Enzymes: The Active Site

Abstract

Enzymes are highly efficient and specific catalysts. They catalyse biochemical reactions with substantial rate enhancement compared to the uncatalysed reactions. The rate enhancement and specificity of enzymes are derived from a network of general acid/base catalysts, nucleophiles and noncovalent interactions in the active site, the part of the enzyme where cataylsis takes place. In catalysis, binding of the substrate and the transition state in the active site is of critical importance. Enzymes catalyse reactions by preferentially binding the transition state and, therefore, lowering the activation energy of the reaction. Enzymes bind their substrates via a network of weak, noncovalent intermolecular interactions such as hydrogen bonding, hydrophobic and electrostatic interactions. Enzymes utilise several mechanisms to accelerate a reaction such as acid/base catalysis, covalent catalysis and metal ion catalysis. Owing to their integral role in all biochemical pathways, enzymes are an attractive target for drug design and development.

Key Concepts:

  • Enzymes are biocatalysts that are involved in all forms of biochemical transformations.

  • Nearly all enzymes are proteins.

  • Enzymes catalyse reactions with a remarkable rate enhancement due primarily to lowering the energy of the transition state.

  • The active site is a cavity in the enzyme structure where catalysis occurs.

  • Amino acid residues in the active site provide the required framework for catalysis.

Keywords: enzymes; catalysis; specificity; noncovalent interactions; active sites

Figure 1.

Examples of the common folding motifs found in protein structure. The all α‐motif is represented in the heme‐binding protein, cytochrome b1 (PDB: 1BCF). The enzyme DFPase (PDB: 1E1A) is an example of all β‐fold. Dihydroorotase (PDB: 1J79) represents the (β/α)8‐barrel fold.

Figure 2.

Noncovalent interactions found in enzyme–substrate and enzyme‐transition state complexes.

Figure 4.

A close‐up view of the active site for the enzyme AChE showing the nucleophile Ser‐200 covalently bound to the transition state analogue TMTFA (shown in green). Different functional groups on the inhibitor are accommodated by the acyl and anionic pockets. Coordinates taken from PDB file: 1AMN.

Figure 6.

A close‐up view of the active site of DHO (PDB: 1J79) showing amino acid residues within approximately 4.5 Å from bound l‐dihydroorotate and carbamoyl‐l‐aspartate. The zinc ions are highlighted in green.

Figure 7.

The proposed mechanism for the hydrolysis and synthesis of l‐dihydroorotate by the enzyme dihydroorotase.

Figure 8.

The reaction mechanism for hydrolysis of the neurotransmitter ACh by the serine protease, AChE.

Scheme
Scheme
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References

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Further Reading

Bugg TDH (1997) An Introduction to Enzyme and Coenzyme Chemistry. Oxford: Blackwell Science.

Copeland RA (2000) Enzymes: A Practical Introduction to Structure, Mechanism and Data Analysis. New York: Wiley‐VCH, Inc.

Copeland RA (2005) Evaluation of Enzyme Inhibitors in Drug Discovery: A Guide for Medicinal Chemists and Pharmacologists. New Jersey: John Wiley & Sons, Inc.

Fersht A (1998) Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. New York: Freeman WH.

Karshikoff A (2006) Non‐Covalent Interactions in Proteins. Hackensack, NJ: World Scientific.

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Ghanem, Eman, and Raushel, Frank M(Oct 2012) Enzymes: The Active Site. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000714.pub2]