Metabolism — urea cycle (final step)
Arginase: hydrolysis of arginine to urea
How the Arginase 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: L-Arginine, H₂O, arginase (Mn₂ site). Conditions: Liver mitochondria/cytosol, pH ~9 optimum, 37 °C. Bonds formed: C–O (urea C=O); N–H; bonds broken: C–N (guanidinium to Nδ); O–H. Stereochemistry: Planar guanidinium attacked from one face; no stereocentre created. Rate and selectivity: Very fast; metal-bridging hydroxide is the nucleophile.
At a glance
Step 1: Mn²⁺-bridged hydroxide from water
Arginase carries a binuclear Mn²⁺ center at its active site. A Mn²⁺-bridged hydroxide is generated from water, so the enzyme holds a ready-made hydroxide nucleophile next to the substrate's guanidinium group.
Step 2: Hydroxide attacks the guanidinium carbon
The Mn²⁺-bound hydroxide attacks the guanidinium carbon (the planar, electron-poor carbon bonded to three nitrogens), forming a tetrahedral intermediate. The metal ions stabilize this intermediate and an active-site aspartate shuttles protons.
Step 3: Collapse releases urea and ornithine
The tetrahedral intermediate collapses, expelling ornithine's δ-amine as the leaving group and releasing urea. This is the last step of the urea cycle: urea carries nitrogen waste out of the body, and ornithine returns to the mitochondria to restart the cycle.
Abbreviations and terms
- R
- R group. Any carbon substituent (alkyl, aryl…) whose identity does not matter for the mechanism.
- L
- Ligand. A Lewis-base group (often a phosphine) bound to a metal centre.
- H2
- Hydrogen gas. Reductant for catalytic hydrogenation.
- Asp
- Aspartate. Acidic amino acid.
How it compares with related reactions
| Arginase | Aconitase | Citrate synthase | |
|---|---|---|---|
| Reagents | L-Arginine, H₂O, arginase (Mn₂ site) | Citrate, [4Fe-4S] cluster (Fe₄ binds OH), enzyme base (Ser) and acid | Acetyl-CoA, oxaloacetate, citrate synthase (His274, His320, Asp375) |
| Conditions | Liver mitochondria/cytosol, pH ~9 optimum, 37 °C | Mitochondrial matrix, pH ≈ 7.4, 37 °C | Mitochondrial matrix, pH ≈ 7.8, 37 °C |
| Stereochemistry | Planar guanidinium attacked from one face; no stereocentre created | Anti elimination; the intermediate flips so water adds to the opposite carbon | Enolate attacks the si face of oxaloacetate; pro-S citrate |
| Rate / selectivity | Very fast; metal-bridging hydroxide is the nucleophile | 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 Arginase?
L-Arginine, H₂O, arginase (Mn₂ site). Conditions: Liver mitochondria/cytosol, pH ~9 optimum, 37 °C.
Which bonds are formed and which are broken?
Formed: C–O (urea C=O); N–H. Broken: C–N (guanidinium to Nδ); O–H.
What is the stereochemical outcome?
Planar guanidinium attacked from one face; no stereocentre created
What controls the rate or the selectivity?
Very fast; metal-bridging hydroxide is the nucleophile
Study guides that help with this reaction
- How to learn reaction mechanisms (without memorising everything)
- Curved-arrow notation: rules and the mistakes students make