What is the Active Site of an Enzyme

Biochemical reactions in living cells are catalyzed by enzymes. The enzymes are synthesized in their inactive form which subsequently converts into the active form. The activity of an enzyme is determined by the amino acid sequence of the primary structure. Substrates bind to the active site of the enzyme in order to specifically accelerate a particular chemical reaction. The active site of an enzyme comprises a substrate binding site and a catalytic site. The specific chemical environment, which is developed by the amino acid residues in the active site, determines which substrates are capable of binding to the enzyme.

This article explains,

1. What are Enzymes and How Do They Work
2. What is the Active Site of an Enzyme
3. How Do an Enzyme and a Substrate Bind

What are Enzymes and How Do They Work

An enzyme is a protein molecule that can act as a biological catalyst. The molecules that enzymes act upon are called substrates. Different molecules that are created by the action of an enzyme upon a particular substrate are called products. Enzymes catalyze biochemical reactions by lowering its activation energy. The catalysis of reaction by an enzyme increases the rate of that particular reaction in the cell. Some enzymes are capable of catalyzing the same reaction. They are called isozymes. A unique set of about 3, 000 enzymes are genetically programmed to be synthesized, giving an individuality to a cell. Other than proteins, RNA molecules like ribozymes can act as enzymes as well. If one enzyme becomes defective, the effect would be disastrous.

Enzymes possess three characteristic features. The primary function of an enzyme is to increase the rate of a reaction. Second, one particular enzyme acts specifically on one particular substrate, producing a product. Thirdly, enzymes can be regulated from a low activity to high activity and vice versa. The binding of a substrate to an enzyme, creating the product by increasing the rate of the reaction and the release of the product are shown in figure 1.

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Figure 1: The action of an enzyme

The activity of an enzyme primarily depends on its amino acid sequence of the protein chain. Enzymes are synthesized as a linear sequence of amino acids called its primary structure. The primary structure spontaneously folds into a 3D structure that is composed of alpha helices and/or beta sheets called secondary structure. The secondary structure of the enzyme folds again into a compact 3D structure called the tertiary structure. The tertiary structure of the enzyme exists in its inactive form.

The polypeptide or protein part of the enzyme complex is referred to as the apoenzyme. The inactive form of the apoenzyme in the originally synthesized structure is known as the proenzyme or zymogen. Several amino acids are removed from the zymogen in order to convert the polypeptide part into an apoenzyme. Most of the times, the apoenzyme combines with other compounds called cofactors in order to catalyze a reaction. The combination of apoenzyme and cofactor is called holoenzyme. The relationship between the apoenzyme, cofactor, and the holoenzyme are shown in figure 2.

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Figure 2: Apoenzyme, cofactor, and holoenzyme

What is the Active Site of an Enzyme

The active site of an enzyme is the region where specific substrates bind to the enzyme, catalyzing the chemical reaction. Substrate binding site along with the catalytic site form the active site of the enzyme. The enzyme binds with a specific substrate in order to catalyze a chemical reaction that changes the substrate in some way. The substrate is smaller in size than its enzyme. The substrate is perfectly oriented inside the enzyme by the active site. One or more substrate binding sites can be found in an enzyme. The catalytic site occurs next to the binding site, carrying out the catalysis. It is composed of around two to four amino acids, involved in the catalysis. The amino acids that form the active site are located in distinct parts of the amino acid sequence of the enzyme. Therefore, the primary structure of the enzyme should fold into its 3D structure, enabling the active site to come together. The active site of the enzyme, the lysozyme, is shown in figure 3. The substrate, peptidoglycan, is shown in black color.

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Figure 3: Active site of the enzyme

Distinct from the active site, enzymes contain pockets that bind to effector molecules, changing the conformation or dynamics of the enzyme. These pockets are known as allosteric sites that are involved in the allosteric regulation of the reaction rate of the enzyme.

How Do an Enzyme and a Substrate Bind

The binding site of the enzyme binds with the substrate in a substrate-specific manner. This binding orients the substrate for catalysis. The amino acid residues that are located in the binding site of the enzyme can be weakly acidic or basic; hydrophilic or hydrophobic; and positively-charged, negatively-charged or neutral. The very specific chemical environment created within the binding site determines the specificity of an enzyme. Temporary covalent interactions like van der Waals forces, hydrophilic/hydrophobic interactions or hydrogen bonds are formed by the active site with the substrate. The enzyme along with the substrate form the enzyme-substrate complex. 

The binding of substrate to the enzyme can occur in two mechanisms: lock-and-key model and induced fit model. The lock-and-key model asserts that substrate fits exactly with the enzyme in one instantaneous step. The binding slightly changes the structure of the enzyme. Only the correctly sized and shaped substrates can bind with the enzyme in lock-and-key model. During the induced fit model, the shape of the active site of enzyme changes continuously in response to substrate binding. This explains why other molecules bind to the active site of the enzyme. However, this dynamic binding of the substrate to an enzyme stabilizes the substrate and increases the rate of the biochemical reaction. Hexokinase is an enzyme that changes its shape, fitting into the shapes of its substrates, adenine triphosphate, and xylose. The induced fit model of hexokinase is shown in figure 4.  Binding sites and the substrates are shown in blue and black colors.

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Figure 4: Induced fit model of hexokinase

The catalysis of a chemical reaction by an enzyme may occur in several ways that lower the activation energy of the chemical reaction. First, enzymes stabilize the transition state by creating complementary charge distribution to that of the transition state, lowering its energy. Second, enzymes promote an alternative reaction pathway that contains a second transition state with lower energy to that of the original transition state. Third, enzymes destabilize the ground state of the substrate.


Enzymes are chemical reactions that increase the rate of biochemical reactions in living cells. Most of the enzymes are proteins that are synthesized in their primary structure. These amino acid chains fold into their 3D structures, producing the active form of enzymes. This folding creates a pocket in the enzyme called active site. Substrates specifically bind to the active site of the enzyme, increasing the rate of the biochemical reactions that occur in the body.

1.”Role of Enzymes in Biochemical Reactions.” Enzymes. N.p., n.d. Web. 21 May 2017. <http://chemistry.elmhurst.edu/vchembook/570enzymes.html>.
2.”Enzymes and the active site.” Khan Academy. N.p., n.d. Web. 21 May 2017. <https://www.khanacademy.org/science/biology/energy-and-enzymes/introduction-to-enzymes/a/enzymes-and-the-active-site>.
3.”Enzyme Active Site and Substrate Specificity.” Boundless. 17 Nov. 2016. Web. 21 May 2017. <https://www.boundless.com/biology/textbooks/boundless-biology-textbook/metabolism-

Image Courtesy:
1. “Induced fit diagram” By Created by TimVickers, vectorized by Fvasconcellos – Provided by TimVickers (Public Domain) via Commons Wikimedia
2. “Enzymes” By Thomas Shafee – Own work (CC BY 4.0)  via Commons Wikimedia
3. “Enzyme structure” By Thomas Shafee – Own work (CC BY 4.0) via Commons Wikimedia
4. “Hexokinase induced fit” By Thomas Shafee – Own work (CC BY 4.0) via Commons Wikimedia

About the Author: Lakna

Lakna, a graduate in Molecular Biology & Biochemistry, is a Molecular Biologist and has a broad and keen interest in the discovery of nature related things

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