2-dehydro-3-deoxy-phosphogluconate Aldolase - Enzyme Mechanism

Enzyme Mechanism

One of the reactions KDPG Aldolase catalyzes, as in the Entner–Doudoroff pathway, is the reversible cleavage of 2-keto-3-deoxy-6-phosphogluconate (KDPG) into pyruvate and D-glyceraldehyde-3-phosphate. This occurs through a stereospecific retro-aldol cleavage. A proton transfer between the zwitterionic pair Glu-45/Lys-133 in the active site activates Lysine to serve as the nucleophile in the first step and Glutamate to aid in the base catalysis involved in the carbon-carbon cleavage. Lysine Residue 133 serves as the nucleophile and attacks the carbonyl group of 2-Keto-3-deoxy-6-phosphogluconate to form a protonated carbinolamine intermediate, also known as a Schiff base intermediate. The intermediate is stabilized by hydrogen bonding with residues in the active site. A three carbon residue, glyceraldehyde 3-phosphate, is cleaved off through base catalysis with a water molecule and residue Glu-45. The pyruvate is generated through the nucleophilic attack of water on the Schiff-base to reform a ketone. Aromatic interaction with Phe-135 ensures the stereospecific addition involved in the reverse process.

KDPG aldolase has also been shown to catalyze the exchange of hydrogen atoms of the methyl groups of pyruvate with protons of the solvent.