rubisco reaction mechanism

Rubisco - reaction mechanism

The enzyme ribulose-1,5-bisphosphate carboxylase (rubisco) catalyzes the addition of gaseous carbon dioxide to ribulose-1,5-bisphosphate (RuBP). Product of the reaction are two molecules of 3-phosphoglyceric acid.

C₅O₃H₈(PO₄^2-)₂ + CO₂ -> 2 C₃O₃H₄PO₄^2-

For the reaction to occur it is neccessary that the protein is activated by the covalent binding of a molecule of carbon dioxide. This CO₂ forms a carbamate with the terminal amino group of lysine²⁰¹. The carbamate itself is labile, it is stabilized in the enzyme by a magnesium ion.

The figures to follow may be viewed in an interactive manner: using the mouse the molecules can be moved; clicking the boxes highlights the described features. Only the first figure is backed by experimental data. Hydrogen atoms (which are not visible in a X-ray data set) were added by a molecular modelling program. The reaction steps were also modeled - there is no claim as to the absolute positions of the atoms concerned. The figures are merely meant to visualize the reaction mechanism.

colour scheme: C H O N P Mg

1

Within the active site of the enzyme the magnesium atom is fixed by amino acids 201 to 204.

Lys²⁰¹

with the carbamate group

Asp²⁰²

Asp²⁰³

Glu²⁰⁴

The magnesium ion is coordinated by six oxygen atoms:

by three amino acids

by one water

twice by the substrate RuBP
- by the keto oxygen off C₂

- by the hydroxyl ogygen off C₃

The oxygen atoms form a somewhat distorted octahedron around the magnesium

(distances in Å).

reset

2

The first step on the reaction pathway is the tautomerisation of RuBP to the enediolate. In this reaction the hydrogen at C₃ (fig. 1)

is bound to the carbamate group of lys²⁰¹

. The oxygen atom at C₂

receives the negative charge of the carbamate oxygen. C₃ has been sp³ hybridized with tetrahedral ligands before. During this step it is hybridized to sp² with a trigonal configuration. The ligands of the C₂-C₃ double bond are in cis (turning the molecule with the mouse will show the planar setting).

reset

3

The next step is the binding of a molecule of CO₂

, which displaces a water molecule. The CO₂ itself is polarized by the vicinity of the metal ion and thus can perform an electrophilic attack on the enediolate. This again is accompanied by a change of positions of hydrogen atoms: the hydrogen of the C₃-hydroxyl

(fig. 2) is translocated to a nitrogen atom

on his²⁹⁴. The hydrogen previously bound to the carbamate on lys²⁰¹

is transferred to the enediolate oxygenon C₂ of the RuBP molecule

. The new covalent bond between CO₂ and RuBP results in a branched C₆ sugar.

reset

4

The covalent bond

between CO₂ and RuBP-C₂ forces C₂ temporarily to a sp³ tetrahedral conformation (a change in hybridization pattern results in diffenrent bonding angels, which causes the side chains to move).
The next step is the hydroxylation of C₃. A water molecule

looses a hydrogen atom to his³²⁷

and the oxygen attacks C₃.

reset

5

The newly formed intermediate with two oxygen atoms bound to C₃ is deprotonated by the aid of lys²⁰¹

. The other oxygen atom on C₃ is held in a deprotonated state by his²⁹⁴

. In this very moment the electron configuration of C₃ is less than optimal. It is brought to a normal state by a cleavage of the bond between C₃ and C₂, so it regains a sp² hybridization characteristic of a carboxyl group with planar ligands.

reset

6

The result is one molecule of 3-phosphoglycerate

. In all reactions so far only the carboxyl carbon of this molecule took part. Thus the conformation of it's chiral (middle) carbon atom remained unchanged. If (with aid of the mouse) you turn the molecule so that (with a vertical orientation of the chain, carboxyl end to the top) both the carboxyl carbon and the terminal carbon (bearing the phosphate group) point to the rear, you may find the hydroxyl group of the middle carbon pointing to the right. That means without doubt this molecule is a D-phosphoglycerate. It is released from the enzyme.
The rest of the carboxylated molecule

remained with a lone electron pair on C₂. Lys¹⁷⁵

supplies a proton as a fourth ligand to C₂.

reset

7

This addition leads from the intermediate to the reaction product. The reaction is stereospecific: another molecule of D-3-phosphoglycerate arises

reset

Literature: C Taylor & I Andersson, J. Mol. Biol. 265 (1997) 432-444