Glycogen synthase (muscle) - 3D Mechanism Simulator

Loading structural data… (7Q13)

References & Databases

START HERE — how to read glycogen(n) + UDPG → glycogen(n+1) + UDP An elongation cartoon on the human GYS1 frame that actually exists: 7Q13 (3.0 Å EM) chain A, activated GYS1–GYG1 with crystal UDP + glucose and allosteric G6P. The soak was UDP-glucose; occupancy is cleaved — never label UDP as UDPG. UDPG is [schematic] (UDP+GLC rebuilt). Crystal GLC is product-like, not glycogen(n). G6P is allosteric, not this pocket. Liver GYS2 has no PDB. Blue is compiled 4-OH nucleophile at the Glu510 seat, not hydride. Measured Å are deposited 7Q13 pairs only.
Crystal structures PDB 7Q13 — human GYS1–GYG1 activated + G6P + UDP + GLC, 3.0 Å EM (McCorvie et al. 2022, PMID 35835870). Coordinates are public. 7Q0B / 7Q0S are inhibited, no catalytic ligands — not this mesh. G6P on 7Q13 has a chirality caveat (C1/C3/C4/C5) — occupancy named, not a sugar-stereochemistry lesson.
Mechanism — glycosyl transfer UniProt P13807 EC 2.4.1.11: glycogen(n) + UDPG + H⁺ → glycogen(n+1) + UDP. Retaining GT-B; no covalent glycosyl-enzyme on this page (A-page). Acceptor glycogen is not deposited — Glu510 ★ names the 4-OH seat. Source: UniProt P13807 · PDB 7Q13 · PMID 35835870
0 — Setup: G6P present, pocket shown empty 7Q13 holds UDP+GLC (cleaved) and allosteric G6P. The catalytic pocket is shown empty so ordered binding can start. G6P stays. Opaque, run:null (no autoplay). Liver GYS2 has no PDB.Source: PDB 7Q13 (3.0 Å EM)
① — UDP-glucose binds Schematic UDPG docks as UDP + glucose rebuilt on the cleaved occupancy — not a deposited UDP-glucose. Never label crystal UDP as UDPG.Source: 7Q13 UDP+GLC occupancy rebuilt
② — Acceptor 4-OH seat — Glu510 Glu510 ★ OE1 ⋯ GLC O4 = 3.07 Å (deposited). Acceptor glycogen(n) is not deposited. Crystal GLC is product-like, not the polymer.Source: 7Q13 Glu510 / GLC O4
③ — 4-OH attacks UDPG C1 → glycogen(n+1) + UDP (hypothetical, lit.-based) Blue nucleophile rides from the Glu510 seat to UDPG C1. UDPG fades in place to crystal UDP + glucose. Acceptor glycogen is identity. No covalent glycosyl-enzyme. Slow-motion on purpose.Source: compiled glycogen-synthase transfer · UniProt P13807
④ — Crystal UDP + glucose are product-like Deposited cleaved occupancy. Arg331 NH2 ⋯ UDP PB = 4.32 Å. UDP PB ⋯ GLC C1 = 5.44 Å is cleaved, not a glycosidic bond (teaching). Allosteric G6P: His291 CA ⋯ G6P P = 13.61 Å (far; not this pocket).Source: 7Q13 UDP / GLC / G6P
⑤ — UDP leaves — GBE1 next UDP departs. G6P stays. Glucose stays as a glycogen(n+1) analog. Branching is GBE1. Liver GYS2 is not this mesh.Source: glycogen-synthesis bookkeeping

How to read this page — a first-pass primer First pass: Setup (G6P present, pocket empty, Glu510 ★) → ① schematic UDPG docks → ② 4-OH seat named → ③ blue seat → C1, fade to UDP+GLC → ④ product-like occupancy named → ⑤ UDP leaves; G6P stays. Second pass: 3.07 / 4.32 Å are crystal facts; 5.44 / 13.61 Å are teaching; UDPG is [schematic]. Third pass: open “Disagreements” for cleaved soak vs UDPG, G6P allosteric vs catalytic, GYS1 vs GYS2, and A-page.
Chemistry primer — glycosyl transfer Glycogen synthase adds glucose from UDP-glucose onto the non-reducing 4-OH of glycogen. UDP leaves. Gold is unused on this page (net H⁺ is in the EC equation, not drawn as a sphere). Blue = compiled 4-OH nucleophile at the Glu510 seat, not hydride. This is not GYG1 (primer) and not GBE1 (branching).
Words used on screen — cleaved soak · allosteric G6P · GYS2 hedge Cleaved soak — 7Q13 was soaked with UDP-glucose; occupancy is UDP + glucose. Allosteric G6P — activator, not the catalytic pocket. GYS2 hedge — liver synthase has no PDB; this mesh is muscle GYS1.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 7Q13 (3.0 Å EM) with UDP, glucose, and G6P; Glu510 OE1 ⋯ GLC O4 = 3.07 Å; Arg331 NH2 ⋯ UDP PB = 4.32 Å. The inferred layer ([schematic]): UDPG, transferring nucleophile sphere, acceptor glycogen identity, product leave. Binding order is compiled staging, not a kinetic fit. The protein mesh is static. PB⋯C1 5.44 Å and His291⋯G6P 13.61 Å are teaching, not attack claims.
Disagreements on record (a) UDP ≠ UDPG. Cleaved soak. (b) Crystal GLC ≠ glycogen(n). Product-like analog. (c) G6P is allosteric, not catalytic. (d) Acceptor glycogen is not deposited — Glu510 names the seat. (e) No covalent glycosyl-enzyme (A-page) — this part is settled: GYS is retaining, and a covalent intermediate has never been demonstrated in any retaining glycosyltransferase. But the sub-step is not settled. Direct SN2-like displacement, front-face SN_i with a short-lived oxocarbenium ion, and an elimination/addition route are all on record; glycogen-synthase-specific work shows a large α-secondary D KIE and a tight UDP/oxocarbenium ion pair, and release of 1,5-anhydro-D-arabino-hex-1-enitol (or its tautomer 1,5-anhydro-D-fructose) when acceptor is absent (Díaz-Vilchis et al., IUBMB Life 2012, PMID:22648728). Step ③ on this page is a direct-displacement staging, not the settled mechanism. (f) GYS2 has no PDB. (g) 7Q0B/7Q0S inhibited, no catalytic ligands. (h) G6P chirality caveat on 7Q13.
Regulation — G6P · phosphorylation · isoforms G6P is an allosteric activator (UniProt BINDING 291–301 / 501 / 582 / 586). Phosphorylation inactivates; this page is the activated EM state. This mesh is GYS1 (muscle). Liver GYS2 (P54840) has no PDB. No GSD allele is simulated.Source: UniProt P13807 · PDB 7Q13 · PMID 35835870
Kinetics scope (no measured timecourse on this page) One glycogen(n) + UDPG → glycogen(n+1) + UDP event is drawn, not a steady-state run. Compiled BRENDA values for EC 2.4.1.11 are not re-asserted here — no measured k_cat/K_m on this page [schematic]. Pair with a kinetics chapter.Source: BRENDA EC 2.4.1.11 — no k_cat/K_m re-asserted
Sequence Human GYS1 UniProt P13807 · NCBI Gene 2997. Screen uses 7Q13 PDB-author numbering (Glu510, Arg331, His291). Chain A. Cα 29–618. Liver GYS2 is P54840.
Simulation map — what you see is what is written Setup = 7Q13 pocket empty, G6P visible (opaque, no autoplay). ① schematic UDPG moves in. ② 4-OH seat named. ③ slow-mo: blue nucleophile seat → C1; UDPG fades to crystal UDP+GLC. ④ product-like occupancy named. ⑤ UDP leaves; G6P stays. Only these events move.
Sources — bibliography of this page S1 — PDB 7Q13: human GYS1–GYG1 activated, 3.0 Å EM, UDP + GLC + G6P — public coordinates; measured Glu510⋯O4 = 3.07 Å · Arg331⋯PB = 4.32 Å S2 — McCorvie et al. 2022, Nat. Struct. Mol. Biol. 29:628 — PMID 35835870 · DOI 10.1038/s41594-022-00799-3 S3 — Sequence: UniProt P13807 (human GYS1) · NCBI Gene 2997 · GYS2 P54840 (no PDB) S4 — Kinetics: BRENDA EC 2.4.1.11 — 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., UDPG, nucleophile flight, acceptor glycogen identity, product release), the pose is drawn schematically and labeled as such in the narration.

N-domainC-domainONnucleophile (blue)