6.2 Catalytic mechanisms
In general terms, the following mechanisms operate at the active site of an enzyme to bring about the conversion of substrate to product:
Charged groups at the enzyme active site alter the distribution of electrons in the substrate. By affecting the electron distributions in key atoms in the substrate, the enzyme can destabilise existing bonds and favour the formation of new bonds. This principle is illustrated below, using as an example the hydrolysis of an amide bond.
In binding the substrate, the enzyme forces it to change its conformation. This conformational change puts a strain on the substrate and drives it towards the transition state.
Many enzymes temporarily form a covalent bond between the substrate and an amino acid side-chain at the active site. This is termed covalent catalysis.
Where an enzyme catalyses a reaction between two substrates (reactants), these will bind at the active site such that they are in close proximity and in the appropriate orientation for the reaction to occur.
Many enzymes require metal ions for catalytic activity (see Section 2.3). These ions may serve to stabilise negative charges in the active site, mediate redox reactions or bind substrates. Catalysis that is driven through the stabilisation of negative charges (by a metal ion or by a positively charged amino acid side-chain) is described as electrophilic catalysis.
An electrophile is an atom, ion or molecule that has an affinity for electrons and can function as an electron acceptor. A nucleophile is an atom, ion or molecule that has an affinity for atomic nuclei and can function as an electron donor.
Refer back to the description of Src tyrosine kinase activity (Section 3.4); note the orientation of the ATP and polypeptide substrates at the active site. How does the orientation of these reactants facilitate the phosphorylation of the polypeptide?
The ATP molecule is bound such that its chain of three phosphates points towards the target tyrosine residue of the polypeptide, thus facilitating the transfer of the terminal γ-phosphate of ATP to the tyrosine residue.