Enzymes: 3D Structure

In enzymes, as with other proteins, function is determined by structure. An enzyme can be:

- A monomeric protein, i.e., containing only one polypeptide chain, typically one hundred or more amino acids; or

- an oligomeric protein consisting of several polypeptide chains, different or identical, that act together as a unit.

As with any protein, each monomer is actually produced as a long, linear chain of amino acids, which folds in a particular fashion to produce a three-dimensional product. Individual monomers may then combine via non-covalent interactions to form a multimeric protein. Many enzymes can be unfolded or inactivated by heating, which destroys the three-dimensional structure of the protein.

A polypetide chain folded into a three-dimensional enzyme molecule

1. substrate molecule bound to the active site of the enzyme molecule
2. amino acid molecule involved in active site formation
3. active site
4. amino acid molecule
5. peptide bond

Most enzymes are larger than the substrates they act on and only a very small portion of the enzyme, around 10 amino acids, come into direct contact with the substrate(s). This region, where binding of the substrate(s) and then the reaction occurs, is known as the active site of the enzyme. Some enzymes contain sites that bind cofactors, which are needed for catalysis. Certain enzymes have binding sites for small molecules, which are often direct or indirect products or substrates of the reaction catalyzed. This binding can serve to increase or decrease the enzyme's activity (depending on the molecule and enzyme), providing a means for feedback regulation.


Many enzymes contain not only a protein part but need additionally various modifications. These modifications are made posttranslational, i.e., after the polypeptide chain is synthesized. Additional groups can be synthesized onto the polypeptide chain, e.g., phosphorylation or glycosylation of the enzyme.

Another kind of posttranslational modification is the cleavage and splicing of the polypeptide chain. Chymotrypsin, a digestive protease, is produced in inactive form as chymotrypsinogen in the pancreas and transported in this form to the stomach where it is activated. This prevents the enzyme from harmful digestion of the pancreas or other tissue. This type of inactive precursor to an enzyme is known as a zymogen.

Enzyme cofactors

Some enzymes do not need any additional components to exhibit full activity. However, others require non-protein molecules to be bound for activity. Cofactors can be either inorganic (e.g., metal ions and Iron-sulfur clusters) or organic compounds, which are also known as coenzymes.

Enzymes that require a cofactor, but do not have one bound are called apoenzymes. An apoenzyme together with its cofactor(s) constitutes a holoenzyme (i.e, the active form). Most cofactors are not covalently bound to an enzyme, but are closely associated. However, some cofactors known as prosthetic groups are covalently bound (e.g., thiamine pyrophosphate in certain enzymes).

Most cofactors are either regenerated or chemically unchanged at the end of the reactions. Many cofactors are vitamin-derivatives and serve as carriers to transfer electrons, atoms, or functional groups from an enzyme to a substrate. Common examples are NAD and NADP, which are involved in electron transfer and coenzyme A, which is involved in the transfer of acetyl groups.

Allosteric modulation

Allosteric enzymes change their structure in response to binding of effectors. Modulation can be direct, where effectors bind directly to binding sites in the enzyme, or indirect, where the effector binds to other proteins or protein subunits that interact with the allosteric enzyme and thus influence catalytic activity.


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