Glucose-6-phosphate Dehydrogenase - 3D Mechanism Simulator

Loading structural data… (2BH9)

References & Databases

START HERE — how to read G6P + NADP⁺ → 6-phosphoglucono-δ-lactone + NADPH + H⁺ A single oxidation cartoon on the human G6PD pocket. Real crystal: 2BH9 (2.5 Å), a deletion variant with two NADP — catalytic coenzyme (residue 799) and structural NADP (residue 811). G6P is not in 2BH9; the sugar pose is a 2BHL BG6 overlay [schematic]. His263 ★ is the general base. Hydride donor is G6P C1 to nicotinamide C4. The product is the δ-lactone, not 6-phosphogluconate (that is PGLS). Gold H⁺ parks on His263; blue H⁻ is the hydride. Two-crystal stitch distances are not geomClaims. Structural NADP ≠ coenzyme.
Crystal structures PDB 2BH9 — human G6PD deletion variant, 2.5 Å, catalytic + structural NADP (Kotaka 2005). Coordinates are public. PDB 2BHL — same variant + BG6 (β-D-glucose 6-phosphate); no NADP on that frame. There is no deposited ternary. 6E08 (activator + structural NADP) is not this mesh. The structural NADP is the well-observed species of 1QKI (Canton R459L, Au 2000): its nicotinamide is fully buried with no hydride access and it sits at/under the dimer interface (Asp421) — the stability site, not a catalytic one.Source: PDB 2BH9 · PDB 1QKI (structural NADP site)
Mechanism — His general base, hydride to C4, δ-lactone product Kotaka et al., Acta Crystallogr D 2005, PMID:15858258 — two NADP sites; His263 as catalytic base. Au et al., Structure 2000, PMID:10745013 — structural NADP and Canton/deficiency context. Hydride leaves G6P C1 for NADP C4; the immediate product is 6-phospho-D-glucono-1,5-lactone (UniProt P11413 · Rhea 15841). PGLS hydrolyses that lactone. Source: Kotaka 2005 · Au 2000 · UniProt P11413
0 — Setup: two NADP, catalytic pocket shown empty 2BH9 holds catalytic NADP (799) + structural NADP (811). The catalytic pocket is shown empty so ordered binding can start. Structural NADP stays visible as a named occupant. Opaque, run:null (no autoplay). His263 ★ is the general base. 2BH9 is a deletion variant.Source: PDB 2BH9
① — Catalytic NADP⁺ binds (residue 799) Crystal catalytic NADP docks. Nicotinamide C4 is the hydride acceptor. Structural NADP does not move. His263 NE2 ⋯ C4N = 8.29 Å on this binary (measured on 2BH9; no G6P in the deposit). NADP-first order is compiled staging, not a fit.Source: 2BH9 NAP 799 pose
② — G6P binds (2BHL overlay) BG6 from 2BHL is seated on the 2BH9 mesh — [schematic] overlay, not a ternary. C1-OH faces His263. Overlay contacts are teaching geometry, not geomClaims. Product of this enzyme is the δ-lactone, not 6-phosphogluconate.Source: 2BHL BG6 overlay onto 2BH9 (Cα RMSD 1.00 Å)
③ — His263 ★ abstracts the C1-OH proton (hypothetical, lit.-based) A gold H⁺ sphere rides a gold arrow from G6P O1 to His263 NE2 and parks. The alkoxide label is a teaching overlay. Compiled G6PD writes this proton transfer with the hydride; this page splits them.Source: Kotaka 2005 · Au 2000 (His263 as base)
④ — Hydride C1 → NADP⁺ C4 → lactone + NADPH (hypothetical, lit.-based) Blue H⁻ (hydride) rides from G6P C1 to NADP C4N. G6P fades in place to schematic δ-lactone; NADP⁺ relabels NADPH. Parked gold H⁺ stays on His263. Overlay C1⋯C4N is a two-crystal stitch, not a measured hydride Å. Slow-motion on purpose.Source: compiled G6PD C1→C4 · UniProt P11413 lactone product
⑤ — H⁺ released — His263 regenerates (hypothetical, lit.-based) The parked gold H⁺ leaves to solvent. Net stoichiometry still needs that H⁺ (EC 1.1.1.49).Source: EC 1.1.1.49 net H⁺
⑥ — Lactone + NADPH leave — PGLS is next [schematic] The δ-lactone and NADPH depart in opposite directions. Structural NADP stays. The lactone is the substrate of PGLS; NADPH is the committed PPP payoff.Source: PPP bookkeeping

How to read this page — a first-pass primer First pass: Setup (structural NADP present, catalytic pocket empty, His263 ★) → ① catalytic NADP⁺ docks → ② G6P overlay docks → ③ gold H⁺ O1 → NE2 (parks) → ④ blue hydride C1 → C4N, G6P becomes δ-lactone, NADP⁺ becomes NADPH → ⑤ gold H⁺ leaves → ⑥ lactone and NADPH leave opposite ways. Second pass: 8.29 Å is a crystal fact on 2BH9; G6P and the H spheres are [schematic]. Third pass: open “Disagreements” for two NADP sites, overlay vs ternary, and concerted vs split.
Chemistry primer — NADP⁺-dependent oxidation to a lactone G6P is a C6 aldose phosphate. Removing the C1-OH proton and the C1 hydride leaves a carbonyl at C1 that is still closed as a six-membered lactone (6-phospho-D-glucono-1,5-lactone). NADP⁺ accepts that hydride at nicotinamide C4. Net H⁺ is released to solvent. Gold = H⁺. Blue = hydride H⁻. 6-Phosphogluconate is made by the next enzyme (PGLS), not here.
Words used on screen — structural NADP · overlay · δ-lactone Structural NADP — the second NADP (2BH9 residue 811) that is not the hydride acceptor; it is a genuine stability cofactor: in Au's 1QKI the nicotinamide ring is entirely buried (no access for hydride, ≥ 16 Å from the active site) and the binding pocket sits at/under the dimer interface, with Asp421 at the interface centre — Class-I deficiency mutations cluster here, and NADP⁺ concentration was long known to control human G6PD stability/oligomerization. Canton / deficiency literature sits here, not in the motion. Overlay — 2BHL BG6 seated on 2BH9 by Cα superposition; not a deposited ternary. δ-lactone — 6-phospho-D-glucono-1,5-lactone, the G6PD product. BG6 — PDB ligand code for β-D-glucose 6-phosphate on 2BHL.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 2BH9 (2.5 Å) with two NADP; His263 NE2 ⋯ catalytic NAP C4N = 8.29 Å. The inferred layer ([schematic]): G6P body (2BHL overlay), δ-lactone, transferring H⁺/H⁻ spheres, NADP⁺→NADPH label switch, product leave, and ⑤ His regeneration. Binding order is compiled staging, not a kinetic fit. The protein mesh is static. Overlay contacts are not geomClaims.
Disagreements on record (a) Two NADP sites. Catalytic coenzyme (799) ≠ structural NADP (811). Mixing them is the classic G6PD error. (b) No ternary. 2BH9 has NADP, 2BHL has G6P; G6P on this mesh is overlay/[schematic]. (c) Concerted vs split. Compiled G6PD writes proton + hydride as one event; this page splits them (③ then ④) for 1-event/1-step teaching. (d) Product identity. Immediate product is the δ-lactone, not 6-phosphogluconate. (e) Variant. 2BH9 is a deletion variant, not full-length WT. (f) NAADP activity (Rhea 86243) is not shown. (g) H6PD (O95479 / 8EM2) is a different gene (ER bifunctional), not this page.
Regulation — NADPH product · variants · isoforms NADPH is both the product here and the main reductive payoff of oxidative PPP — named, not drawn as a G6PD·NADPH crystal. Class-I variants (Canton and others) often map near the structural NADP site (Au 2000) — named, not simulated. Cytosolic G6PD (this page) vs microsomal H6PD are different genes.Source: Au 2000 PMID:10745013 · textbook G6PD vs H6PD
Kinetics scope (no measured timecourse on this page) One G6P → δ-lactone + NADPH + H⁺ event is drawn, not a steady-state run. Compiled BRENDA values for EC 1.1.1.49 are not re-asserted here — no measured k_cat/K_m on this page [schematic]. Pair with a kinetics chapter.Source: BRENDA EC 1.1.1.49 — no k_cat/K_m re-asserted
Sequence Human G6PD UniProt P11413 · NCBI Gene 2539. Screen uses 2BH9 PDB-author numbering (His263). The construct is an N-terminal deletion variant (first residue Val, not His).
Simulation map — what you see is what is written Setup = 2BH9 catalytic pocket empty, structural NADP visible (opaque, run:null). ① catalytic NADP⁺ moves in (crystal 799). ② G6P moves in (2BHL overlay). ③ gold H⁺ + gold arrow O1 → His263 NE2 (parks). ④ slow-mo: blue hydride H⁻ + blue arrow C1 → C4N; G6P fades to δ-lactone; NADP⁺ relabels NADPH; parked gold H⁺ remains. ⑤ gold H⁺ leaves to solvent. ⑥ lactone and NADPH leave opposite ways; structural NADP stays. Only these events move.
Sources — bibliography of this page S1 — PDB 2BH9: human G6PD deletion variant, 2.5 Å, catalytic NADP (799) + structural NADP (811) — public coordinates; measured NE2⋯C4N = 8.29 Å S2 — PDB 2BHL: same variant + BG6 (β-D-glucose 6-phosphate); overlay onto 2BH9 (Cα RMSD 1.00 Å) — [schematic] G6P pose, not a ternary S3 — Kotaka et al., Acta Crystallogr D 2005, PMID:15858258 · Au et al., Structure 8:293 (2000), PMID:10745013 · PDB 1QKI — two NADP sites; His263 base; structural NADP is a stability cofactor (nicotinamide buried, near dimer interface, Class-I mutations cluster there) S4 — Sequence: UniProt P11413 (human G6PD) · NCBI Gene 2539 · Rhea 15841 S5 — Kinetics: BRENDA EC 1.1.1.49 — no k_cat/K_m re-asserted on this page

› Backbones and ligand poses are taken directly from the listed PDB entries, superposed into one common frame. Where no crystalline state exists for a step (e.g., G6P on 2BH9, lactone identity, H⁺/H⁻ flight, product release), the pose is drawn schematically and labeled as such in the narration.

NADP-binding domainC-domainONH⁺ (gold)H⁻ hydride (blue)