Transaldolase - 3D Mechanism Simulator

Loading structural data… (1F05)

References & Databases

START HERE — how to read S7P + GAP ⇌ E4P + F6P A class-I aldolase cartoon on an apo human TALDO pocket. Real crystal: 1F05 (2.45 Å) with deposited Lys142 ★ waiting — no sugar is in this deposit. S7P, E4P, GAP, F6P are [schematic]. Lys142 forms a Schiff base with S7P C2; retro-aldol releases E4P; GAP condenses to F6P. Measured Å is the deposited Glu106⋯Lys142 NZ pair only. Net: S7P + GAP ⇌ E4P + F6P — no net H⁺. F6P and GAP return to glycolysis. This is not TKT (that enzyme uses TPP).
Crystal structure PDB 1F05 — human transaldolase apo, 2.45 Å (Thorell et al. 2000, PMID 10869557). Coordinates are public. Mesh = chain A, residues 11–332 (DIMERIC A+B in the deposit; one pocket drawn). UniProt P37837. NCBI Gene 6888 (TALDO1).
Mechanism — Schiff Lys142, retro-aldol, aldol EC 2.2.1.2 is a class-I transaldolase. This page: Lys142 ★ ε-amine attacks S7P C2; C3–C4 cleavage releases E4P; GAP condenses and the imine hydrolyzes to F6P. Glu106 ★ is the nearby acid. 1F05 is apo — unlike aldolase 1ZAI, there is no deposited imine. Compiled TALDO writes Schiff + cleavage as one cycle; the screen splits them. Source: UniProt P37837 · Rhea 17053 · PDB 1F05 · PMID 10869557
0 — Setup: empty pocket, Lys142 waiting The pocket presents apo Lys142 ★. Opaque, run:null (no autoplay). No sugar is deposited. Glu106 ★ is the nearby acid.Source: PDB 1F05 (2.45 Å)
① — S7P binds (schematic ketose) [schematic] S7P (a TKT product) docks with carbonyl C2 toward Lys142. Not a deposited ternary.Source: schematic pose off 1F05 Lys142 NZ
② — Schiff base (deposited Glu106⋯NZ) (hypothetical, lit.-based) Lys142 ★ attacks S7P C2. The covalent imine is [schematic] — 1F05 is apo. Deposited pocket contact: Glu106 OE1 ⋯ Lys142 NZ = 4.32 Å. Overlay S7P C2⋯NZ is teaching geometry, not a geomClaim. Slow-motion on purpose.Source: 1F05 Glu106 / Lys142 · compiled EC 2.2.1.2
③ — Retro-aldol: E4P leaves (hypothetical, lit.-based) The C3–C4 bond of the Schiff adduct breaks. E4P leaves; a C3 ketol stays on Lys142. S7P cross-fades toward E4P. Slow-motion on purpose.Source: compiled EC 2.2.1.2 · Thorell 2000
④ — GAP binds [schematic] GAP docks as the second aldose. E4P has left; the ketol remains on Lys142.Source: schematic acceptor on 1F05 Lys142 seat
⑤ — Aldol: GAP + ketol → F6P (hypothetical, lit.-based) GAP condenses with the Lys142 ketol. The imine hydrolyzes and F6P appears in place. Lys142 is regenerated. Slow-motion on purpose.Source: compiled EC 2.2.1.2 · Rhea 17053
⑥ — F6P leaves — return to glycolysis [schematic] F6P departs. Net: S7P + GAP ⇌ E4P + F6P — no net H⁺. F6P and GAP (from TKT) return to glycolysis.Source: PPP bookkeeping · EC 2.2.1.2

How to read this page — a first-pass primer First pass: Setup (apo Lys142) → ① S7P docks → ② Schiff (Glu106⋯NZ measured) → ③ E4P leaves → ④ GAP docks → ⑤ F6P appears → ⑥ F6P leaves. Second pass: only Glu106⋯NZ Å is printed — sugars are schematic. Third pass: open “Disagreements” for apo vs 1ZAI imine, Schiff vs one-cycle, and dimer.
Chemistry primer — class-I transaldolase S7P is a ketose (carbonyl at C2). Lys142 makes a Schiff imine. Retro-aldol cuts C3–C4 (E4P leaves). GAP condenses to F6P and the imine hydrolyzes. Net: S7P + GAP ⇌ E4P + F6P. No TPP, no NADP, no net H⁺. TKT is the TPP enzyme, not this page.
Words used on screen — Schiff · retro-aldol · schematic Schiff — the covalent Lys142–C2 imine, drawn as a teaching label on an apo frame. Retro-aldol — C3–C4 cleavage that releases E4P. Schematic — sugars are teaching poses off Lys142 NZ, not a deposited ternary.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 1F05 (2.45 Å) human TALDO apo with Lys142 / Glu106. The inferred layer (all [schematic]): S7P, E4P, GAP, F6P, the Schiff adduct, retro-aldol, aldol, and product leave. Glu106⋯NZ is the geomClaim. Schematic sugar contacts are not. Binding order is compiled staging, not a kinetic fit. The protein mesh is static.
Disagreements on record (a) Apo vs imine crystal. 1F05 holds no sugar; aldolase 1ZAI holds a real Lys–FBP imine. This page does not borrow 1ZAI geometry. (b) Schiff vs one-cycle. Compiled TALDO writes Schiff + cleavage as one event; this page splits them (② then ③). (c) Dimer. 1F05 is A+B; one chain-A pocket is drawn. (d) TKT vs TALDO. TKT uses TPP; TALDO uses a lysine Schiff. (e) Schematic S7P C2⋯NZ is not a geomClaim.
Regulation — non-oxidative PPP · isoforms TALDO sits after TKT on non-oxidative PPP and returns F6P + GAP toward glycolysis. Human TALDO1 (P37837) is the gene named. No allosteric crystal is claimed here.Source: UniProt P37837 · textbook TKT → TALDO
Kinetics scope (no measured timecourse on this page) One S7P + GAP ⇌ E4P + F6P event is drawn, not a steady-state run. Compiled BRENDA values for EC 2.2.1.2 are not re-asserted here — no measured k_cat/K_m on this page [schematic]. Pair with a kinetics chapter.Source: BRENDA EC 2.2.1.2 — no k_cat/K_m re-asserted
Sequence Human TALDO1 UniProt P37837 · NCBI Gene 6888. Residue numbers on this screen are 1F05 (Lys142, Glu106).
Simulation map — what you see is what is written Setup = 1F05 apo pocket (opaque, run:null). ① S7P moves in (schematic). ② slow-mo: Lys142 Schiff; Glu106⋯NZ 4.32 Å after dock. ③ slow-mo: S7P fades to E4P. ④ GAP docks. ⑤ slow-mo: GAP fades to F6P. ⑥ F6P leaves. Only these events move.
Sources — bibliography of this page S1 — PDB 1F05: human TALDO apo, 2.45 Å — public coordinates (Thorell 2000, PMID 10869557) S2 — Sequence: UniProt P37837 · NCBI Gene 6888 · Rhea 17053 S3 — Kinetics: BRENDA EC 2.2.1.2 — no k_cat/K_m re-asserted on this page

› Backbones and Lys142 occupancy are taken directly from the listed PDB entry. 1F05 is apo — no sugar is deposited. Where no crystalline state exists on this frame (S7P, E4P, GAP, F6P, Schiff adduct, product release), the pose is drawn schematically and labeled as such in the narration.

N-domainC-domainON