RuBisCO — Carbon Fixation

1RCX

Mechanism: Andersson & Backlund, 2008; structure: Taylor & Andersson, 1997 (PDB 1RCX).

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Catalytic cycle

1Diffusion · An activator CO₂ wanders through the crowded cytoplasm — Brownian motion carries it toward the active site
2Carbamylation · CO₂ reacts with the ε-amino group of Lys201, forming a carbamate
3Mg²⁺ activation · A Mg²⁺ ion clamps onto the carbamate — the enzyme is now switched on
4RuBP binds · The five-carbon substrate ribulose-1,5-bisphosphate docks into the activated site
5CO₂ capture · A second CO₂ attacks the RuBP enediol — carboxylation builds a six-carbon intermediate
6Products · The intermediate is cleaved — two molecules of 3-phosphoglycerate are released

Molecules

Activator CO₂ · CO₂carbamylates the active-site lysine
Magnesium ion · Mg²⁺clamps the carbamate — switches the enzyme on
Ribulose-1,5-bisphosphate · RuBPthe five-carbon sugar substrate
Substrate CO₂ · CO₂the carbon that actually gets fixed
3-phosphoglycerate · 3-PGAproduct — two molecules released per turnover

How it works

RuBisCO fixes inorganic CO₂ into sugar — the first committed step of the Calvin cycle and the gateway for nearly all carbon entering the biosphere. Catalysis needs two separate CO₂ molecules with very different jobs. First an ACTIVATOR CO₂ diffuses in and reacts with the ε-amino group of an active-site lysine to form a carbamate; a Mg²⁺ ion then clamps onto that carbamate, switching the enzyme on. Only now can the five-carbon substrate ribulose-1,5-bisphosphate (RuBP) bind. RuBisCO abstracts a proton to make a reactive enediol, and a SECOND CO₂ — the substrate carbon that actually gets fixed — attacks it, building a six-carbon intermediate. That intermediate is hydrated and split, releasing two molecules of 3-phosphoglycerate (3-PGA). It is famously sluggish (~3 turnovers per second) and confuses O₂ for CO₂ about a fifth of the time, which is why there is so much of it.