Hexokinase I - 3D Mechanism Simulator

Loading structural data… (4FOI · 1HKB · 1QHA)

References & Databases

Structure Aleshin AE et al. Structure 1998;6:39–50 — HKI·glucose·G6P (PDB 1HKB) PMID:9493266; the viewer scaffold 4FOI (HK1 D413N + Glc-1,6BP) has no standalone PMID. The catalytic-nucleotide co-structure 1DGK exists (mutant monomeric HK1 with ADP seated at the C-terminal active site, Aleshin AE et al., J Mol Biol 2000, PMID:10686099) and is disclosed here but not loaded — this page keeps 1QHA's re-aligned AMP-PNP as its ATP pose and labels it [schematic].
ATP complex Rosano C et al. Structure 1999;7:1427–37 — AMP-PNP·Mg (PDB 1QHA) PMID:10574795
① Glucose binding (induced fit) Ordered mechanism — glucose binds first, then Mg·ATP docks opposite the 6-OH. Caveat (1HKC, Aleshin AE et al., J Mol Biol 1998, PMID:9735292): in the catalytically active C-terminal half, glucose bound alone does not by itself stabilize a closed cleft — a stable closed half requires ATP (or G6P) along with glucose, so the clamp shown here is schematic and completes as ATP docks (next step). Bound-glucose pose from HKI·glucose·G6P 1HKB (Aleshin AE et al., Structure 1998, PMID:9493266).Source: ordered binding (glucose first) — Structure card; pose from PDB 1HKB (Aleshin 1998); clamp schematic until ATP docks — 1HKC caveat (PMID:9735292)
② Mg·ATP docks opposite O6 [schematic] Gamma-P of ATP positioned ~3.4 Å behind O6 on the backside-attack line (pose from the AMP-PNP·Mg complex 1QHA, re-aligned). Mg²⁺ chelates the β/γ phosphates.Source: pose re-aligned from PDB 1QHA (AMP-PNP·Mg, PMID:10574795); ~3.4 Å Michaelis geometry = registered schematic, not measured (no HK1 Michaelis crystal — "Why is the Mg·ATP pose labeled [schematic]?" card)
③ Asp657 deprotonates the C6-OH (HT) [schematic · hypothetical, lit.-based] Asp657 deprotonates the C6-OH (general-base proposal, M-CSA Entry 696); the alkoxide attacks Pγ in-line through a trigonal-bipyramidal transition state; configuration inverts.Source: general-base proposal — M-CSA Entry 696 (hypothetical, lit.-based); measured 6-OH·Asp657 Oδ2 = 2.77 Å (PDB 1HKB assembled frame, manifest geomClaim)
④ In-line S_N2 transfer (inversion) [schematic] direct in-line phosphoryl transfer (no dissociative/free-metaphosphate branch). Ser603 lines up the O6–Pγ line; Arg539 · Asp532 · Asp657 (M-CSA catalytic residues) coordinate Mg²⁺ (here via water), and Mg²⁺ stabilizes the TS (M-CSA Entry 696).Source: in-line Sₙ2 without dissociative/Sₙ1 branch — Mechanism fidelity card ("GT"); Pγ–N3B bridge 1.60 Å measured (PDB 1QHA, manifest geomClaim); residue roles & TS stabilization — M-CSA Entry 696
⑤ Products leave — G6P + ADP + H⁺ G6P dissociates in its crystallographic pose; ADP follows; the H⁺ product regenerates Asp657 (M-CSA step 2). Glucose / G6P pose from 1HKB.Source: G6P pose — PDB 1HKB (GLC/G6P seat, Aleshin 1998); H⁺ regenerates Asp657 — M-CSA Entry 696 step 2
Sequence DNA/gene NCBI Gene 3098 · protein UniProt P19367

Legend & Fidelity

Mechanism fidelity — the Asp657 "general base" is a proposal, not a direct measurement M-CSA Entry 696 records the 6-OH ⋯ γ-P ≈ 3 Å in-line geometry with Asp657 abstracting the C6-OH proton, but it also notes a recent HK crystal structure whose data suggest the pKa of Asp657 is too low to abstract that proton — the proton may instead transfer later, on phosphate-bond formation.
· HT (③): we animate the classical general-base proposal and label it "(hypothetical, lit.-based)"; a later-step H⁺ transfer would keep the same in-line associative Sₙ2 chemistry and inversion.
· GT (④): in-line Sₙ2, associative — no dissociative / free-metaphosphate (Sₙ1) branch is proposed for HK1.
· Frame honesty: the scene stitches 4FOI + 1HKB + 1QHA into one frame. The deposited 1QHA Mg sits ≈ 8.7 Å from Pγ at a non-catalytic surface site and is re-anchored ≈ 2.1 Å onto the γ-oxygen cap; mid-flight the O6 ⋯ Pγ ⋯ β-P triangle reads ≈ 94°, not 180° — the in-line Sₙ2 statement is carried by the drawn flight axis (the equatorial rig), not by every intermediate atom.
Why is the Mg·ATP pose labeled "[schematic]"? The AMP-PNP·Mg copy deposited in 1QHA binds a non-catalytic surface site on the N-terminal domain — not the catalytic cleft. The adenosine + Mg²⁺ are real 1QHA coordinates; the γ-PO₃ is rotated so Pγ faces O6 at ≈ 3.4 Å on the backside line — a Michaelis complex no HK1 crystal has yet captured. Glucose, G6P, Asp657, Ser603, Arg539 and Asp532 are real 1HKB geometry.
Assembly & scaffold — one monomer per frame HK1 is biologically a monomer (UniProt P19367 SUBUNIT; Aleshin AE et al., J Mol Biol 2000); it homodimerizes only at the elevated concentrations used for crystallization. PDBe author-assigned assemblies: 1HKB monomer ×2 · 1QHA dimer · 1HKC dimer · 4FOI dimer · 1DGK monomer. Each step therefore renders a single HK1 chain (4FOI chain A scaffold).
Physiological regulation — HK1 in context Feedback: the product G6P potently inhibits HK1, and inorganic phosphate relieves that inhibition via the N-terminal regulatory site — the classic product brake on glycolysis step 1. The inhibition is debated between competition with ATP at the catalytic site and an allosteric G6P site in the N-terminal half; 1HKB shows G6P's 6-phosphate occupying the catalytic ATP seat (supporting competitive product inhibition), while a secondary N-terminal-half G6P/regulatory site is also recognized — both relieved by Pi (1HKC + mutagenesis place the phosphate regulatory site in the N-terminal half). Localization: the N-terminal half of HK1 attaches to the outer mitochondrial membrane via VDAC (porin), letting the enzyme use matrix ATP and linking glucose catabolism to cell survival (prominent in neurons); G6P promotes its release. Isozyme contrast: HK1 has a low K_m for glucose (≈ 0.05–0.1 mM) and is G6P-sensitive, unlike glucokinase (GCK, hexokinase IV) whose high K_m (~5–10 mM) and lack of G6P inhibition make it the liver/β-cell glucose sensor — the two are not the same enzyme, though names are sometimes conflated.
Kinetics scope — context, not simulator outputs Stoichiometric context only — human HK1 runs K_m(glucose) ≈ 0.05–0.1 mM and K_m(Mg·ATP) ≈ 0.6–1.2 mM (BRENDA EC 2.7.1.1 · ref 640237).
Sources — bibliography of this page S1 — PDB 1HKB: HKI·glucose·G6P — bound-glucose pose and the G6P 6-phosphate occupying the catalytic ATP seat; Aleshin AE et al., Structure 1998, PMID:9493266; the measured 6-OH⋯Asp657 Oδ2 separation is quoted on the Mechanism fidelity card (assembled 1HKB frame, tools/manifests/hk.json) S2 — PDB 1HKC: catalytically active C-terminal half — glucose alone does not stabilize a closed C-terminal cleft, so the drawn clamp is schematic until ATP docks; Aleshin AE et al., J Mol Biol 1998, PMID:9735292 S3 — PDB 1QHA: AMP-PNP·Mg complex — ATP/adenosine + Mg²⁺ pose source (its Mg sits a non-catalytic surface site and is re-anchored onto the γ-O cap; ζ-PO₃ rotated to the backside-attack line — distances quoted on the Mechanism fidelity card = registered schematic, no HK1 Michaelis crystal), PMID:10574795; Pγ–N3B bridge measured value also on the fidelity card (manifest) S4 — PDB 4FOI: scaffold frame (chain A); HK1 is a monomer by biology, homodimerizing only at crystallization concentrations — assembly assignments from Aleshin AE et al., J Mol Biol 2000 (Assembly card) S5 — M-CSA entry 696: Asp657 general-base HT proposal and the in-line associative Sₙ2 TS; a recent HK structure questions the Asp657 pKa, so the HT step is drawn (hypothetical, lit.-based) — no dissociative/free-metaphosphate branch S6 — Kinetics context: BRENDA EC 2.7.1.1 · ref 640237 — human HK1 K_m(glucose) and K_m(Mg·ATP) values quoted in the EvidenceView body S7 — UniProt P19367 (HK1) · NCBI Gene 3098 S8 — Repo display conventions: 4FOI + 1HKB + 1QHA stitched into one frame, Mg re-anchor and ζ-PO₃ rotation stated as frame honesty (Mechanism fidelity card) · Rule 30 (narrated claims reconstructible from the scene) · 4 geomClaims in tools/manifests/hk.json · [schematic] = re-anchored pose on the measured frame, no deposition claimed

› 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., Michaelis geometry), the pose is drawn schematically using PubChem 3D geometries and is labeled as such in the narration. Residue numbers follow UniProt P19367 (HK1) and match the structure papers. Where inter-state transitions are stitched, the recomposed coordinates are schematic — see "Mechanism fidelity" above.

N-terminal half (regulatory)C-terminal half (catalytic)ONPMg/K