Metabolism — citric acid cycle (step 3)
Isocitrate dehydrogenase: oxidative decarboxylation
How the Isocitrate dehydrogenase works, in 3 steps. Each step shows the structures and the curved arrows that move the electrons.
In short. A 3-step mechanism. Typical reagents: Isocitrate, NAD⁺ (or NADP⁺), Mn²⁺ or Mg²⁺. Conditions: Mitochondrial matrix, pH ≈ 7.4. Bonds formed: C=O (ketone); NADH; CO₂; C=C then C–H; bonds broken: C–H (carbinol); C–C (CO₂). Stereochemistry: Hydride to one face of NAD⁺ (4R/4S-H); new CH₂ stereo-free. Rate and selectivity: Rate-controlling step of the cycle; allosterically activated by ADP, inhibited by ATP and NADH.
At a glance
Step 1: Hydride transfer to NAD⁺
A hydride transfers from isocitrate's secondary alcohol carbon to NAD⁺ (or NADP⁺), oxidizing it to a ketone (oxalosuccinate) — the same hydride-transfer oxidation mechanism as malate dehydrogenase, covered next in this cycle.
Step 2: β-Keto acid sets up a cyclic TS
This new ketone, positioned beta to a carboxylate group, sets up exactly the six-membered cyclic transition state used in the standalone β-keto acid decarboxylation entry covered much earlier in this library.
Step 3: CO₂ lost; enol tautomerizes
Loss of CO₂ through that same concerted, retro-ene-like mechanism gives α-ketoglutarate — this single step both oxidizes the substrate and releases the cycle's first equivalent of CO₂, and it's the primary rate-controlling, regulated step of the entire citric acid cycle.
Abbreviations and terms
- R
- R group. Any carbon substituent (alkyl, aryl…) whose identity does not matter for the mechanism.
- H2
- Hydrogen gas. Reductant for catalytic hydrogenation.
- TS
- Transition state. The highest-energy point on the pathway between two minima; it cannot be isolated.
- ATP
- Adenosine triphosphate. The cell’s energy currency; transfers phosphate groups.
- ADP
- Adenosine diphosphate. ATP after losing one phosphate.
- NAD+
- Nicotinamide adenine dinucleotide (oxidised). Hydride-accepting coenzyme in oxidations.
- NADH
- Nicotinamide adenine dinucleotide (reduced). Hydride-donating coenzyme.
- NADP
- NADP⁺ / NADPH. Phosphorylated NAD cousin used mainly in biosynthetic reductions.
How it compares with related reactions
| Isocitrate dehydrogenase | Aconitase | Citrate synthase | |
|---|---|---|---|
| Reagents | Isocitrate, NAD⁺ (or NADP⁺), Mn²⁺ or Mg²⁺ | Citrate, [4Fe-4S] cluster (Fe₄ binds OH), enzyme base (Ser) and acid | Acetyl-CoA, oxaloacetate, citrate synthase (His274, His320, Asp375) |
| Conditions | Mitochondrial matrix, pH ≈ 7.4 | Mitochondrial matrix, pH ≈ 7.4, 37 °C | Mitochondrial matrix, pH ≈ 7.8, 37 °C |
| Stereochemistry | Hydride to one face of NAD⁺ (4R/4S-H); new CH₂ stereo-free | Anti elimination; the intermediate flips so water adds to the opposite carbon | Enolate attacks the si face of oxaloacetate; pro-S citrate |
| Rate / selectivity | Rate-controlling step of the cycle; allosterically activated by ADP, inhibited by ATP and NADH | Near-equilibrium; citrate:isocitrate ≈ 90:10 at equilibrium | Hydrolysis of citryl-CoA (ΔG°′ ≈ −32 kJ/mol overall) makes the step irreversible |
Test yourself
Try to answer each question before opening it.
Which reagents and conditions are typical for the Isocitrate dehydrogenase?
Isocitrate, NAD⁺ (or NADP⁺), Mn²⁺ or Mg²⁺. Conditions: Mitochondrial matrix, pH ≈ 7.4.
Which bonds are formed and which are broken?
Formed: C=O (ketone); NADH; CO₂; C=C then C–H. Broken: C–H (carbinol); C–C (CO₂).
What is the stereochemical outcome?
Hydride to one face of NAD⁺ (4R/4S-H); new CH₂ stereo-free
What controls the rate or the selectivity?
Rate-controlling step of the cycle; allosterically activated by ADP, inhibited by ATP and NADH
Study guides that help with this reaction
- How to learn reaction mechanisms (without memorising everything)
- Curved-arrow notation: rules and the mistakes students make