Phosphoglycerate Kinase - 3D Mechanism Simulator

Loading structural data… (2XE7 · 3-PG + ADP semi-closed ternary)

References & Databases

Reaction-cycle structure — the semi-closed ternary · 2XE7 Human PGK1 semi-closed ternary with 3-PG + ADP — the state where the two substrates have met in the cleft before the domains complete the closing motion (Zerrad L et al., J Biol Chem 286:14040–14048, 2011; RCSB 2XE7, PMID:21349853, DOI 10.1074/jbc.M110.206813). A human fully-closed TSA ternary IS published — 2WZB (ADP + 3-PG + MgF₃⁻, 1.47 Å; 2WZC = AlF₄⁻ variant, 2WZD = K219A), Cliff et al., JACS 132:6507–6516, 2010, PMID:20397725 — it fixes the closed-state donor–acceptor window 3.9–4.3 Å quoted here. This page keeps the 2XE7 frame, so the closing motion of ③ is a schematic translation of the nucleotide toward the acyl phosphate (hinge-swing ≈ 33° [schematic] arc drawn; 3.9–4.3 Å recorded as literature [lit.] context, kept off-screen as numbers).
① 1,3-BPG — real slot, schematic acyl-phosphate The 3-PG skeleton + the 3-phosphate are the deposited 2XE7 coordinates; 1,3-BPG itself is too labile to be co-crystallized, so the C1 acyl phosphate (C1–O2–P2) is a [schematic] add-on. Arg122 (basic patch: Arg65/Arg170/Arg38 + His62) clamps the substrate phosphate: Arg122 NH1 ⋯ O2P = 2.78 Å (measured from the assembled data, geomClaim).Source: 3-PG pose, PDB 2XE7 (Zerrad et al. 2011); Arg122 ⋯ O2P 2.78 Å measured from the assembled data (manifest geomClaim) · C1 acyl phosphate = [schematic] add-on, 1,3-BPG not co-crystallized
② ADP · Mg²⁺ — deposited ADP, schematic metal ADP uses the deposited 2XE7 pose; 2XE7 carries no metal, so Mg²⁺ is [schematic]. Lys219 anchors the nucleotide α-phosphate: Lys219 NZ ⋯ O2A = 3.75 Å (measured, geomClaim); the Lys219/Asn336/Glu343/Asp218 network cradles the phosphates. Catalytic Lys215 ★ waits to swing onto the β-phosphate during closure.Source: ADP pose, PDB 2XE7 (Zerrad et al. 2011); Lys219 ⋯ O2A 3.75 Å measured (manifest geomClaim) · Mg²⁺ absent from 2XE7, placed [schematic]
③ In-line S_N2 — the moving step is a schematic template in-line phosphoryl transfer with inversion: the ADP β-oxygen O3B attacks the acyl-P2 as the C1–O2 bond breaks (O3B ⋯ P2 8.73 Å open → ≈ 3 Å closed, in line; measured open distance + target geometry). The gold arrow, equatorial TS ring and cross-fades are bookkeeping cartoons, not an observed transition state — 13BPG→3-PG and ADP→ATP re-annotate the same skeleton in place (the ATP γ-PO₃ is [schematic]). No proton is consumed; Mg²⁺ and the Lys network neutralize the anionic TS.Source: open O3B ⋯ P2 = 8.73 Å measured from the assembled 2XE7 common frame (manifest geomClaim) · ≈3 Å closed target = schematic goal geometry, not a claim · closed-state window 3.9–4.3 Å, 2WZB: Cliff et al. 2010 [lit.] · TS ring/arrows = Rule 30 cartoons, TS unobserved
④ Products leave + reverse chemistry ATP, 3-PG and Mg²⁺ release along different trajectories as the cleft reopens — the first substrate-level ATP of glycolysis. In gluconeogenesis PGK runs the same in-line S_N2 backwards (ATP phosphorylates 3-PG → 1,3-BPG).Source: Rule 4 — display convention, separate exits (no external geometry claimed) · reverse gluconeogenesis direction = same in-line S_N2 (REACTION_EQUATIONS.md ## pgk)

Legend & Fidelity

How to tell measurement from reconstruction on screen Numbers labeled with an Å value (2.78 / 3.75 / 8.73) are measured from the assembled coordinates and re-checked (Rule 34 geomClaims). Everything tagged [schematic] — the acyl phosphate, Mg²⁺, γ-PO₃, the closure translation, the S_N2 arrows/rig, the ≈33° hinge arc — is a declaration of reconstruction, and is disclosed again here and at the top of the narration.
Mechanism fidelity — measured vs. inferred The measured layer: the 2XE7 backbone with the deposited 3-PG and ADP poses — the three interatomic distances are re-derived from that frame and re-checked (Rule 34 geomClaims; see the card above). The inferred layer: what the deposit could not capture — the 1,3-BPG C1 acyl phosphate, Mg²⁺, the ATP γ-PO₃, the closure translation, and the S_N2 trajectory markers. The 2XE7 frame is semi-closed, so the catalytic approach is assembled from literature geometry (closed-state window 3.9–4.3 Å from the fully-closed 2WZB complex) and tagged [schematic] step by step.
Why is the closed state "[schematic]"? Because the frame used here (2XE7) is a semi-closed ternary — a fully-closed human complex with both substrates and a tetrahedral transfer-state analog does exist (2WZB, 1.47 Å), but this page's narrative is built on the semi-closed 2XE7 deposit, so closure is drawn as the nucleotide sliding toward the acyl phosphate along a hinge arc, not a measured trajectory. 2WZB fixes the reacting-pair separation in the closed state — 3.9–4.3 Å — quoted in the first card while the on-screen approach distance is own target geometry; the open-state measurements are the crystallographic part.
First-pass primer (read me once) Ignore labels on ①, watch ①-② (substrate meet in the open cleft), then ③-④ (they react and leave). The reaction is one transfer of a phosphate group — the acyl-phosphate P2 is handed from 1,3-BPG onto the ADP β-oxygen O3B, in-line. PGK makes the first ATP you can keep from glycolysis (the 2 ATP invested earlier are spent). The two domain colors (blue = 3-PG / 1,3-BPG side, orange = ADP/ATP nucleotide side) just show where each substrate sits.
Chemistry primer — why an acyl phosphate can make ATP 1,3-BPG carries an acyl phosphate (anhydride-like) — a high-energy phosphate (the same acyl-phosphate payoff already created by GAPDH's Step 6; a specific ΔG°′ figure was not re-verified this review — see Kinetics scope). S_N2 at P runs in-line (nucleophile O3B, leaving group O2, 180° geometry) and produces inversion — the geometry taught for phosphoryl transfer; the equatorial ring + flip on ③ marks that, as a cartoon. No proton is used: the anionic TS is neutralized by Mg²⁺ and the Lys219/Lys215/Arg122 network. ATP made here is substrate-level (direct enzyme-transfer, not oxidative phosphorylation).
Hinge motion — what the static mesh can and cannot show PGK works by hinge-bending: the two domains open and close over the bound substrates. On-screen the protein is a static mesh of the semi-closed state (Rule 24); closure is conveyed by translating the nucleotide along the C1→P2 axis with the ≈33° hinge-swing arc drawn as an overlay — a schematic stylization, since the page keeps the 2XE7 semi-closed frame rather than the fully-closed 2WZB complex. Real opening is entropic and continuous; the discrete move you see is a pedagogical beat, not a measured trajectory.
Physiological regulation PGK1 is not an allosteric gate: its flux is set by energy charge, substrate availability (1,3-BPG delivered by GAPDH · a specific K_m figure was not re-verified this review — see Kinetics scope) and product feedback (3-PG / ATP product inhibition; a very high [ATP] can push the near-equilibrium step backward). The enzyme is a monomer in the cytoplasm; the same protein moonlights as a surface-bound disulfide reductase and interacts with angiostatin machinery when secreted — involvement that is not part of the glycolysis step shown here.
Kinetics scope (no measured timecourse on this page) This page shows one catalytic event, no timecourse and no steady-state modeling (see the scope badge). Earlier versions quoted BRENDA-compiled reference values — kcat ≈ 200 s⁻¹ (BRENDA EC 2.7.2.3 r=722979; derived specific activity ≈ 650–700 µmol·min⁻¹·mg⁻¹), K_m(1,3-BPG) ≈ 6.86 µM, K_m(3-PG) ≈ 186 µM, K_m(ADP) ≈ 221 µM (r=761524), and |ΔG°′| ≈ 1 kJ·mol⁻¹ — those numbers are withdrawn pending verification: UniProt P00558 carries no K_m/k_cat for this reaction (its K_m 0.56 mM ATP entry is PMID 26942675, a mitochondrial protein kinase EC 2.7.11.1 — unrelated), and the BRENDA entries could not be re-confirmed in the latest review (2026-09-19). PGK is nonetheless treated as a near-equilibrium step on textbook grounds.
Residue numbering Human PGK1, PDB-author numbering = UniProt P00558 − 1 (the mature chain loses Met1: author Arg38 = UniProt Arg39). Residues 4–416 on screen; N-domain 4–201 (3-PG / 1,3-BPG side, blue) · C-domain 202–416 (ADP/ATP nucleotide side, orange) — matching UniProt's 3-PG-binding region (author 22–170) and nucleotide-binding region (author 213–375). Catalytic/marking residues: Arg122 ★, Lys215 ★, Lys219, plus the Arg170 / Arg65 / Arg38 basic patch (author numbers).
Sequence & databases DNA/gene NCBI Gene 5230 · protein UniProt P00558 · EC 2.7.2.3 BRENDA registry · catalysis record M-CSA (PGK family).
Sources — bibliography of this page S1 — PDB 2XE7: human PGK1 semi-closed ternary, single frame — the 3-PG slot and deposited ADP pose (no organism mixing, no superposition seam); measured annotations Arg122 clamp / Lys219 anchor / open O3B⋯P2 (3 geomClaims in tools/manifests/pgk.json; Å values on the cards); 2XE7 carries no Mg²⁺ — metal placed [schematic] S2 — PDB 2WZB (1.47 Å): fully-closed human ternary with a tetrahedral transfer-state analog — fixes the closed-state reacting-pair window (lit., quoted in ③ card); Cliff MJ et al., 2010, PMID:20397725. Used as the closed reference; the page keeps 2XE7 as its frame, so closure is drawn as a [schematic] hinge arc (value on the ③ card) S3 — Kinetics: the BRENDA compiled values quoted in the EvidenceView body (k_cat, K_m(1,3-BPG), K_m(3-PG), K_m(ADP), |ΔG°′|) are withdrawn pending verification — UniProt P00558 carries no K_m/k_cat for this reaction (its only ATP entry is PMID 26942675, an unrelated mitochondrial protein kinase EC 2.7.11.1), and the BRENDA entries could not be re-confirmed (review 2026-09-19) S4 — Sequence & databases: NCBI Gene 5230 · UniProt P00558 (PDB-author numbering = UniProt − 1, mature chain loses Met1) · EC 2.7.2.3 (BRENDA) · M-CSA (PGK family) S5 — Repo display conventions: Rule 30 (gold attack arrow, equatorial TS ring, hinge arc = cartoon; S_N2 TS unobserved) · Rule 34 geometry (geomClaims: every Å a single measured value from the assembled 2XE7 common frame; closed target = own goal geometry beside the 2WZB closed-state window quoted in ③) · Rule 4 (separate product exits) · [schematic] = 1,3-BPG C1 acyl phosphate, Mg²⁺, ATP γ-PO₃, closure translation, 13BPG→3-PG / ADP→ATP re-annotations · REACTION_EQUATIONS.md ## pgk for the reverse gluconeogenesis direction

› Backbones and the ADP / 3-PG ligand poses are taken directly from 2XE7 (human semi-closed ternary, single frame) — no organism mixing and no superposition seam. The 1,3-BPG C1 acyl phosphate, the ATP γ-PO₃, Mg²⁺, the hinge-swing closure translation and the S_N2 arrows/rig are schematic reconstructions, each labeled and disclosed. Distances shown on screen (2.78 / 3.75 / 8.73 Å) are measured from the assembled data; the ≈ 3 Å closed target is own target geometry beside the literature closed-state window 3.9–4.3 Å (2WZB), as labeled.

N-domain (3-PG / 1,3-BPG)C-domain (ADP/ATP nucleotide)ONPMg