Types of Enzyme Catalysis

Here are the 5 main types of catalytic mechanisms employed by enzymes:

  1. Acid/Base Catalysis
  2. Covalent Catalysis
  3. Metal Ion Catalysis
  4. Proximity and Orientation Effects
  5. Preferential binding of the transition state complex

Acid/Base Catalysis:

  • Here the enzyme protonates or deprotonates the substrate to lower the free energy of the transition state.
    • The enzyme can either act as an acid or base
  • Examples of Acid/Base Catalysis
    • RNAase A
      • A hydrolase that hydrolyzes phosphodiester bonds in RNA
      • Active sites has two Histidines
      • Involves a 23 cyclic nucleotide intermediate
      • Mostly beta sheet
      • His 12 acts as a general base and His 119 as a general acid to promote nucleophilic attack and bond cleavage.

Covalent Catalysis:

  • A catalytic mechanism that involved an enzyme-substrate covalent intermediate
  • Transient formation of the complex increases reaction rates
  • The enzyme nucleophilically attacks the substrate (also called nucleophilic catalysis)
  • Reversible

Metal Ion Catalysis:

Catalysis involving a metal ion can occur via several different mechanisms:

  • Coordinate substrates and orient them properly
  • Mediate redox reactions by acting as electron donor or acceptor
  • Stabilize or shield negatively charges species (usually to allow nucleophile to enter)
  • Make coordinated waters more acidic (better nucleophile

Example: Carbonic Anhydrase

  • Requires Zn2+ which is coordinated by 3 His and 1 H2O

Proximity/Orientation:

  • Enzymes bring substrates into contact with catalytic groups
  • Restricts rotational and translational motion of substrated when bound
  • Can increase reaction rates by 107

Preferential Transition State Binding:

  • Reaction rates increase by increasing the concentration of the transition state
  • Some enzymes bind tighter to the T.S. than to the substrate
  • Binding substrate force it to adopt the T.S. by straining the molecule towards that molecule.
  • T.S. analogs will be potent inhibitors of these enzymes

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