Glycogen branching enzyme - 3D Mechanism Simulator

Loading structural data… (5CLW)

References & Databases

START HERE — how to read α-1,4 segment → α-1,6 branch A branching cartoon on the human GBE1 frame that actually exists: 5CLW (2.8 Å) chain A. Deposited maltoheptaose (chain D) sits ~36 Å from Asp357 — surface crystal sugar, not the catalytic occupancy, and it is not moved into this pocket. Donor and acceptor sugars are [schematic] at Asp357 / Glu412. Acarbose 5CLT is a named overlay, not this mesh. Apo 4BZY is not this mesh. Retaining GH13: Asp357 ★ is the nucleophile (covalent E~glycosyl, disclosed). Glu412 is the compiled proton donor. Blue is aspartate-oxygen nucleophile, not hydride. Measured Å are deposited 5CLW pairs only.
Crystal structures PDB 5CLW — human GBE1 (UniProt fragment 38–700) + maltoheptaose, 2.8 Å, SGC deposit (to be published). Coordinates are public. Surface chain-D maltoheptaose is named, not catalytic. 5CLT is acarbose analog — named overlay only, not extracted. 4BZY is apo — not this mesh.
Mechanism — retaining GH13 branch UniProt Q04446 EC 2.4.1.18: an α-1,4 segment is transferred to a C6-OH (α-1,6 branch). Asp357 is the nucleophile; covalent glycosyl-enzyme is compiled and disclosed (not a pure A-page). Glu412 is the compiled proton donor; gold H⁺ is not drawn. Source: UniProt Q04446 · PDB 5CLW
0 — Setup: empty catalytic pocket 5CLW holds surface maltoheptaose ~36 Å from Asp357. The catalytic pocket is shown empty so schematic binding can start. Surface sugar is not moved. Opaque, run:null (no autoplay). 5CLT / 4BZY are not this mesh.Source: PDB 5CLW (2.8 Å)
① — α-1,4 donor segment binds Schematic donor docks at Asp357 — [schematic], not the deposited surface maltoheptaose. Binding order is compiled staging, not a kinetic fit.Source: compiled GH13 donor seat on 5CLW Asp357 / Glu412
② — Asp357 nucleophile · Glu412 proton donor Asp357 ★ OD1 ⋯ Glu412 OE1 = 3.11 Å (deposited 5CLW). Schematic donor C1⋯OD1 is teaching, not a geomClaim. Surface maltoheptaose is not this pair.Source: 5CLW Asp357 / Glu412
③ — Asp357 attacks donor C1 → E~glycosyl (hypothetical, lit.-based) Blue nucleophile rides from Asp357 OD1 to schematic donor C1. Product is covalent E~glycosyl identity on this stick — not a third crystal and not surface maltoheptaose. Glu412 proton-donor role is compiled; gold H⁺ is not drawn. Slow-motion on purpose. Not a pure A-page.Source: compiled retaining GH13 · UniProt Q04446
④ — C6 acceptor — α-1,6 attachment (hypothetical, lit.-based) Schematic C6 acceptor docks — the α-1,6 attachment site, not a 5CLW sugar. Compiled: acceptor C6-OH resolves the E~glycosyl to a branch. This page does not polymerize glycogen and does not hydrolyse like AGL. 5CLT acarbose is a named analog overlay, not this ligand.Source: compiled GH13 branch transfer
⑤ — Branch analog leaves The α-1,6 branched unit — donor and acceptor joined by the new C1–O6 bond — leaves as one species on a shared vector. The enzyme is left clean, no glycosyl on Asp357. This page does not elongate (that is GYS1) and does not debranch (that is AGL).Source: glycogen-synthesis bookkeeping

How to read this page — a first-pass primer First pass: Setup (pocket empty, Asp357 ★; surface maltoheptaose named far) → ① schematic donor docks → ② pocket named → ③ blue Asp357 → C1, E~glycosyl identity → ④ schematic C6 acceptor docks → ⑤ branched unit leaves together; enzyme clean. Second pass: 3.11 Å is a crystal fact; ~36 Å is teaching (surface sugar); donor/acceptor are [schematic]. Third pass: open “Disagreements” for surface vs catalytic sugar, 5CLT overlay, covalent vs A-page, and GYS1/AGL.
Chemistry primer — retaining GH13 branch Glycogen branching enzyme cuts an α-1,4 segment and reattaches it as an α-1,6 branch. That segment is more than 6 glucose units long (GBE1 cuts every ~8–14 residues from the non-reducing end); this page draws one ring as a mono-unit proxy for its anomeric centre, so the bond chemistry shown is right but the product is an oligosaccharide, not a diglucoside. The nucleophile is a catalytic aspartate (covalent glycosyl-enzyme). A glutamate is the compiled proton donor. Gold is unused on this page (proton-donor role is compiled, not drawn as a sphere). Blue = nucleophile (aspartate oxygen), not hydride. This is not GYS1 (elongation) and not AGL (debranching).
Words used on screen — surface maltoheptaose · E~glycosyl · 5CLT overlay Surface maltoheptaose — 5CLW chain-D sugar ~36 Å from Asp357; not this pocket. E~glycosyl — covalent Asp357–sugar intermediate, identity on the schematic donor stick. 5CLT overlay — acarbose analog, named, not extracted.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 5CLW (2.8 Å) chain A; Asp357 OD1 ⋯ Glu412 OE1 = 3.11 Å. The inferred layer ([schematic]): donor sugar, acceptor sugar, transferring nucleophile sphere, E~glycosyl identity, product leave. Binding order is compiled staging, not a kinetic fit. The protein mesh is static. Surface maltoheptaose ~36 Å is teaching, not a catalytic claim. Schematic donor C1⋯OD1 is not a geomClaim.
Disagreements on record (a) Crystal maltoheptaose ≠ catalytic occupancy. Chain D is surface (~36 Å). (b) Donor / acceptor are schematic, not 5CLW sugars. (c) 5CLT acarbose is overlay, not this ligand. (d) Covalent E~glycosyl is compiled — not a trapped glycosyl-Asp crystal on 5CLW (not a pure A-page). (e) Glu412 proton donor is compiled; gold H⁺ is not drawn. (f) 4BZY apo is not this mesh. (g) This page does not elongate (GYS1) and does not debranch (AGL). (h) One ring is drawn, but the real transferred unit is a segment. GBE1 cuts an α-1,4 chain every ~8–14 residues and transfers a piece of more than 6 glucose units to a C6-OH. The C1→O6 bond and the glycosyl-Asp357 shown here sit on that segment's anomeric residue, so the local chemistry is right; the other ~6 units are not drawn, and the product is an oligosaccharide, not the diglucoside the two rings might suggest.
Regulation — isoforms · GSD IV This mesh is GBE1 (one human gene). GSD IV (Andersen) is named, not simulated. No allele is drawn. This page does not show glycogenin primer or synthase elongation.Source: UniProt Q04446 · PDB 5CLW
Kinetics scope (no measured timecourse on this page) One α-1,4 → α-1,6 transfer event is drawn, not a steady-state run. Compiled BRENDA values for EC 2.4.1.18 are not re-asserted here — no measured k_cat/K_m on this page [schematic]. Pair with a kinetics chapter.Source: BRENDA EC 2.4.1.18 — no k_cat/K_m re-asserted
Sequence Human GBE1 UniProt Q04446 · NCBI Gene 2632. Screen uses 5CLW PDB-author numbering (Asp357, Glu412). Chain A. Cα 43–700 (UniProt fragment 38–700).
Simulation map — what you see is what is written Setup = 5CLW pocket empty (opaque, no autoplay); surface maltoheptaose named far, not moved. ① schematic donor moves in. ② pocket named. ③ slow-mo: blue nucleophile Asp357 → C1; E~glycosyl identity. ④ schematic C6 acceptor docks. ⑤ branched unit (donor+acceptor joined) leaves together; enzyme clean. Only these events move.
Sources — bibliography of this page S1 — PDB 5CLW: human GBE1, 2.8 Å, maltoheptaose surface occupancy — public coordinates; measured Asp357 OD1⋯Glu412 OE1 = 3.11 Å; SGC deposit, to be published (no PMID) S2 — Overlay named only: PDB 5CLT acarbose analog · apo companion 4BZY — not this mesh S3 — Sequence: UniProt Q04446 (human GBE1) · NCBI Gene 2632 S4 — Kinetics: BRENDA EC 2.4.1.18 — 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., donor/acceptor sugars, nucleophile flight, E~glycosyl identity, product release), the pose is drawn schematically and labeled as such in the narration.

N-domainC-domainONnucleophile (blue)