide is co-crystallized in 1ZY8 — [schematic].Source: PDB 1ZY8 (2.59 Å, X-ray, cited on page) — cited in Fidelity card: "No nucleotide is co-crystallized with 1ZY8, so the NAD⁺/NADH poses are schematic"; NAD⁺ acceptor role — Patel et al. 2014 (PMID:24798336)
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E3 ③ — Reoxidation → lipoamide + NADH
The lipoyl disulfide re-forms; electrons pass from the arm into the FAD isoalloxazine N5 (arrow tip), then on to NAD⁺ — the enzyme disulfide between arm and flavin is text-only (no Cys sidechains in frame). Magenta marker flies both relay legs (arm → N5, FAD → NAD⁺). A stacked nicotinamide–FAD geometry of this kind is documented in the NADH-bound DLD structure (Bräutigam et al.).Source: electron relay arm → FAD N5 → NAD⁺ — Patel et al. 2014 (PMID:24798336); real FAD — PDB 1ZY8 (2.59 Å, cited on page); stacked nicotinamide–FAD geometry — Bräutigam et al. (this card; no page link)
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E3 ④ — Lipoamide + NADH depart
Lipoamide swings back to E1 for the next acetyl group; NADH feeds the electron transport chain.Source: lipoamide recycle to E1, NADH → ETC — Overall reaction card / Patel et al. 2014 (PMID:24798336); departures are display poses, no measured exit geometry
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Overall reaction
Pyruvate + CoA + NAD⁺ → Acetyl-CoA + CO₂ + NADH + H⁺ (essentially irreversible — a quantitative ΔG°′ ≈ −8 kcal/mol value is withdrawn pending verification, see Kinetics scope). The lipoyl group is covalently bound to a conserved Lys ε-amino group on each E2 lipoyl domain (the "swinging arm").
Legend & Fidelity
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Mechanism fidelity — measured vs. inferred
The measured layer: the E1 protein + TPP + pocket residues (1NI4) and the E3 DLD homodimer + FAD (1ZY8) are deposited coordinates. (In 1NI4 the two αβ dimers pack crosswise in the deposited file — chains A+D and C+B — and each α-pocket's Mg²⁺ is instanced on the partner α-chain, so the metal that anchors the displayed chain-A pocket carries chain letter C; the residue contacts and numbers named on this page are authentic 1NI4 contacts.) The inferred layer: the E2 pocket, every substrate and intermediate pose (pyruvate, LThDP, HE-TPP, the three lipoyl-arm states, CoA, acetyl-CoA, NAD⁺/NADH), the tautomer/proton path, and the arm swing path are literature-based reconstructions, labeled [schematic] where shown.
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Why are the arm and the E2 pocket "[schematic]"?
Three gaps force it. (1) No human E2 catalytic pocket is co-crystallized in this frame — the E2 tab draws a schematic pocket on the E1 frame, and 7B9K (E. coli E2p core) is cited for the channeling principle only. (2) The lipoyl arm is a protein domain tethered to the E2 core, but the mesh is static — its large rotation is summarized by the moving S–S group, not a true domain swing. (3) No nucleotide is co-crystallized with 1ZY8, so the NAD⁺/NADH poses are schematic even though the FAD beside them is real.
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Physiological regulation
Regulated by covalent modification: pyruvate dehydrogenase kinase (PDK) phosphorylates and inactivates E1; PDH phosphatase (PDP) dephosphorylates and reactivates. Dichloroacetate inhibits PDK and thereby holds PDH on. — see Patel et al. 2014 review (PMID:24798336).
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Kinetics scope
This tool animates a single catalytic event; it does not model timecourses, steady-state kinetics, or Km / kcat / Vmax behavior. The overall reaction is strongly exergonic — effectively irreversible — but no quantitative ΔG°′ value is stated on this page (values quoted in earlier versions are withdrawn pending verification). For enzyme parameters see BRENDA (EC 1.2.4.1 · 2.3.1.12 · 1.8.1.4) — this page's outputs are not kinetic data.
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Sources — bibliography of this page
S1 — PDB 1NI4: human PDH E1 holoenzyme with genuine TPP / Mg²⁺ (deposited coordinates; the two αβ dimers pack crosswise — chains A+D and C+B — and each α-pocket's Mg²⁺ is instanced on the partner α-chain, so the metal anchoring the displayed chain-A pocket carries chain letter C; the residue contacts named on this page are authentic 1NI4 contacts)
S2 — PDB 1ZY8: E3 DLD homodimer with genuine FAD (2.59 Å, X-ray) — deposited coordinates; no nucleotide is co-crystallized, so the NAD⁺/NADH poses are [schematic]; stacked nicotinamide–FAD geometry documented in the NADH-bound DLD structure (Bräutigam et al., this card — no page link)
S3 — E2 channeling principle only: PDB 7B9K (E. coli E2p core), Škerlová et al., 2021, PMID:34489474 — the human E2 catalytic pocket is not co-crystallized in this frame, so the E2 tab draws a schematic pocket on the E1 frame
S4 — Mechanism & regulation review: Patel MS et al. 2014, PMID:24798336 — transacetylation (CoA-SH ↔ acetylated arm thioester), electron relay arm → FAD N5 → NAD⁺, and the PDK phosphorylation / PDP dephosphorylation control of E1; dichloroacetate inhibits PDK
S5 — Kinetics scope: BRENDA EC 1.2.4.1 · 2.3.1.12 · 1.8.1.4 — no quantitative ΔG°′ stated (earlier values withdrawn pending verification)
S6 — Repo display conventions: measured layer = E1 protein + TPP + pocket residues (1NI4) and the E3 DLD homodimer + FAD (1ZY8); every substrate/intermediate pose (pyruvate, LThDP, HE-TPP, the three lipoyl-arm states, CoA, acetyl-CoA, NAD⁺/NADH), the E2 pocket, the tautomer/proton path and the arm swing path are [schematic] literature-based reconstructions (
tools/manifests/pdh.json: 3 geomClaims, 2 narrativeNumbers) · departures are display poses, no measured exit geometry
› The 3D protein is the real E1 holoenzyme (PDB 1NI4) with its genuine TPP / Mg²⁺, and the real E3 DLD homodimer with its genuine FAD (PDB 1ZY8). Substrates, products and the E2 transacetylase pocket are drawn as compact schematic molecules posed at the active-site pockets and are labeled [schematic].