RuBisCO: Difference between revisions

The structure of spinach Rubisco bound to the naturally occurring inhibitor 2-carboxylarabinitol-1,5-bisphosphate (CAP) and Mg²⁺ ([[8ruc]]<ref>PMID:8648644</ref>), implicates residues that are involved in the catalytic mechanism [[Image:RubiscoMechanism.pdf]]. [[Image:CAP.jpg|left|]] The structure of CAP (left figure) is similar to the hydrated reaction intermediate that is formed following the addition of CO₂ to RUBP. Here is an <scene name='46/463261/8ruc_active-site/1'>isolated α-β barrel</scene> (cartoon and colored for secondary structure) with CAP and and Mg²⁺ in CPK spacefill.  This <scene name='46/463261/8ruc_active-site/5'> overview of the active site</scene> in which the helices have been removed, shows that CAP sits at one end of the α-β barrel, and only residues from the beta strands (gold ball & stick) and loops that link them to helices (white ball & stick) are involved in binding RUBP and Mg²⁺ (the RUBP-bidning residue contributed by the N-terminal lobe of the adjacent subunit is not shown). The <scene name='46/463261/8ruc_active-site/6'>types of residues</scene> involved are <font color='red'>acidic</font> residues that interact with Mg²⁺, <font color='blue'>basic</font> residues and <font color='lightblue'>histidines</font> that interact with phosphate and hydroxyl groups, <font color='orchid'>polar</font> residues that interact with hydroxyl groups, one <font color='slategray'>hydrophobic</font> residue, and backbone atoms (white ball & stick) of several residues.

<scene name='46/463261/8ruc_active-site/10'>Residues that are involved in catalysis</scene> are shown shown here in CPK ball & stick. Asp 203 and Glu 204 bind to and position the magnesium ion. The carbamylated lysine residue KCX 201 coordinates Mg²⁺ and initiates catalysis by extracting a proton from C3 of RUBP. Note the proximity of the carbamyl group to carbon 3 in this structure. His 294 acts as a catalytic base in the carboxylation step of the mechanism and accepts a proton from the hydroxyl of carbon 3. Mg²⁺ is coordinated by six ligands. In addition to oxygen atoms in the three residues already mentioned, the ion binds to two oxygen atoms of RUBP. The 6th ligand is either water or in the carboxylation step it binds the incoming CO₂. In the structure shown, Mg²⁺ is bound to the carboxyl group in CAP that corresponds to the fixed CO₂ in the hydrated intermediate.