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Structure (frame)
Human PGI 1JLH (Cordeiro AT et al., BBA 2003, PMID:12573240) — full-side-chain frame; sugar-phosphate analog complex (erythrose-4-P) 1IRI (Tanaka N et al., J Mol Biol 2002, PMID:12054796) marked the pocket. The 1IRI analog itself is not drawn as a substrate — only its faint deposited pose appears as the anchor in the Setup frame; see "Why is the substrate schematic?" below.
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① Ring opening — Lys519 base · His389′ acid
Lys519 (candidate ring-opening base — the role split is debated, see ④; rabbit 1HOX / mouse 1U0F ortholog context) abstracts the C1-OH proton while His389′ (partner subunit) donates H⁺ to the ring oxygen [schematic], converting the glucopyranose into the open-chain aldehyde. His389′ already sits over the pocket in the apo frame (Nε2 ≈ 7 Å above the ring-oxygen side; the same-chain His389 is 33 Å away and catalytically irrelevant); the base Lys519-NZ sits ≈ 9 Å from the C1-OH below. A true H⁺ transfer needs ≈ 2.5–3 Å, so both proton legs close through the substrate-induced fit [schematic] — the base leg is shown as a schematic dock across the full ≈ 9 Å, not a real proton hop. [lit.-based, schematic]Source: PDB 1JLH/1IRI measured contacts (geomClaims pgi-cleft-glu357-his388 · pgi-his388b-e4p-c1-ringslot · pgi-same-chain-his388-noncatalytic): partner-subunit His389′ NE2 ≈ 7 Å over the ring-oxygen slot, same-chain His389 ≈ 33 Å — not drawn, no 30-Å cleft swing; Lys519-NZ ≈ 9 Å from the C1-OH (≈ 8.2 Å E4P-P in 1IRI, geomClaim pgi-e4p-p-lysnz); Lys519 base + His389′ acid ring-opening split = disputed literature assignment (see "Mechanism (curated database)" card), drawn [schematic]
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② cis-enediol(ate) — the shared transition state
Glu358 abstracts the pro-R C2-H (pro-R/Re stereo from isotope-labeling work — see ⑤); the carbonyl pivots C1→C2 through the planar cis-enediol(ate), stabilized by Arg273 / Lys211 electrostatics (O1⁻); Lys519 holds a catalytic water / cradles the C6-phosphate. Only stable ene-diolate–mimic inhibitor analogs have been crystallized with rabbit PGI (5-phospho-D-arabinonate, 5PAA; 5-phospho-D-arabinonohydroxamate, 5PAH) — mimics of the enediol(ate), not a captured reaction intermediate; our planar drawing is a [schematic] stylization.Source: proposal, lit.-based — Glu358 pro-R C2-H abstraction and Arg273/Lys211 enediol(ate) electrostatics inferred from crystal geometry + kinetics; pro-R/Re stereospecificity comes from isotope-labeling work (Rose IA et al.), not the cited abstracts (see "Ring opening & enediol(ate) — crystal evidence" card); enediol(ate) precedent = crystallized rabbit PGI·5PAA/5PAH inhibitor analogs (Jeffery et al. 2001), not a captured intermediate; planar drawing registered as schematic (species cis-enediol(ate) in
tools/manifests/pgi.json)
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③ Proton return — ketose recloses to F6P
The same proton returns to C1 (Re face) so C2 becomes the carbonyl (ketose); the open chain recloses to the furanose F6P. Fully reversible — the same shuttle runs backward in gluconeogenesis. The pro-R C2-H / Re-face C1 assignments rest on isotope-labeling work (see ⑤). [lit.-based, schematic]Source: registered step "Proton return — ketose recloses to F6P" (step 4 of
tools/manifests/pgi.json; REACTION_EQUATIONS.md ## pgi) — H⁺ returns to C1 (Re face) so C2 becomes the carbonyl, open chain recloses to furanose F6P, Glu358 shuttle; Re-face/pro-R stereospecificity is from isotope-labeling (Rose IA et al., see "Ring opening & enediol(ate) — crystal evidence" card), so the shuttle motion is [lit.-based, schematic], not measured
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④ Mechanism (curated database)
M-CSA entry #842 — "Glucose-6-phosphate isomerase" (m-csa entries) is curated on the rabbit enzyme (UniProt Q9N1E2 / crystal 1dqr — not the human protein): it assigns Glu358 (1dqr-author "Glu357A", i.e. UniProt − 1) as the C2→C1 proton shuttle and Arg273/Lys211 (1dqr 272/210) as the enediolate electrostatics — matching the shuttle drawn here. But the curated ring-opening role split differs from the rabbit crystal papers in ⑤: M-CSA Step 1 names the partner-chain His389 (chain B) as proton acceptor (base) and Lys519 as proton donor (acid), whereas Lee 2001 protonates the ring oxygen with His389′ (acid) while Lys519 holds the catalytic water. So the partner-chain-His ring-opening step is a disputed literature assignment — here drawn [schematic], not independently confirmed.Source: M-CSA entry #842 ("Glucose-6-phosphate isomerase", curated on the rabbit enzyme, UniProt Q9N1E2 / crystal 1dqr) — assigns Glu358 (1dqr-author Glu357A) as C2→C1 shuttle and Arg273/Lys211 (272/210) as enediolate electrostatics; its ring-opening role split (Step 1: partner-chain His389B acceptor, Lys519 donor) reverses the drawn Lys519-base/His389′-acid split from the rabbit crystal papers (Lee 2001) — disputed literature assignment, drawn [schematic]
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⑤ Ring opening & enediol(ate) — crystal evidence
Lee JH et al., Biochemistry 2001, 40:7799–7805, DOI 10.1021/bi002916o — rabbit PGI·F6P (crystal 1HOX): His388 protonates the ring oxygen, Glu216 positions that His, and a water held by Lys518/Thr214 accepts the C2-OH proton. Jeffery CJ et al., Biochemistry 2001, 40:1560–1566, DOI 10.1021/bi0018483 — rabbit PGI·5PAA (5-phospho-D-arabinonate, an ene-diolate–mimic inhibitor): Glu357 is the proposed C2↔C1 proton shuttle, Arg272/Lys210 the electrostatics, inferred from the 5PAA orientation. These papers number residues in the 1dqr-author frame (= UniProt − 1: His388 = His389, Glu216 = Glu217, Lys518 = Lys519, Glu357 = Glu358, Arg272/Lys210 = Arg273/Lys211). Their abstracts never state the pro-R C2-H or Re-face C1 return — that stereospecificity comes from isotope-labeling studies (Rose IA et al.), so the stereo-specific arrows carry a [schematic] flag.Source: Lee et al. 2001 (rabbit PGI·F6P, crystal 1HOX): His388 protonates the ring oxygen, Glu216 positions it, water held by Lys518/Thr214 accepts the C2-OH proton · Jeffery et al. 2001 (rabbit PGI·5PAA): Glu357 proposed C2↔C1 shuttle, Arg272/Lys210 electrostatics, inferred from the 5PAA orientation — neither abstract states pro-R or Re-face; that stereospecificity comes from isotope-labeling studies (Rose IA et al.), hence the [schematic] flag on the stereo arrows
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Kinetics — a fast near-equilibrium step (human PGI, UniProt P06744)
Wild-type human PGI is very fast: BRENDA (EC 5.3.1.9, UniProt P06744) lists a high kcat and a sub-millimolar Km(G6P) — a specificity ratio kcat/Km of order 10⁶ M⁻¹ s⁻¹, i.e. roughly two orders below a true diffusion limit (≈ 10⁸–10⁹ M⁻¹ s⁻¹): the enzyme does not turn over every collision. These numbers are compiled context, not re-derived here (Tsuboi 1971's PubMed record carries no numeric kinetics), so they are stated qualitatively. "Perfect" in the card above means the textbook near-equilibrium, mass-action sweet spot — not literally diffusion-limited. Direction is set by bulk concentrations (Keq ≈ 0.4 favors G6P, see below), not by an asymmetric intrinsic preference of the enzyme. Sources: BRENDA EC 5.3.1.9 (P06744); Tsuboi KK et al., J Biol Chem 1971, 246:7586–7594 (human erythrocyte PGI).
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Protonation states at pH 7 [schematic]
Why the shuttle residues are drawn in these forms: at pH 7, Glu358 is the carboxylate (pKa ≈ 4) — already deprotonated, the idle C2↔C1 shuttle base; His389′ imidazole (pKa ≈ 6–7) can donate H⁺ to the ring oxygen in its neutral form; Lys519's ε-amine has pKa ≈ 10.5, so at pH 7 the bulk is NH₃⁺ — for it to abstract the C1-OH proton its pKa must be shifted down by the phosphate-cradle microenvironment, and the neutral ε-amine is drawn as that catalytically competent (transiently deprotonated) state, not a pH-7 bulk ground state [schematic].
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Sequence
DNA/gene NCBI Gene 2821 · protein UniProt P06744 (residue numbering used on screen)
Legend & Fidelity
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Mechanism fidelity — measured vs. inferred
The measured layer: 1JLH side chains (Glu358/His389/Arg273/Lys519; the 1JLH-author numbers are UniProt − 1) and the 1IRI E4P-analog pocket. The inferred layer (labeled [schematic]/PROPOSAL): the ring-opening proton bookkeeping (role split disputed — see ④), the pro-R C2-H shuttle, the Arg273 O1⁻ contact, and the proton-transfer trajectory of His389′ onto the ring oxygen (shown as the green dashed). His389′ is the partner subunit's histidine (apo reach and closing fit detailed in card ①) — because it already sits over the pocket, no 30-Å cleft swing is drawn; both proton legs ride the schematic substrate-induced fit.
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Why is the substrate "schematic"?
No intact human PGI·G6P (or PGI·F6P) complex is deposited — the crystal only trapped a 4-carbon sugar-4P analog (1IRI, E4P) that marked the pocket (that trapped E4P is the faint fragment in the Setup frame). Intact sugar complexes of the orthologs are deposited (rabbit 1HOX·F6P, mouse 1U0F·G6P at 1.6 Å; note 1U0G is a separate mouse E4P complex, not a G6P complex) and the human pocket is drawn onto those poses. G6P and F6P are therefore PubChem 3D schematics re-anchored by centroid onto the E4P pocket pose (phosphate toward Arg273/Lys519, ring over Glu358). The anomeric C1 / ring oxygen positions are drawn, not measured.
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Physiological regulation — a near-equilibrium step, mass action not allostery
PGI isomerization sits near equilibrium: [F6P]/[G6P] ≈ 0.4 (Km-independent), ΔG°′ ≈ +2 kJ/mol, and the enzyme has no allosteric regulator. Net glycolytic flux is therefore driven by mass action: hexokinase pulls substrate in, and PFK-1 drains F6P downstream — this is the classic "near-equilibrium" middle of glycolysis. The same protein moonlights as secreted autocrine motility factor (AMF) and a neurotrophic factor (neuroleukin), unrelated to catalysis. Glucokinase (GCK) is a different enzyme and plays no role here.
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Kinetics scope — one turnover's chemistry
The motion is one G6P → F6P isomerization; rates and equilibria are context, not outputs (qualitative context in "Kinetics" above). The step sits near equilibrium (ΔG°′ ≈ +2 kJ/mol), so what you see is mass-action steering — no allostery or cooperative dynamics to simulate.
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Sources — bibliography of this page
S1 — PDB 1JLH: human PGI full-side-chain frame; Cordeiro AT et al., BBA 2003, PMID:12573240
S2 — PDB 1IRI: sugar-4-P analog complex (erythrose-4-P) that marked the pocket; Tanaka N et al., J Mol Biol 2002, PMID:12054796 — that analog is not drawn as substrate, only its faint deposited pose anchors the Setup frame
S3 — Rabbit PGI·F6P crystal 1HOX: Lee JH et al., Biochemistry 2001, 40:7799–7805, DOI 10.1021/bi002916o — ring-opening roles (His protonates the ring oxygen, Glu positions it, water held by Lys/Thr accepts the C2-OH proton)
S4 — Jeffery CJ et al., Biochemistry 2001, 40:1560–1566, DOI 10.1021/bi0018483 — rabbit PGI·5PAA ene-diolate-mimic inhibitor; Glu357 proposed C2↔C1 shuttle, Arg272/Lys210 electrostatics
S5 — Intact sugar complexes of the orthologs: rabbit PGI·F6P 1HOX · mouse PGI·G6P 1U0F (1.6 Å) · mouse PGI·E4P 1U0G (a separate E4P complex, not a G6P complex); the human pocket is drawn onto these poses
S6 — M-CSA entry 842, curated on the rabbit enzyme (UniProt Q9N1E2 / crystal 1dqr): Glu358 (1dqr-author Glu357A) C2→C1 shuttle, Arg273/Lys211 electrostatics, and a disputed ring-opening role split vs. Lee 2001 — drawn [schematic]
S7 — Kinetics/sequence context: BRENDA EC 5.3.1.9 (P06744) · Tsuboi KK et al., J Biol Chem 1971, 246:7586–7594 (human erythrocyte PGI, qualitative) · UniProt P06744 (numbering on screen) · NCBI Gene 2821
S8 — Repo display conventions: Rule 4 (separate product exits) · Rule 30 (narrated claims reconstructible from the scene) · 6 geomClaims in
tools/manifests/pgi.json · pro-R C2-H / Re-face C1 stereospecificity from isotope labeling (Rose IA et al.) carries a [schematic] flag · G6P/F6P = PubChem 3D schematics re-anchored onto the E4P pocket pose, no intact human substrate complex deposited
› Backbones and residue side chains are taken directly from 1JLH; the 1IRI E4P analog is
rendered only as the faint deposited anchor in the Setup frame (its pose oriented the substrate dock).
No intact human PGI·sugar product complex is deposited,
so G6P/F6P and the open-chain/enediolate species are schematic (PubChem 3D geometries re-anchored,
and hand-built open forms) and are labeled as such in the narration.
Where inter-state transitions are stitched, the recomposed coordinates are schematic — see
"Mechanism fidelity" above.