Biological context
Central to glycolysis and gluconeogenesis. Defines the TIM-barrel (β/α)₈ fold — the most common fold in nature.
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Isomerase · Triosephosphate isomerase family
Triosephosphate isomerase
EC EC 5.3.1.1PDB 1YPISaccharomyces cerevisiae
A catalytically perfect enzyme — its reaction is limited only by diffusion. Interconverts GAP and DHAP via a cis-enediol(ate) intermediate.
Mechanistic insight
TIM is the textbook example of a diffusion-limited enzyme (kcat/KM ≈ 10^8 M⁻¹s⁻¹). The active site is gated by a flexible Ω-loop (residues 166–176) whose closure is essential for catalysis and prevents methylglyoxal leakage.
isomeraseTIM barrelloop dynamicsdiffusion-limitedglycolysis
Catalytic mechanism
Type: General acid/base with cis-enediolate intermediate
Rate-limiting: At neutral pH, intramolecular proton transfer between C1 and C2 (or diffusion for GAP→DHAP)
Overall reaction
D-glyceraldehyde-3-phosphate ⇌ Dihydroxyacetone phosphate
01
Substrate binds and the Ω-loop closes
DHAP (or GAP) binds in the active site with its phosphate anchored by Asn11, Lys13 and the N-terminus of helix α6. Loop 6 (residues 166–176) closes over the active site, sequestering the substrate from bulk solvent and pre-organising the electrostatics. Loop 7 (residues 208–213) also contributes.
A:165A:95A:13A:11
Loop closure is essential: open-loop TIM is catalytically inert and leaks methylglyoxal via enediolate decomposition.
Step 1 / 5
References (3)
- Knowles JR. Enzyme catalysis: not different, just better. Nature 350:121–124 (1991).
- Richard JP. A paradigm for enzyme-catalyzed proton transfer at carbon: triosephosphate isomerase. Biochemistry 51:2652–2661 (2012).
- Wierenga RK, Kapetaniou EG, Venkatesan R. Triosephosphate isomerase: a highly evolved biocatalyst. Cell Mol Life Sci 67:3961–3982 (2010).
Kinetic parameters
Steady-state kcat, KM and specificity constants from literature.
| Substrate | kcat (s⁻¹) | KM (mM) | kcat/KM (M⁻¹s⁻¹) | pH | T (°C) | Source |
|---|---|---|---|---|---|---|
| D-glyceraldehyde-3-phosphate (GAP) | 4.30 × 10³ | 0.47 | 9.10 × 10⁶ | 7.6 | 30 | Albery & Knowles, Biochemistry 1976 |
| Dihydroxyacetone phosphate (DHAP) | 430 | 0.97 | 4.40 × 10⁵ | 7.6 | 30 | Albery & Knowles, Biochemistry 1976 |
kcat/KM for GAP → DHAP is ~10^7–10^8 M⁻¹s⁻¹, approaching the diffusion limit. The reaction is near-thermoneutral (Keq ≈ 22 favouring DHAP).
Michaelis–Menten · steady-state simulator
Run TIM in silico.
Integrate the reaction v = Vmax·[S] / (Km,app + [S]) in closed form with RK4, across any [S], [E], and an optional reversible inhibitor. Defaults are drawn from the curated kinetic record for this enzyme where available.
Progress curve · [S](t) and [P](t)30 s window
substrate [S]product [P]
Saturation · v vs. [S]Km,app = 0.470 mM · Vmax,app = 4.30 mM/s
Inhibitor
Curated kinetic record
Defaults seeded from D-glyceraldehyde-3-phosphate (GAP) at pH 7.6 / 30 °C — source: Albery & Knowles, Biochemistry 1976.
Why this enzyme is in the catalog
Showcase for: loop dynamics, electrostatic catalysis, enzyme perfection, the classic β/α barrel architecture.