1. Catalysts

Enzyme and Active Site Size

Enzymes are typically much larger than the substrate they bind–sometimes 200x larger! They’re also much larger than their active sites. A few reasons why:

  1. The 3D folding allows the correct positions of catalytic residues
  2. The region of the protein allows for induced fit
  3. The need to regulate the activities of the enzyme
  4. Regions are involved in protein-to-protein interactions. In some cases, enzymes assemble multi-functional complexes.
  5. Supports sequential reactions and complex pathways.

For example, if an enzyme is too short, there will be limited folding possibilities, inflexibility and fixed angles. Useless!

Size can also contribute to the enzyme’s specificity. In some cases, there is a three-point attachment pattern (the TPA model) between the substrate and the active site. Chiral orientation.


Regions outside the active site can be critical too since conformational changes occur once binding happens. A good example is the first step in the Citric Acid Cycle with sitrate synthase (CS).

Citrate synthase can’t bind to Acetyl-CoA, only oxaloacetate (Oxal). However, once Oxal binds to CS, there’s a conformation (induced fit) that creates the binding site for Ac-CoA. This create the reaction intermediate called Citroyl Coenzyme A (CoA), the result of a covalent bond between the Acetyl group of Ac-CoA and Oxal. This then leads a second conformation of CS, which triggers the hydrolysis of the acetyl group and release of CoA.

Enzyme activity is regulated by different signals in the cell

An example can be found in the following transient covalent modification:

  • The addition of a phosphate group catalyzed by a kinase
  • The removal of a phosphate group catalyzed by a phosphatase

The phosphorylation or de-phosphorylation can either activate or inhibit an enzyme.

Example: phosphofructokinase-2 (PFK-2), determines “fate” of glucose in liver cells. This will be covered extensively in a later lecture.

PFK-2 is one protein in two domains one a kinase, the other a phosphatase. It’s a bi-functional enzyme: when the K-domain is phosphorylated (on serine), it becomes inactive turning PFK-2 into a phosphatase. In the absence of the phosphate group in the K-domain, PFK-2 acts as a kinase. So de/phosphorylation changes its function.

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