Enzyme Specificity | Impact of metabolic network context

The Relationship Between Enzyme Specificity and Promiscuity

What is the difference between absolute and stereochemical specificity of enzymes? What influences enzyme specificity and promiscuity? How do the metabolic network context and environmental conditions affect enzyme activity? Here is an animation to help students visualize the concept.

Absolute enzyme specificity

Absolute enzyme specificity refers to an enzyme that catalyzes a reaction expressly limited to one particular substrate. For example, lactase is an enzyme specific to lactose degradation, breaking down lactose into two monosaccharides, and glutamate dehydrogenase phosphorylates glucose to glucose-6-phosphate. Absolute specificity is a critical aspect of enzyme catalysis, determining the correct type of physiological phenotype for a particular reaction.

Relative specificity can be described as how a biological molecule can interact with its cognate substrates and targets differentially. Although relative specificity is an essential regulatory mechanism in many biological processes, it has not been investigated explicitly in the most complex biochemical systems. Here we review recent large-scale studies on relative specificity, showing its pervasiveness in diverse biological systems and pointing out its impact on disease processes.

The extent to which an enzyme is stereochemically specific can be determined. The optical properties of a substrate influence the activity of an enzyme. If the enzymes are stereochemically specific, they only bind substrates with certain properties. For instance, cellulose-binding enzymes will react with beta-glycosidic bonds and will not interact with alpha-glycosidic bonds found in starch.

Not always easy to determine

While absolute specificity is not always easy to determine, some methods can help with this process. One method is called BRASS. This method is beneficial for characterizing broad substrate specificity. The BRASS method uses the electrostatic and spatial properties of the enzyme’s active site to determine which molecules it recognizes. It can also identify enzymes that are more than 90% specific. This approach benefits detecting enzymes with high degrees of specificity and stereoselectivity.

The other method of determining the degree of absolute enzyme specificity involves analyzing the interaction between an enzyme and a specific substrate. The enzymes’ specificity is based on how they react with the specific substrate. These enzymes may recognize aromatic side chains in amino acids. In addition, enzymes may recognize specific phosphorylation sites on a substrate. The phosphorylation of multiple hexoses, six-carbon sugars, is another example of absolute enzyme specificity.

Enzyme specificity and catalytic promiscuity

To understand the relationship between enzyme specificity and catalytic promiscuity, we need to examine the evolution of protein sequences. Promiscuous enzymes are springboards for functional evolution, as they promote multiple reactions and avoid functional loss during adaptation. Promiscuous enzymes are part of the alkaline phosphatase (AP) superfamily, which maps a likely transition zone between PMHs and ASs. Kinetic analysis of the AP superfamily reveals four different chemical activities that catalyze phosphoryl and sulfoesterase reactions, which are remarkably high. The rate acceleration is over ten thousand times higher for the promiscuous reactions than promiscuous reactions, suggesting that catalytic promiscuity is highly prevalent in AP enzymes.

Glycoside transposes (GTAs) are a class of enzymes that catalyze a wide range of sugar-addition reactions on various organic substrates. Although GTPases are composed of a small number of structural classes, they span a wide range of substrate preferences. The most promiscuous GTAs (b4GalT1), b-1,3GlcNAcT1, and b1-3,3GlcNAcT1 are characterized by their ability to accommodate a wide range of donors and acceptors. The extreme case of the enzyme’s specificity is represented by N-glycan core GTPases, which act on one single acceptor under physiological conditions.

Ambiguity and substrate specificity

The concepts of substrate ambiguity and substrate specificity are closely related. In enzyme superfamilies, thioesterases and HADs exhibit substrate ambiguity. In addition, these enzymes show substrate ambiguity, despite multiple sites of interaction with the substrate. Despite the resemblances between the two concepts, the concepts are very different. Catalytic promiscuity and enzyme specificity are important for biotechnology. The in-silico protein engineering techniques allow scientists to incorporate latent catalytic activities into enzymes. This technique complements wet-lab methods.

In addition, catalytic promiscuity also extends to the cleavage of other compounds. One mutant of NosL exhibits this property, which results in simultaneous cleavage of the Ca-Cb and Ca-COO(H) bonds. This property is a common feature of promiscuous enzymes, but it is possible to design a specific OP-degrading enzyme that exhibits broader stereospecificity.

Impact of metabolic network context

Metabolic networks contain both weakly branched and linear pathways. High-degree metabolites are considered major intersections of several pathways. High-degree metabolites are highly related to organisms of similar evolutionary history. They span metabolic distances of up to D = 7.

Enzyme evolution toward high specificity can be influenced by environmental conditions, which are reflected in the evolution of specificity. Enzymes with extensive metabolic regulation tend to have increased specificity. Furthermore, the metabolic network context of the organism influences the evolution of enzyme specificity. A study conducted on the metabolism of Saccharomyces cerevisiae revealed that the enzymes possessed high specificity, while the generalists were more common.

Korbel et al. showed that operons form a complex picture using genomic data. They found 23 modules containing genes from one operon, including murein, thiamin, and histidine biosynthesis. However, most of the modules comprise genes from multiple operons. This finding confirms the hypothesis that operon organization is correlated with metabolic pathways. Genomic associations were used to identify the functional modules.

A metabolic network are enriched

This study shows that amino acid residues in a metabolic network are enriched in particular clusters. This is a consequence of their proximity to specific metabolic subsystems. These clusters are composed of generalist enzymes and specialists. Generalist enzymes are enriched in those clusters with few flux changes. The latter group contains more PTMs, whereas the specialists are enriched in those with many flux changes.

Moreover, these findings support the hypothesis that evolutionary rates of metabolism genes are much lower than those of other genes. This suggests that positive selection occurs in specific residue sites, which shapes the evolution of enzymes. However, the relationship between gene essentiality and metabolic function may modulate evolution rates. In addition, 3D protein structure mapping also indicates that amino acid residues are positively evolving, even if they are distant from essential metabolic sites.

The impact of metabolic network context on enzyme specificity and promiscuity has been a critical element in determining the evolution of plants. The evolution of plants relied on enzyme promiscuity, which has resulted in new functions and metabolic pathways. This inefficiency can impair plant survival, and thus plants have evolved a strategy to manage promiscuity. One such strategy involves the bendability of a homolog to the enzyme involved in the flavonoid pathway. This, in turn, narrows the specificity of the enzyme and facilitates its recruitment.

Influence of environmental conditions

Many factors affect the evolution of enzyme specificity, including environment, genetics, and metabolism. Previous studies have overlooked the influence of environment on enzyme specificity. For example, a dry season can ruin crop yields, while the temperature of an egg can influence a reptile’s sex. In addition, enzyme specificity can be influenced by the composition of the enzyme-substrate. Understanding this complexity of factors may aid in the design of better enzymes.

The temperature and pH of an enzyme’s circumstances affect its activity. Enzymes function most efficiently at temperatures above 41 degrees Celsius, making them move faster and form more hydrogen bonds. Very high or low temperatures, on the other hand, can denature enzymes or change their activity. High pH and temperature changes can also disrupt hydrogen bonds, impairing enzyme activity. This is why environmental conditions and pH affect enzyme activity.

The active site must fit a molecule into its active site. The enzyme will not catalyze the reaction if the substrate cannot fit into this active site. In contrast, a protein may be particular for one molecule and not react with another. Hence, the substrate must fit into the enzyme’s active site. Ultimately, it is possible to design an enzyme that can react with different chemicals.

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