Phosphoglucomutase-1 - 3D Mechanism Simulator

Loading structural data… (6SNO)

References & Databases

START HERE — how to read α-G1P ⇌ α-G6P A ping-pong phospho-relay cartoon on the human PGM1 frame that actually exists: 6SNO (2.7 Å) isoform 2 with crystal G1P and Zn. Residue 117 is VAL on this occupancy — the phospho-Ser is SEP135, not Ser117. Crystal Zn stands in for physiological Mg (named). G6P is a 6SNQ overlay [schematic], not a 6SNO ternary. G1,6BP is an identity label on the same G1P mesh, not a third sugar. Covalent E~P is disclosed (not a pure A-page). White is phosphoryl transfer (PO₃), not hydride. Measured Å are deposited 6SNO pairs only. Overlay RMSD is named, not a geomClaim.
Crystal structures PDB 6SNO — human PGM1 isoform 2 + G1P + Zn, 2.7 Å (Backe 2020). Coordinates are public. PDB 6SNQ supplies the G6P overlay only. 5EPC is WT 1.85 Å with no sugar — companion, not this mesh. Disease variants 5F9C / 5JN5 / 5TR2 are not used.
Mechanism — ping-pong via G1,6BP UniProt P36871 EC 5.4.2.2: α-G1P ⇌ α-G6P. Backe et al., Sci Rep 2020, PMID:32221390 — isoform 2 + G1P / G6P. Compiled PGM: E~P + G1P ⇌ G1,6BP ⇌ E~P + G6P. This page splits the two phosphate throws. Overlay contacts are not geomClaims. Source: UniProt P36871 · Backe 2020
0 — Setup: Zn present, sugar pocket shown empty 6SNO holds G1P and Zn. The sugar pocket is shown empty so ordered binding can start. Zn stays as a named occupant (physiological metal is Mg). Opaque, run:null (no autoplay). Residue 117 is VAL.Source: PDB 6SNO (2.7 Å)
① — Glucose 1-phosphate binds Crystal G1P docks as deposited. Thr525 OG1 ⋯ G1P P = 3.01 Å. This is not glycogen and not G6P.Source: 6SNO G1P pose
② — Phospho-Ser135 faces G1P O6 SEP135 is the covalent E~P occupancy. Residue 117 is VAL — not Ser117. Ser135 OG ⋯ Zn = 2.35 Å. Ser135 OG ⋯ G1P O6 = 4.90 Å is a deposited contact, far from ping-pong attack geometry (named teaching contact, not a Michaelis claim). Crystal Zn ≠ physiological Mg.Source: 6SNO SEP135 / Zn
③ — O6 attacks Ser135-P → G1,6BP (hypothetical, lit.-based) White nucleophile rides from G1P O6 to SEP135 P. G1,6BP is an identity label on the same G1P mesh — extra phosphate atoms at O6 are not drawn. Compiled PGM writes both halves as one cycle; this page splits them. Slow-motion on purpose.Source: compiled PGM ping-pong · UniProt P36871
④ — Bisphosphate: C1-P is now the donor (hypothetical, lit.-based) Still the 6SNO G1P mesh, now teaching-G1,6BP. C1-P will return phosphate to Ser135. No reorientation movie — the protein is static.Source: compiled ping-pong bookkeeping
⑤ — C1-P returns to Ser135 → G6P (hypothetical, lit.-based) White nucleophile rides from G1P P to Ser135 OG. G1P fades in place to overlay G6P (6SNQ). Overlay contacts are not geomClaims. E~P occupancy stays. Slow-motion on purpose.Source: 6SNQ overlay onto 6SNO · EC 5.4.2.2
⑥ — G6P leaves — glycolysis / UGP2 next [schematic overlay] G6P departs. Zn stays. G6P feeds glycolysis (PGI) and can return toward synthesis via UGP2. This page does not make UDP-glucose.Source: glycogen-breakdown bookkeeping

How to read this page — a first-pass primer First pass: Setup (Zn present, sugar pocket empty, Ser135 ★) → ① crystal G1P docks → ② SEP135 named vs Val117 → ③ white O6 → Ser135-P (G1,6BP identity) → ④ C1-P is now the donor → ⑤ white C1-P → Ser135 OG, G1P becomes overlay G6P → ⑥ G6P leaves; Zn stays. Second pass: 3.01 Å / 2.35 Å / 2.01 Å metal shell are crystal facts on 6SNO; G6P and G1,6BP identity are [schematic]. Third pass: open “Disagreements” for isoform-2 Val117, Zn vs Mg, overlay vs ternary, and E~P vs A-page.
Chemistry primer — ping-pong phospho-relay PGM1 moves the phosphate from C1 to C6 via a covalent phospho-Ser and a glucose 1,6-bisphosphate intermediate. Gold is unused on this page (no net H⁺ in the EC equation). White = phosphoryl transfer (PO₃), not hydride. Net: α-G1P ⇌ α-G6P. This is not PYGL (G1P from glycogen) and not UGP2 (UDPG from G1P).
Words used on screen — isoform 2 · SEP135 · overlay G6P Isoform 2 — residue 117 is VAL; isoform-1 Ser117 numbering does not apply to this mesh. SEP135 — deposited phospho-Ser (E~P). Overlay G6P — 6SNQ Kabsch-fit onto 6SNO, not a 6SNO ternary. Zn — crystal occupant; physiological metal is Mg.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 6SNO (2.7 Å) with G1P and Zn; Ser135 OG ⋯ Zn = 2.35 Å; Asp306 OD2 ⋯ Zn = 1.98 Å; Asp308 OD1 ⋯ Zn = 2.01 Å; Asp310 OD1 ⋯ Zn = 2.01 Å; Thr525 OG1 ⋯ G1P P = 3.01 Å. The inferred layer ([schematic]): G1,6BP identity, transferring nucleophile spheres, G6P overlay (6SNQ), product leave. Binding order is compiled staging, not a kinetic fit. The protein mesh is static. Overlay contacts and the 4.90 Å O6 teaching contact are not geomClaims. Two deposited residue-pair distances plus the metal shell are the claim set.
Disagreements on record (a) Isoform 2 ≠ isoform 1 numbering. Residue 117 is VAL; phospho-Ser is SEP135. (b) Zn ≠ physiological metal. UniProt lists Mg; 6SNO holds Zn. (c) 6SNQ overlay ≠ 6SNO ternary. G6P is schematic on this mesh. (d) E~P vs A-page. Covalent phospho-Ser is disclosed. (e) Concerted vs split. Compiled PGM writes both phosphate throws as one ping-pong cycle; this page splits them (③ then ⑤). (f) 4.90 Å O6 contact is deposited but far from attack geometry — teaching, not a Michaelis claim. (g) 5EPC WT apo is not this sugar story.
Regulation — isoforms · GSD XIV This mesh is PGM1 isoform 2. Isoform 1 numbering (Ser117) is not this occupancy. PGM2 / PGM3 are other genes. GSD XIV (PGM1-CDG) is named, not simulated. Cytosolic mutase feeding G6P into glycolysis or back toward UDPG via UGP2.Source: UniProt P36871 · Backe 2020 PMID:32221390
Kinetics scope (no measured timecourse on this page) One α-G1P ⇌ α-G6P event is drawn, not a steady-state run. Compiled BRENDA values for EC 5.4.2.2 are not re-asserted here — no measured k_cat/K_m on this page [schematic]. Pair with a kinetics chapter.Source: BRENDA EC 5.4.2.2 — no k_cat/K_m re-asserted
Sequence Human PGM1 UniProt P36871 · NCBI Gene 5236. Screen uses 6SNO PDB-author numbering (SEP135, Val117, Asp306). Chain A. Cα 6–580.
Simulation map — what you see is what is written Setup = 6SNO sugar pocket empty, Zn visible (opaque, no autoplay). ① crystal G1P moves in. ② SEP135 / Zn named. ③ slow-mo: white nucleophile O6 → Ser135-P (G1,6BP identity). ④ C1-P named as donor. ⑤ slow-mo: white nucleophile C1-P → Ser135 OG; G1P fades to overlay G6P. ⑥ G6P leaves; Zn stays. Only these events move.
Sources — bibliography of this page S1 — PDB 6SNO: human PGM1 isoform 2, 2.7 Å, G1P + Zn — public coordinates; measured OG⋯Zn = 2.35 Å · OG1⋯P = 3.01 Å S2 — PDB 6SNQ: G6P overlay onto 6SNO — [schematic] product, not a 6SNO ternary S3 — Backe et al., Sci Rep 2020, PMID:32221390 — human PGM1 isoform 2 S4 — Sequence: UniProt P36871 (human PGM1) · NCBI Gene 5236 S5 — Kinetics: BRENDA EC 5.4.2.2 — 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., G1,6BP identity, phosphate-flight, G6P on 6SNO, product release), the pose is drawn schematically and labeled as such in the narration.

N-domainC-domainONphosphoryl (white)