Glycogenin-1 - 3D Mechanism Simulator

Loading structural data… (3T7O)

References & Databases

START HERE — how to read Tyr-OH + UDPG → Glc-Tyr + UDP A primer-glycosylation cartoon on the human GYG1 frame that actually exists: 3T7O (1.85 Å) chain A with crystal UPG and Mn. The attacking OH on this occupancy is partner-chain B Tyr197 (6.78 Å from UPG C1′) — UniProt primer is Tyr195, whose chain-A OH is 18 Å away (dimer hedge). UDP is [schematic] (UPG without glucose). Crystal GLC is a second sugar occupancy, not Tyr-Glc. Blue is tyrosine-oxygen nucleophile, not hydride. Measured Å are deposited 3T7O pairs only. GYG2 is another gene.
Crystal structures PDB 3T7O — human GYG1 + UPG + MN + GLC, 1.85 Å. Coordinates are public. 3T7M is UDP + MN, no glucose donor — not this mesh.
Mechanism — primer glycosylation UniProt P46976 EC 2.4.1.186: Tyr-OH + UDPG + H⁺ → Glc-Tyr + UDP. Chaikuad et al. occupancy on 3T7O. This page is chain A plus the partner Tyr197 stick. Source: UniProt P46976 · PDB 3T7O
0 — Setup: Mn present, pocket shown empty 3T7O holds UPG and catalytic Mn. The pocket is shown empty so ordered binding can start. Mn stays. Opaque, run:null (no autoplay). UniProt primer is Tyr195; closest OH is B Tyr197.Source: PDB 3T7O (1.85 Å)
① — UDP-glucose binds Crystal UPG docks as deposited — real donor occupancy, not a schematic. Glucose C1′ faces the partner tyrosine.Source: 3T7O UPG occupancy
② — Primer tyrosine — dimer hedge B Tyr197 OH ⋯ UPG C1′ = 6.78 Å (deposited, far from attack — teaching). UniProt primer is Tyr195; chain-A OH is 18 Å from this C1′. Crystal GLC is not Tyr-Glc.Source: 3T7O chain B Tyr197 / chain A Tyr195
③ — Tyr-OH attacks UPG C1′ → Glc-Tyr + UDP (hypothetical, lit.-based) Blue nucleophile rides from B Tyr197 OH to UPG C1′. UPG fades in place to schematic UDP. Glucose becomes covalent Glc-Tyr identity — not crystal GLC, not a catalytic E~glycosyl that turns over. Slow-motion on purpose.Source: compiled glycogenin autoglycosylation · UniProt P46976
④ — Mn shell on the donor phosphates Catalytic Mn is deposited. Mn ⋯ UPG O1A = 1.97 Å. Asp102 OD2 ⋯ Mn = 2.00 Å. Asp104 OD1 ⋯ Mn = 1.99 Å. Mn ⋯ O1B = 1.98 Å. Lewis-acid role is compiled; this page claims the deposited shell only.Source: 3T7O MN / Asp102 / Asp104
⑤ — UDP leaves — GYS1 next [schematic UDP] UDP departs. Mn stays. The primer is the start for GYS1 elongation. This page does not polymerize glycogen.Source: glycogen-synthesis bookkeeping

How to read this page — a first-pass primer First pass: Setup (Mn present, pocket empty, Tyr197 ★) → ① crystal UPG docks → ② dimer hedge named → ③ blue Tyr-OH → C1′, fade to UDP → ④ Mn shell named → ⑤ UDP leaves; Mn stays. Second pass: 1.97 / 2.00 / 1.99 / 1.98 Å are crystal facts; 6.78 Å is teaching; UDP is [schematic]. Third pass: open “Disagreements” for Tyr195 vs Tyr197, dimer vs monomer, GLC vs Tyr-Glc, and GYG2.
Chemistry primer — primer glycosylation Glycogenin starts glycogen by attaching glucose to its own tyrosine. The tyrosine oxygen attacks UDP-glucose C1; UDP leaves. Product is Glc-Tyr, the primer for glycogen synthase. Gold is unused on this page (net H⁺ is in the EC equation, not drawn as a sphere). Blue = nucleophile (tyrosine oxygen), not hydride. This is not UGP2 (UDPG synthesis) and not GYS1 (elongation).
Words used on screen — dimer hedge · Tyr-Glc identity · crystal GLC Dimer hedge — UniProt primer is Tyr195; the attacking OH on 3T7O-A UPG is partner-chain B Tyr197. Tyr-Glc identity — covalent primer product, not a third crystal. Crystal GLC — a second sugar occupancy, not the primer product.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 3T7O (1.85 Å) with UPG and Mn; Mn ⋯ O1A = 1.97 Å; Asp102 ⋯ Mn = 2.00 Å; Asp104 ⋯ Mn = 1.99 Å; Mn ⋯ O1B = 1.98 Å. The inferred layer ([schematic]): UDP, transferring nucleophile sphere, Glc-Tyr identity, product leave. Binding order is compiled staging, not a kinetic fit. The protein mesh is static. B Tyr197 OH ⋯ C1′ 6.78 Å and A Tyr195 18 Å are teaching, not attack claims.
Disagreements on record (a) Tyr195 ≠ the attacking OH on this occupancy. UniProt primer is Tyr195; closest OH is B Tyr197. (b) 6.78 Å is far from attack. Teaching, not Michaelis. (c) Crystal GLC ≠ Tyr-Glc. (d) UDP is schematic (UPG without glucose). (e) Not a catalytic E~glycosyl turnover — primer identity. (f) GYG2 is another gene. (g) 3T7M has no glucose donor.
Regulation — isoforms · dimer This mesh is GYG1. Biological unit is a dimer; this cartoon is chain A plus the partner Tyr197 stick. GYG2 is another gene. No GSD allele is simulated.Source: UniProt P46976 · PDB 3T7O
Kinetics scope (no measured timecourse on this page) One Tyr-OH + UDPG → Glc-Tyr + UDP event is drawn, not a steady-state run. Compiled BRENDA values for EC 2.4.1.186 are not re-asserted here — no measured k_cat/K_m on this page [schematic]. Pair with a kinetics chapter.Source: BRENDA EC 2.4.1.186 — no k_cat/K_m re-asserted
Sequence Human GYG1 UniProt P46976 · NCBI Gene 2992. Screen uses 3T7O PDB-author numbering (Tyr195, Tyr197, Asp102, Asp104). Chain A + partner B Tyr197 stick. Cα 0–262.
Simulation map — what you see is what is written Setup = 3T7O pocket empty, Mn visible (opaque, no autoplay). ① crystal UPG moves in. ② dimer hedge named. ③ slow-mo: blue nucleophile Tyr-OH → C1′; UPG fades to schematic UDP. ④ Mn shell named. ⑤ UDP leaves; Mn stays. Only these events move.
Sources — bibliography of this page S1 — PDB 3T7O: human GYG1, 1.85 Å, UPG + MN — public coordinates; measured Mn⋯O1A = 1.97 Å · Asp102⋯Mn = 2.00 Å S2 — Companion: PDB 3T7M UDP + MN, no glucose donor — not this mesh S3 — Sequence: UniProt P46976 (human GYG1) · NCBI Gene 2992 S4 — Kinetics: BRENDA EC 2.4.1.186 — 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., UDP, nucleophile flight, Tyr-Glc identity, product release), the pose is drawn schematically and labeled as such in the narration.

N-domainC-domainONnucleophile (blue)