Transketolase - 3D Mechanism Simulator

Loading structural data… (3MOS)

References & Databases

START HERE — how to read two TKT shuffles One enzyme, two carbon-shuffles, one crystal. Real frame: human TKT 3MOS (1.75 Å) with deposited TPP (residue 700) and Ca²⁺. No sugar is in this deposit — Xu5P, R5P, S7P, GAP, E4P, F6P are [schematic]. Tab 1: Xu5P + R5P ⇌ S7P + GAP. Tab 2: Xu5P + E4P ⇌ F6P + GAP. TPP C2 ylide takes a ketol and transfers it. Measured Å are Ca–ligand pairs on 3MOS only. EDO / Na⁺ are crystallization buffer, not extracted. No net H⁺. TALDO uses S7P + GAP next.
Crystal structure PDB 3MOS — human transketolase + TPP + Ca²⁺, 1.75 Å (Mitschke et al. 2010, PMID 20667822). Coordinates are public. Mesh = chain A, residues 3–618 (ASU is monomer; BIOMT dimer not drawn). UniProt P29401. NCBI Gene 7086 (TKT).
Mechanism — TPP ylide, covalent ketol, two acceptors EC 2.2.1.1 transfers a C2 ketol from a ketose donor (Xu5P) onto an aldose acceptor. This page: TPP C2 ylide attacks Xu5P; the adduct waits; R5P (tab 1) or E4P (tab 2) accepts the ketol. His258 ★ / Glu160 ★ line the ylide. Ca²⁺ clamps the pyrophosphate. Compiled TKT writes adduct + transfer as one cycle; the screen splits donor vs acceptor beats. Source: UniProt P29401 · Rhea 27626 / 10508 · PDB 3MOS · PMID 20667822
0 — Setup: TPP + Ca²⁺, empty sugar pocket The pocket presents deposited TPP and Ca²⁺ as occupancy. Opaque, run:null (no autoplay). No sugar is deposited. EDO / Na⁺ are buffer.Source: PDB 3MOS (1.75 Å)
① — Xu5P binds (schematic ketol donor) [schematic] Open-chain Xu5P is seated with C2 toward TPP C2. Not a deposited ternary. Xu5P is the RPE product.Source: schematic pose off 3MOS TPP C2
② — Ca²⁺ clamps TPP (deposited Å) Deposited: Asp155 OD1 ⋯ CA = 2.22 Å on 3MOS. Asn185 OD1 ⋯ CA = 2.18 Å; TPP O1A ⋯ CA = 2.15 Å; TPP O1B ⋯ CA = 2.16 Å. Overlay sugar⋯TPP distances are not geomClaims. Ca²⁺ is a Lewis-acid clamp, not a redox metal.Source: 3MOS CA + Asp155 / Asn185 / TPP O1A / O1B
③ — TPP ylide takes the C2 ketol (hypothetical, lit.-based) The thiazolium C2 ylide attacks Xu5P C2. A covalent ketol adduct forms on TPP [schematic]. Xu5P fades (donor consumed). His258 ★ / Glu160 ★ pin for the arrow window. Slow-motion on purpose.Source: compiled EC 2.2.1.1 · Mitschke 2010
④ — Acceptor binds (R5P or E4P) [schematic] Tab 1 docks R5P; tab 2 docks E4P. The ketol still sits on TPP. Not a deposited ternary.Source: schematic acceptor on 3MOS TPP seat
⑤ — Ketol transfers — product + GAP (hypothetical, lit.-based) The C2-ketol is transferred onto the acceptor. Tab 1: R5P → S7P + GAP. Tab 2: E4P → F6P + GAP. TPP is regenerated. Slow-motion on purpose.Source: compiled EC 2.2.1.1 · Rhea 27626 / 10508
⑥ — Products leave — TPP stays [schematic] Products depart opposite ways. Deposited TPP and Ca²⁺ stay. Net: Xu5P + R5P ⇌ S7P + GAP, or Xu5P + E4P ⇌ F6P + GAP — no net H⁺. TALDO uses S7P + GAP next.Source: PPP bookkeeping · EC 2.2.1.1

How to read this page — a first-pass primer First pass: Setup (TPP + Ca occupancy) → ① Xu5P docks → ② Ca clamp measured → ③ ylide adduct → ④ acceptor docks → ⑤ ketol transfer → ⑥ products leave. Second pass: only Ca–ligand Å are printed — sugars are schematic. Third pass: open “Disagreements” for one enzyme / two shuffles, adduct vs one-cycle, and EDO buffer.
Chemistry primer — TPP ketol transfer Xu5P is a ketose donor (carbonyl at C2). TPP C2 ylide takes that C2-ketol as a covalent adduct. An aldose acceptor (R5P or E4P) receives it, making a longer ketose (S7P or F6P) plus GAP. Net: no NADP, no net H⁺. Two shuffles, one cofactor.
Words used on screen — ylide · ketol · schematic Ylide — the deprotonated TPP thiazolium C2 that attacks the donor. Ketol — the C2 fragment transferred from Xu5P. Schematic — sugars are teaching poses off TPP C2, not a deposited ternary.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 3MOS (1.75 Å) human TKT with TPP and Ca²⁺ and Asp155 / Asn185 / TPP O1A / O1B. The inferred layer (all [schematic]): Xu5P, R5P, S7P, GAP, E4P, F6P, the ylide adduct, and product leave. Ca–ligand Å are geomClaims. Schematic sugar contacts are not. Binding order is compiled staging, not a kinetic fit. The protein mesh is static.
Disagreements on record (a) One enzyme, two shuffles. Both pairs run on the same TPP; this page splits them into tabs, not two URLs. (b) Adduct vs one-cycle. Compiled TKT writes ylide attack + transfer as one catalytic cycle; this page splits donor vs acceptor beats (③ then ⑤). (c) No sugar co-crystal. 3MOS holds TPP + Ca, not a ternary. Overlay sugar Å are not geomClaims. (d) ASU vs dimer. 3MOS deposits chain A; BIOMT dimer is not drawn. (e) EDO / Na⁺ are crystallization buffer, not substrate. (f) Phe359 is PHE on this frame, not Arg.
Regulation — non-oxidative PPP · isoforms TKT sits after RPE / RPI on non-oxidative PPP. Human TKT (P29401) is the gene named; TKTL1 / TKTL2 are other genes, not this mesh. No allosteric crystal is claimed here.Source: UniProt P29401 · textbook RPE/RPI → TKT → TALDO
Kinetics scope (no measured timecourse on this page) One shuffle event is drawn per tab, not a steady-state run. Compiled BRENDA values for EC 2.2.1.1 are not re-asserted here — no measured k_cat/K_m on this page [schematic]. Pair with a kinetics chapter.Source: BRENDA EC 2.2.1.1 — no k_cat/K_m re-asserted
Sequence Human TKT UniProt P29401 · NCBI Gene 7086. Residue numbers on this screen are 3MOS (His258, Glu160, Asp155, Asn185).
Simulation map — what you see is what is written Setup = 3MOS pocket with TPP + Ca occupancy (opaque, run:null). ① Xu5P moves in (schematic). ② Asp155⋯CA 2.22 Å after dock. ③ slow-mo: ylide adduct; Xu5P fades. ④ acceptor docks. ⑤ slow-mo: ketol transfer; product + GAP appear. ⑥ products leave; TPP stays. Only these events move.
Sources — bibliography of this page S1 — PDB 3MOS: human TKT + TPP + Ca²⁺, 1.75 Å — public coordinates (Mitschke 2010, PMID 20667822) S2 — Sequence: UniProt P29401 · NCBI Gene 7086 · Rhea 27626 / 10508 S3 — Kinetics: BRENDA EC 2.2.1.1 — no k_cat/K_m re-asserted on this page

› Backbones and TPP/Ca occupancy are taken directly from the listed PDB entry. 3MOS holds TPP + Ca²⁺, not a sugar ternary. Where no crystalline state exists on this frame (Xu5P, R5P, S7P, GAP, E4P, F6P, ylide adduct, product release), the pose is drawn schematically and labeled as such in the narration.

N-domainC-domainON