Enzyme Structure
Crystallographic studies have observed that the active form of IPP isomerase is a monomer with alternating α-helices and β-sheets. The active site of IPP isomerase is deeply buried within the enzyme and consists of a glutamic acid residue and a cysteine residue that interact with opposite sides of the IPP substrate, consistent with the antarafacial stereochemistry of isomerization. The origin of the initial protonation step has not been conclusively established. Recent evidence suggests that the glutamic acid residue is involved in the protonating step despite the observation that its carboxylic acid side chain is stabilized in its carboxylate form. This discrepancy has been addressed by the discovery of a water molecule in the active site of human IPP isomerase, suggesting a mechanism where the glutamine residue polarizes the double bond of IPP and makes it more susceptible to protonation by water.
IPP isomerase also requires a divalent cation to fold into its active conformation. The enzyme contains several amino acids, including the catalytic glutamate, that are involved in coordinating with Mg2+ or Mn2+. The coordination of the metal cation to the glutamate residue stabilizes the carbiocation intermediate after protonation.
Read more about this topic: Isopentenyl-diphosphate Delta Isomerase
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