Pyruvate Kinase - 3D Mechanism Simulator

Loading structural data… (3SRD)

References & Databases

Product complex Human PKM2 allosteric regulation and catalysis: Dombrauckas JD et al., Biochemistry 2005, PMID:15996096 (1T5A, FBP + oxalate). FBP-bound M2PYK R-state structures and nutrient-sensing mechanism: Morgan HP et al., PNAS 2013, PMID:23530218. Note: the scaffold in the viewer is 3SRD, a related FBP+oxalate M2 deposition that itself has no standalone PMID; the mechanism and ligand set are those in the cited published literature. 3SRD itself contains no ATP — the ATP product pose is modeled from 4FXF.
① PEP binds — Lys270 neutralizes carboxylate [schematic] PEP enters with Lys270 neutralizing its carboxylate while Asp296 coordinates Mg²⁺, positioning the enol-phosphate for transfer (pose snapped into the real oxalate/pyruvate-analog slot).Source: [schematic] — no PKM2·PEP crystal deposited; pose snapped into the 3SRD oxalate (pyruvate-analog) slot · Lys270/Asp296 roles on the real scaffold: Dombrauckas et al. 2005
② ADP binds — Michaelis assembly [schematic] ADP docks with its β-phosphate facing PEP's phosphate; Mg²⁺ chelates the α,β-phosphates and Lys270 stabilizes the β oxygens for in-line attack.Source: [schematic] — no PKM2·ADP crystal deposited; ADP seat = modeled ATP pose (4FXF-based, 4FXF; see Product complex card)
③ S_N2 phosphoryl transfer [schematic] The ADP β-oxygen attacks PEP's phosphorus in-line (S_N2) while the P–O bond to the enol carbon breaks in the same step — no covalent intermediate; Mg²⁺ stabilizes the developing enolate (snaps PEP→oxalate, ADP→ATP).Source: [schematic] — direct in-line phosphoryl transfer, no covalent intermediate (REACTION_EQUATIONS.md ## pk, associative S_N2) · TS unobserved, arrows/rig = cartoons (see Mechanism fidelity card)
④ Enol → keto tautomerization [schematic] The enol-pyruvate tautomerizes to the stable keto pyruvate on-enzyme (enolpyruvate intermediate from the Seeholzer–Rose mechanism; stereospecific ketonization after Kuo & Rose — see the fidelity card) — drawn as one intramolecular O→C3 proton hop (both endpoints on screen); the enzyme-mediated path is collapsed into that hop and any external donor is unidentified. 1A49 finds no obvious residue candidate near the enolate face (Larsen 1998).Source: enolpyruvate intermediate — Seeholzer & Rose 1991 · stereospecific ketonization — Kuo & Rose (see fidelity card) · single intramolecular O→C3 hop = [schematic], external donor unidentified (1A49, Larsen 1998)
⑤ Products release Pyruvate (oxalate-analog position) leaves before ATP (a preferred dissociation order — a specific kinetic attribution was not re-verified this review) while K⁺/Mg²⁺ stay home — the second ATP payoff; per glucose, PK yields 2 pyruvate + 2 ATP.Source: ordered release (pyruvate first) = registered schematic — kinetic attribution not re-verified (card wording) · K⁺/Mg²⁺ resident in 3SRD · 2 pyruvate + 2 ATP per glucose = pathway stoichiometry (REACTION_EQUATIONS.md ## pk)

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: the 3SRD scaffold — chain, FBP, the oxalate pyruvate-analog, the K⁺/Mg²⁺ sphere, and the starred catalytic side chains (Lys270, Asp296 & c.) are deposited coordinates (see "Product complex"). The inferred layer (every substrate step tagged [schematic], cards ①–⑤): the PEP and ADP Michaelis poses, the associative in-line S_N2 transition state, and the enol-pyruvate→keto reversion drawn as a single collapsed intramolecular proton hop (enolpyruvate intermediate: Seeholzer & Rose, J Biol Chem 266:14283, 1991, PMID:1988060; stereospecific ketonization: Kuo & Rose, 1989/1991) whose external donor is unidentified — 1A49 (Larsen 1998) reports no crystallographically obvious base at the enolate face. No PKM2 co-structure with PEP or ADP has been deposited, so everything before product release is a literature pose mounted on the real scaffold, labeled [schematic] wherever that is the case.
Why is the Michaelis complex "[schematic]"? Because no crystal has captured PKM2 bound to PEP or ADP — the depositions (3SRD, 1T5A) exist only in product/trapped-analog form: oxalate standing in for pyruvate and no ATP in sight. The substrate geometry is therefore assembled: PEP is snapped into the real oxalate slot, ADP docks onto the β-phosphate position with Mg²⁺ chelation, and the ATP product pose is carried over from 4FXF (its Mg·ATP geometry, re-anchored onto the real P-site). The scaffold, ions, oxalate and residue side chains are measured coordinates; everything stitched between them is literature geometry and carries the [schematic] tag.
Physiological regulation & moonlightingPKM2 is feedforward-activated by FBP (PFK-1 product) into the R-state tetramer, and by serine (Chaneton 2012); inhibited by Phe/Ala, T3, PML and pTyr-peptide FBP release (Christofk 2008); Y105 phosphorylation, K433 acetylation and TEPP-46-class activators tune the tetramer–dimer balance (dimer: low-activity, nuclear protein-kinase moonlighting on STAT3/H3T11). M1 (adult, constitutive) vs M2 (embryo/cancer). Tetramer shown as monomer.
Kinetics scope (no measured timecourse on this page)One phosphoenolpyruvate transfer is drawn — R-state/substrate-depletion dynamics are not simulated. K_m(PEP) 2.7→0.17 mM and K_m(ADP) 0.34→0.24 mM with FBP are UniProt P14618 entries attributed to Dombrauckas 2005 (one condition set: +FBP, 32°C, pH 8). The k_cat estimate and the net-reaction ΔG°′ ≈ −31.4 kJ·mol⁻¹ are withdrawn pending verification (not in UniProt; BRENDA/other sources could not be re-confirmed in the latest review, 2026-09-19).
Sequence DNA/gene NCBI Gene 5315 · protein UniProt P14618
Sources — bibliography of this page S1 — PDB 3SRD (no standalone PMID): the viewer scaffold — FBP-bound R-state PKM2 with the oxalate pyruvate-analog and the K⁺/Mg²⁺ sphere (measured coordinates); 3SRD contains no ATP — the deposit exists only in product/trapped-analog form (oxalate standing in for pyruvate) S2 — PDB 1T5A (FBP + oxalate): Dombrauckas JD et al., Biochemistry 2005, PMID:15996096 — Lys270 / Asp296 catalytic roles on the real scaffold; mechanism and ligand set of this page follow the cited published literature S3 — PDB 4FXF: Morgan HP et al., PNAS 2013, PMID:23530218 — FBP-bound M2PYK R-state/nutrient-sensing mechanism; the ATP product pose used in the S_N2 step is modeled from 4FXF (ATP + FBP + Mg²⁺ + K⁺; PDBe "phenylalanine" title inconsistent — the Phe ligand belongs to the sister deposit 4FXJ; ATP sits in only half the chains, coexisting with that crystal's own oxalate) S4 — Mechanism: direct in-line associative S_N2, no covalent intermediate (REACTION_EQUATIONS.md ## pk) · enolpyruvate intermediate — Seeholzer & Rose, J Biol Chem 266:14283, 1991, PMID:1988060 · stereospecific ketonization — Kuo & Rose (see fidelity card) · 1A49 (Larsen 1998) reports no crystallographically obvious base at the enolate face; the O→C3 hop is [schematic], external donor unidentified S5 — Kinetics: K_m(PEP) and K_m(ADP) with FBP (values on the Kinetics scope card) are UniProt P14618 entries attributed to Dombrauckas 2005 (one condition set: +FBP, 32 °C, pH 8); the k_cat estimate and net-reaction ΔG°′ are withdrawn pending verification (review 2026-09-19) S6 — Sequence: NCBI Gene 5315 · UniProt P14618 (PKM2) S7 — Repo display conventions: Rule 30 (S_N2 arrows/rig = cartoons, TS unobserved) · [schematic] = PEP / ADP Michaelis poses (no PKM2·PEP or PKM2·ADP crystal deposited), enol → keto single intramolecular O→C3 proton hop (external donor unidentified), product release order (pyruvate first) = registered schematic (kinetic attribution not re-verified) · 4FXF ATP pose re-anchored on the real P-site · Rule 4 separate exits · K⁺/Mg²⁺ resident in 3SRD

› 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.

N-domainA/B/C domainsONPMg/K