Here are the 5 main types of catalytic mechanisms employed by enzymes:
- Acid/Base Catalysis
- Covalent Catalysis
- Metal Ion Catalysis
- Proximity and Orientation Effects
- 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 2‘3‘ 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.
- RNAase A
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