Enzyme

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Holoenzyme
)

glucosidase converts the sugar maltose into two glucose sugars. Active site residues in red, maltose substrate in black, and NAD cofactor in yellow. (PDB: 1OBB
​)

Enzymes (

molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. Almost all metabolic processes in the cell need enzyme catalysis in order to occur at rates fast enough to sustain life.[1]: 8.1  Metabolic pathways depend upon enzymes to catalyze individual steps. The study of enzymes is called enzymology and the field of pseudoenzyme analysis recognizes that during evolution, some enzymes have lost the ability to carry out biological catalysis, which is often reflected in their amino acid sequences and unusual 'pseudocatalytic' properties.[2][3]

Enzymes are known to catalyze more than 5,000 biochemical reaction types.

three-dimensional structure
.

IUPAC definition for enzymes

Like all catalysts, enzymes increase the reaction rate by lowering its activation energy. Some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example is orotidine 5'-phosphate decarboxylase, which allows a reaction that would otherwise take millions of years to occur in milliseconds.[5][6] Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, nor do they alter the equilibrium of a reaction. Enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules: inhibitors are molecules that decrease enzyme activity, and activators are molecules that increase activity. Many therapeutic drugs and poisons are enzyme inhibitors. An enzyme's activity decreases markedly outside its optimal temperature and pH, and many enzymes are (permanently) denatured when exposed to excessive heat, losing their structure and catalytic properties.

Some enzymes are used commercially, for example, in the synthesis of antibiotics. Some household products use enzymes to speed up chemical reactions: enzymes in biological washing powders break down protein, starch or fat stains on clothes, and enzymes in meat tenderizer break down proteins into smaller molecules, making the meat easier to chew.

Etymology and history

Photograph of Eduard Buchner.
Eduard Buchner

By the late 17th and early 18th centuries, the digestion of meat by stomach secretions[7] and the conversion of starch to sugars by plant extracts and saliva were known but the mechanisms by which these occurred had not been identified.[8]

French chemist

vital force contained within the yeast cells called "ferments", which were thought to function only within living organisms. He wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells."[10]

In 1877, German physiologist

Ancient Greek ἔνζυμον (énzymon) 'leavened, in yeast', to describe this process.[11] The word enzyme was used later to refer to nonliving substances such as pepsin, and the word ferment was used to refer to chemical activity produced by living organisms.[12]

substrate (e.g., lactase is the enzyme that cleaves lactose) or to the type of reaction (e.g., DNA polymerase forms DNA polymers).[15]

The biochemical identity of enzymes was still unknown in the early 1900s. Many scientists observed that enzymatic activity was associated with proteins, but others (such as Nobel laureate Richard Willstätter) argued that proteins were merely carriers for the true enzymes and that proteins per se were incapable of catalysis.[16] In 1926, James B. Sumner showed that the enzyme urease was a pure protein and crystallized it; he did likewise for the enzyme catalase in 1937. The conclusion that pure proteins can be enzymes was definitively demonstrated by John Howard Northrop and Wendell Meredith Stanley, who worked on the digestive enzymes pepsin (1930), trypsin and chymotrypsin. These three scientists were awarded the 1946 Nobel Prize in Chemistry.[17]

The discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography. This was first done for lysozyme, an enzyme found in tears, saliva and egg whites that digests the coating of some bacteria; the structure was solved by a group led by David Chilton Phillips and published in 1965.[18] This high-resolution structure of lysozyme marked the beginning of the field of structural biology and the effort to understand how enzymes work at an atomic level of detail.[19]

Classification and nomenclature

Enzymes can be classified by two main criteria: either amino acid sequence similarity (and thus evolutionary relationship) or enzymatic activity.

Enzyme activity. An enzyme's name is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase.[1]: 8.1.3  Examples are lactase, alcohol dehydrogenase and DNA polymerase. Different enzymes that catalyze the same chemical reaction are called isozymes.[1]: 10.3 

The International Union of Biochemistry and Molecular Biology have developed a nomenclature for enzymes, the EC numbers (for "Enzyme Commission"). Each enzyme is described by "EC" followed by a sequence of four numbers which represent the hierarchy of enzymatic activity (from very general to very specific). That is, the first number broadly classifies the enzyme based on its mechanism while the other digits add more and more specificity.[20]

The top-level classification is:

These sections are subdivided by other features such as the substrate, products, and

chemical mechanism. An enzyme is fully specified by four numerical designations. For example, hexokinase (EC 2.7.1.1) is a transferase (EC 2) that adds a phosphate group (EC 2.7) to a hexose sugar, a molecule containing an alcohol group (EC 2.7.1).[21]

Sequence similarity. EC categories do not reflect sequence similarity. For instance, two ligases of the same EC number that catalyze exactly the same reaction can have completely different sequences. Independent of their function, enzymes, like any other proteins, have been classified by their sequence similarity into numerous families. These families have been documented in dozens of different protein and protein family databases such as Pfam.[22]

Non-homologous isofunctional enzymes. Unrelated enzymes that have the same enzymatic activity have been called non-homologous isofunctional enzymes.[23] Horizontal gene transfer may spread these genes to unrelated species, especially bacteria where they can replace endogenous genes of the same function, leading to hon-homologous gene displacement.

Structure

rate of reaction
at an intermediate temperature.

Enzymes are generally globular proteins, acting alone or in larger complexes. The sequence of the amino acids specifies the structure which in turn determines the catalytic activity of the enzyme.[24] Although structure determines function, a novel enzymatic activity cannot yet be predicted from structure alone.[25] Enzyme structures unfold (denature) when heated or exposed to chemical denaturants and this disruption to the structure typically causes a loss of activity.[26] Enzyme denaturation is normally linked to temperatures above a species' normal level; as a result, enzymes from bacteria living in volcanic environments such as hot springs are prized by industrial users for their ability to function at high temperatures, allowing enzyme-catalysed reactions to be operated at a very high rate.

Enzymes are usually much larger than their substrates. Sizes range from just 62 amino acid residues, for the monomer of 4-oxalocrotonate tautomerase,[27] to over 2,500 residues in the animal fatty acid synthase.[28] Only a small portion of their structure (around 2–4 amino acids) is directly involved in catalysis: the catalytic site.[29] This catalytic site is located next to one or more binding sites where residues orient the substrates. The catalytic site and binding site together compose the enzyme's active site. The remaining majority of the enzyme structure serves to maintain the precise orientation and dynamics of the active site.[30]

In some enzymes, no amino acids are directly involved in catalysis; instead, the enzyme contains sites to bind and orient catalytic

allosteric sites where the binding of a small molecule causes a conformational change that increases or decreases activity.[31]

A small number of

RNA-based biological catalysts called ribozymes exist, which again can act alone or in complex with proteins. The most common of these is the ribosome which is a complex of protein and catalytic RNA components.[1]
: 2.2 

Mechanism

Lysozyme displayed as an opaque globular surface with a pronounced cleft which the substrate depicted as a stick diagram snuggly fits into.
Organisation of enzyme structure and lysozyme example. Binding sites in blue, catalytic site in red and peptidoglycan substrate in black. (PDB: 9LYZ​)

Substrate binding

Enzymes must bind their substrates before they can catalyse any chemical reaction. Enzymes are usually very specific as to what

hydrophobic characteristics to the substrates. Enzymes can therefore distinguish between very similar substrate molecules to be chemoselective, regioselective and stereospecific.[32]

Some of the enzymes showing the highest specificity and accuracy are involved in the copying and expression of the genome. Some of these enzymes have "proof-reading" mechanisms. Here, an enzyme such as DNA polymerase catalyzes a reaction in a first step and then checks that the product is correct in a second step.[33] This two-step process results in average error rates of less than 1 error in 100 million reactions in high-fidelity mammalian polymerases.[1]: 5.3.1  Similar proofreading mechanisms are also found in RNA polymerase,[34] aminoacyl tRNA synthetases[35] and ribosomes.[36]

Conversely, some enzymes display

neutrally), which may be the starting point for the evolutionary selection of a new function.[37][38]

Hexokinase displayed as an opaque surface with a pronounced open binding cleft next to unbound substrate (top) and the same enzyme with more closed cleft that surrounds the bound substrate (bottom)
Enzyme changes shape by induced fit upon substrate binding to form enzyme-substrate complex. Hexokinase has a large induced fit motion that closes over the substrates adenosine triphosphate and xylose. Binding sites in blue, substrates in black and Mg2+ cofactor in yellow. (PDB: 2E2N​, 2E2Q​)

"Lock and key" model

To explain the observed specificity of enzymes, in 1894

Emil Fischer proposed that both the enzyme and the substrate possess specific complementary geometric shapes that fit exactly into one another.[39] This is often referred to as "the lock and key" model.[1]: 8.3.2  This early model explains enzyme specificity, but fails to explain the stabilization of the transition state that enzymes achieve.[40]

Induced fit model

In 1958,

glycosidases, the substrate molecule also changes shape slightly as it enters the active site.[42] The active site continues to change until the substrate is completely bound, at which point the final shape and charge distribution is determined.[43]
Induced fit may enhance the fidelity of molecular recognition in the presence of competition and noise via the conformational proofreading mechanism.[44]

Catalysis

Enzymes can accelerate reactions in several ways, all of which lower the activation energy (ΔG, Gibbs free energy)[45]

  1. By stabilizing the transition state:
    • Creating an environment with a charge distribution complementary to that of the transition state to lower its energy[46]
  2. By providing an alternative reaction pathway:
    • Temporarily reacting with the substrate, forming a covalent intermediate to provide a lower energy transition state[47]
  3. By destabilising the substrate ground state:
    • Distorting bound substrate(s) into their transition state form to reduce the energy required to reach the transition state[48]
    • By orienting the substrates into a productive arrangement to reduce the reaction entropy change[49] (the contribution of this mechanism to catalysis is relatively small)[50]

Enzymes may use several of these mechanisms simultaneously. For example, proteases such as trypsin perform covalent catalysis using a catalytic triad, stabilise charge build-up on the transition states using an oxyanion hole, complete hydrolysis using an oriented water substrate.[51]

Dynamics

Enzymes are not rigid, static structures; instead they have complex internal dynamic motions – that is, movements of parts of the enzyme's structure such as individual amino acid residues, groups of residues forming a

conformational ensemble of slightly different structures that interconvert with one another at equilibrium. Different states within this ensemble may be associated with different aspects of an enzyme's function. For example, different conformations of the enzyme dihydrofolate reductase are associated with the substrate binding, catalysis, cofactor release, and product release steps of the catalytic cycle,[52] consistent with catalytic resonance theory
.

Substrate presentation

Substrate presentation is a process where the enzyme is sequestered away from its substrate. Enzymes can be sequestered to the plasma membrane away from a substrate in the nucleus or cytosol. Or within the membrane, an enzyme can be sequestered into lipid rafts away from its substrate in the disordered region. When the enzyme is released it mixes with its substrate. Alternatively, the enzyme can be sequestered near its substrate to activate the enzyme. For example, the enzyme can be soluble and upon activation bind to a lipid in the plasma membrane and then act upon molecules in the plasma membrane.

Allosteric modulation

Allosteric sites are pockets on the enzyme, distinct from the active site, that bind to molecules in the cellular environment. These molecules then cause a change in the conformation or dynamics of the enzyme that is transduced to the active site and thus affects the reaction rate of the enzyme.[53] In this way, allosteric interactions can either inhibit or activate enzymes. Allosteric interactions with metabolites upstream or downstream in an enzyme's metabolic pathway cause feedback regulation, altering the activity of the enzyme according to the flux through the rest of the pathway.[54]

Cofactors

Thiamine pyrophosphate displayed as an opaque globular surface with an open binding cleft where the substrate and cofactor both depicted as stick diagrams fit into.
Chemical structure for thiamine pyrophosphate and protein structure of transketolase. Thiamine pyrophosphate cofactor in yellow and xylulose 5-phosphate substrate in black. (PDB: 4KXV​)

Some enzymes do not need additional components to show full activity. Others require non-protein molecules called cofactors to be bound for activity.

prosthetic groups, which are tightly bound to an enzyme. Organic prosthetic groups can be covalently bound (e.g., biotin in enzymes such as pyruvate carboxylase).[57]

An example of an enzyme that contains a cofactor is carbonic anhydrase, which uses a zinc cofactor bound as part of its active site.[58] These tightly bound ions or molecules are usually found in the active site and are involved in catalysis.[1]: 8.1.1  For example, flavin and heme cofactors are often involved in redox reactions.[1]: 17 

Enzymes that require a cofactor but do not have one bound are called apoenzymes or apoproteins. An enzyme together with the cofactor(s) required for activity is called a holoenzyme (or haloenzyme). The term holoenzyme can also be applied to enzymes that contain multiple protein subunits, such as the DNA polymerases; here the holoenzyme is the complete complex containing all the subunits needed for activity.[1]: 8.1.1 

Coenzymes

Coenzymes are small organic molecules that can be loosely or tightly bound to an enzyme. Coenzymes transport chemical groups from one enzyme to another.

tetrahydrofolate (THF), are derived from vitamins. These coenzymes cannot be synthesized by the body de novo
and closely related compounds (vitamins) must be acquired from the diet. The chemical groups carried include:

Since coenzymes are chemically changed as a consequence of enzyme action, it is useful to consider coenzymes to be a special class of substrates, or second substrates, which are common to many different enzymes. For example, about 1000 enzymes are known to use the coenzyme NADH.[60]

Coenzymes are usually continuously regenerated and their concentrations maintained at a steady level inside the cell. For example, NADPH is regenerated through the

methionine adenosyltransferase. This continuous regeneration means that small amounts of coenzymes can be used very intensively. For example, the human body turns over its own weight in ATP each day.[61]

Thermodynamics

A two dimensional plot of reaction coordinate (x-axis) vs. energy (y-axis) for catalyzed and uncatalyzed reactions. The energy of the system steadily increases from reactants (x = 0) until a maximum is reached at the transition state (x = 0.5), and steadily decreases to the products (x = 1). However, in an enzyme catalysed reaction, binding generates an enzyme-substrate complex (with slightly reduced energy) then increases up to a transition state with a smaller maximum than the uncatalysed reaction.
The energies of the stages of a chemical reaction. Uncatalysed (dashed line), substrates need a lot of activation energy to reach a transition state, which then decays into lower-energy products. When enzyme catalysed (solid line), the enzyme binds the substrates (ES), then stabilizes the transition state (ES) to reduce the activation energy required to produce products (EP) which are finally released.

As with all catalysts, enzymes do not alter the position of the chemical equilibrium of the reaction. In the presence of an enzyme, the reaction runs in the same direction as it would without the enzyme, just more quickly.[1]: 8.2.3  For example, carbonic anhydrase catalyzes its reaction in either direction depending on the concentration of its reactants:[62]

(in tissues; high CO2 concentration)

 

 

 

 

(1)

(in lungs; low CO2 concentration)

 

 

 

 

(2)

The rate of a reaction is dependent on the activation energy needed to form the transition state which then decays into products. Enzymes increase reaction rates by lowering the energy of the transition state. First, binding forms a low energy enzyme-substrate complex (ES). Second, the enzyme stabilises the transition state such that it requires less energy to achieve compared to the uncatalyzed reaction (ES). Finally the enzyme-product complex (EP) dissociates to release the products.[1]: 8.3 

Enzymes can couple two or more reactions, so that a thermodynamically favorable reaction can be used to "drive" a thermodynamically unfavourable one so that the combined energy of the products is lower than the substrates. For example, the hydrolysis of ATP is often used to drive other chemical reactions.[63]

Kinetics

Schematic reaction diagrams for uncatalzyed (Substrate to Product) and catalyzed (Enzyme + Substrate to Enzyme/Substrate complex to Enzyme + Product)
A chemical reaction mechanism with or without enzyme catalysis. The enzyme (E) binds substrate (S) to produce product (P).
A two dimensional plot of substrate concentration (x axis) vs. reaction rate (y axis). The shape of the curve is hyperbolic. The rate of the reaction is zero at zero concentration of substrate and the rate asymptotically reaches a maximum at high substrate concentration.
Saturation curve for an enzyme reaction showing the relation between the substrate concentration and reaction rate.

Enzyme kinetics is the investigation of how enzymes bind substrates and turn them into products.

Maud Leonora Menten proposed a quantitative theory of enzyme kinetics, which is referred to as Michaelis–Menten kinetics.[65] The major contribution of Michaelis and Menten was to think of enzyme reactions in two stages. In the first, the substrate binds reversibly to the enzyme, forming the enzyme-substrate complex. This is sometimes called the Michaelis–Menten complex in their honor. The enzyme then catalyzes the chemical step in the reaction and releases the product. This work was further developed by G. E. Briggs and J. B. S. Haldane, who derived kinetic equations that are still widely used today.[66]

Enzyme rates depend on solution conditions and substrate concentration. To find the maximum speed of an enzymatic reaction, the substrate concentration is increased until a constant rate of product formation is seen. This is shown in the saturation curve on the right. Saturation happens because, as substrate concentration increases, more and more of the free enzyme is converted into the substrate-bound ES complex. At the maximum reaction rate (Vmax) of the enzyme, all the enzyme active sites are bound to substrate, and the amount of ES complex is the same as the total amount of enzyme.[1]: 8.4 

Vmax is only one of several important kinetic parameters. The amount of substrate needed to achieve a given rate of reaction is also important. This is given by the

Michaelis–Menten constant (Km), which is the substrate concentration required for an enzyme to reach one-half its maximum reaction rate; generally, each enzyme has a characteristic KM for a given substrate. Another useful constant is kcat, also called the turnover number, which is the number of substrate molecules handled by one active site per second.[1]
: 8.4 

The efficiency of an enzyme can be expressed in terms of kcat/Km. This is also called the specificity constant and incorporates the

β-lactamase, and superoxide dismutase.[1]: 8.4.2  The turnover of such enzymes can reach several million reactions per second.[1]
: 9.2  But most enzymes are far from perfect: the average values of and are about and , respectively.[67]

Michaelis–Menten kinetics relies on the law of mass action, which is derived from the assumptions of free diffusion and thermodynamically driven random collision. Many biochemical or cellular processes deviate significantly from these conditions, because of macromolecular crowding and constrained molecular movement.[68] More recent, complex extensions of the model attempt to correct for these effects.[69]

Inhibition

Enzyme reaction rates can be decreased by various types of enzyme inhibitors.[70]: 73–74 

Types of inhibition

Competitive

A

dihydrofolate to tetrahydrofolate.[72] The similarity between the structures of dihydrofolate and this drug are shown in the accompanying figure. This type of inhibition can be overcome with high substrate concentration. In some cases, the inhibitor can bind to a site other than the binding-site of the usual substrate and exert an allosteric effect to change the shape of the usual binding-site.[73]

Non-competitive

A non-competitive inhibitor binds to a site other than where the substrate binds. The substrate still binds with its usual affinity and hence Km remains the same. However the inhibitor reduces the catalytic efficiency of the enzyme so that Vmax is reduced. In contrast to competitive inhibition, non-competitive inhibition cannot be overcome with high substrate concentration.[70]: 76–78 

Uncompetitive

An

uncompetitive inhibitor cannot bind to the free enzyme, only to the enzyme-substrate complex; hence, these types of inhibitors are most effective at high substrate concentration. In the presence of the inhibitor, the enzyme-substrate complex is inactive.[70]: 78  This type of inhibition is rare.[74]

Mixed

A mixed inhibitor binds to an allosteric site and the binding of the substrate and the inhibitor affect each other. The enzyme's function is reduced but not eliminated when bound to the inhibitor. This type of inhibitor does not follow the Michaelis–Menten equation.[70]: 76–78 

Irreversible

An

irreversible inhibitor permanently inactivates the enzyme, usually by forming a covalent bond to the protein.[75] Penicillin[76] and aspirin[77]
are common drugs that act in this manner.

Functions of inhibitors

In many organisms, inhibitors may act as part of a feedback mechanism. If an enzyme produces too much of one substance in the organism, that substance may act as an inhibitor for the enzyme at the beginning of the pathway that produces it, causing production of the substance to slow down or stop when there is sufficient amount. This is a form of negative feedback. Major metabolic pathways such as the citric acid cycle make use of this mechanism.[1]: 17.2.2 

Since inhibitors modulate the function of enzymes they are often used as drugs. Many such drugs are reversible competitive inhibitors that resemble the enzyme's native substrate, similar to

retroviral infections such as HIV.[79] A common example of an irreversible inhibitor that is used as a drug is aspirin, which inhibits the COX-1 and COX-2 enzymes that produce the inflammation messenger prostaglandin.[77] Other enzyme inhibitors are poisons. For example, the poison cyanide is an irreversible enzyme inhibitor that combines with the copper and iron in the active site of the enzyme cytochrome c oxidase and blocks cellular respiration.[80]

Factors affecting enzyme activity

As enzymes are made up of proteins, their actions are sensitive to change in many physio chemical factors such as pH, temperature, substrate concentration, etc.

The following table shows pH optima for various enzymes.[81]

Enzyme Optimum pH pH description
Pepsin 1.5–1.6 Highly acidic
Invertase 4.5 Acidic
Lipase (stomach) 4.0–5.0 Acidic
Lipase (castor oil) 4.7 Acidic
Lipase (pancreas) 8.0 Alkaline
Amylase (malt) 4.6–5.2 Acidic
Amylase (pancreas) 6.7–7.0 Acidic-neutral
Cellobiase 5.0 Acidic
Maltase 6.1–6.8 Acidic
Sucrase 6.2 Acidic
Catalase 7.0 Neutral
Urease 7.0 Neutral
Cholinesterase 7.0 Neutral
Ribonuclease 7.0–7.5 Neutral
Fumarase 7.8 Alkaline
Trypsin 7.8–8.7 Alkaline
Adenosine triphosphate 9.0 Alkaline
Arginase 10.0 Highly alkaline

Biological function

Enzymes serve a wide variety of

HIV integrase and reverse transcriptase, or for viral release from cells, like the influenza virus neuraminidase.[85]

An important function of enzymes is in the

herbivorous diets, microorganisms in the gut produce another enzyme, cellulase, to break down the cellulose cell walls of plant fiber.[86]

Metabolism

pyruvate
via a series of intermediate metabolites. Each chemical modification (red box) is performed by a different enzyme.

Several enzymes can work together in a specific order, creating metabolic pathways.[1]: 30.1  In a metabolic pathway, one enzyme takes the product of another enzyme as a substrate. After the catalytic reaction, the product is then passed on to another enzyme. Sometimes more than one enzyme can catalyze the same reaction in parallel; this can allow more complex regulation: with, for example, a low constant activity provided by one enzyme but an inducible high activity from a second enzyme.[87]

Enzymes determine what steps occur in these pathways. Without enzymes, metabolism would neither progress through the same steps and could not be regulated to serve the needs of the cell. Most central metabolic pathways are regulated at a few key steps, typically through enzymes whose activity involves the hydrolysis of ATP. Because this reaction releases so much energy, other reactions that are

thermodynamically unfavorable can be coupled to ATP hydrolysis, driving the overall series of linked metabolic reactions.[1]
: 30.1 

Control of activity

There are five main ways that enzyme activity is controlled in the cell.[1]: 30.1.1 

Regulation

Enzymes can be either activated or inhibited by other molecules. For example, the end product(s) of a metabolic pathway are often inhibitors for one of the first enzymes of the pathway (usually the first irreversible step, called committed step), thus regulating the amount of end product made by the pathways. Such a regulatory mechanism is called a negative feedback mechanism, because the amount of the end product produced is regulated by its own concentration.[88]: 141–48  Negative feedback mechanism can effectively adjust the rate of synthesis of intermediate metabolites according to the demands of the cells. This helps with effective allocations of materials and energy economy, and it prevents the excess manufacture of end products. Like other homeostatic devices, the control of enzymatic action helps to maintain a stable internal environment in living organisms.[88]: 141 

Post-translational modification

Examples of

blood sugar.[89] Another example of post-translational modification is the cleavage 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 stops the enzyme from digesting the pancreas or other tissues before it enters the gut. This type of inactive precursor to an enzyme is known as a zymogen[88]
: 149–53  or proenzyme.

Quantity

Enzyme production (

enzyme repression
.

Subcellular distribution

Enzymes can be compartmentalized, with different metabolic pathways occurring in different

β-oxidation.[92] In addition, trafficking of the enzyme to different compartments may change the degree of protonation (e.g., the neutral cytoplasm and the acidic lysosome) or oxidative state (e.g., oxidizing periplasm or reducing cytoplasm) which in turn affects enzyme activity.[93] In contrast to partitioning into membrane bound organelles, enzyme subcellular localisation may also be altered through polymerisation of enzymes into macromolecular cytoplasmic filaments.[94][95]

Organ specialization

In

blood sugar and regulating insulin production.[97]

Involvement in disease

Ribbon diagram of phenylalanine hydroxylase with bound cofactor, coenzyme and substrate
In phenylalanine hydroxylase over 300 different mutations throughout the structure cause phenylketonuria. Phenylalanine substrate and tetrahydrobiopterin coenzyme in black, and Fe2+ cofactor in yellow. (PDB: 1KW0​)
recessive
fashion because the enzymes from the unaffected genes are generally sufficient to prevent symptoms in carriers.

Since the tight control of enzyme activity is essential for homeostasis, any malfunction (mutation, overproduction, underproduction or deletion) of a single critical enzyme can lead to a genetic disease. The malfunction of just one type of enzyme out of the thousands of types present in the human body can be fatal. An example of a fatal genetic disease due to enzyme insufficiency is Tay–Sachs disease, in which patients lack the enzyme hexosaminidase.[98][99]

One example of enzyme deficiency is the most common type of phenylketonuria. Many different single amino acid mutations in the enzyme phenylalanine hydroxylase, which catalyzes the first step in the degradation of phenylalanine, result in build-up of phenylalanine and related products. Some mutations are in the active site, directly disrupting binding and catalysis, but many are far from the active site and reduce activity by destabilising the protein structure, or affecting correct oligomerisation.[100][101] This can lead to intellectual disability if the disease is untreated.[102] Another example is pseudocholinesterase deficiency, in which the body's ability to break down choline ester drugs is impaired.[103] Oral administration of enzymes can be used to treat some functional enzyme deficiencies, such as

pancreatic insufficiency[104] and lactose intolerance.[105]

Another way enzyme malfunctions can cause disease comes from

Evolution

Similar to any other protein, enzymes change over time through mutations and sequence divergence. Given their central role in metabolism, enzyme evolution plays a critical role in adaptation. A key question is therefore whether and how enzymes can change their enzymatic activities alongside. It is generally accepted that many new enzyme activities have evolved through gene duplication and mutation of the duplicate copies although evolution can also happen without duplication. One example of an enzyme that has changed its activity is the ancestor of methionyl aminopeptidase (MAP) and creatine amidinohydrolase (creatinase) which are clearly homologous but catalyze very different reactions (MAP removes the amino-terminal methionine in new proteins while creatinase hydrolyses creatine to sarcosine and urea). In addition, MAP is metal-ion dependent while creatinase is not, hence this property was also lost over time.[108] Small changes of enzymatic activity are extremely common among enzymes. In particular, substrate binding specificity (see above) can easily and quickly change with single amino acid changes in their substrate binding pockets. This is frequently seen in the main enzyme classes such as kinases.[109]

Artificial (in vitro) evolution is now commonly used to modify enzyme activity or specificity for industrial applications (see below).

Industrial applications

Enzymes are used in the

organic solvents and at high temperatures. As a consequence, protein engineering is an active area of research and involves attempts to create new enzymes with novel properties, either through rational design or in vitro evolution.[110][111] These efforts have begun to be successful, and a few enzymes have now been designed "from scratch" to catalyze reactions that do not occur in nature.[112]

Application Enzymes used Uses
Biofuel industry Cellulases Break down cellulose into sugars that can be fermented to produce cellulosic ethanol.[113]
Ligninases
Pretreatment of biomass for biofuel production.[113]
Biological detergent
Proteases, amylases, lipases Remove protein, starch, and fat or oil stains from laundry and dishware.[114]
Mannanases
Remove food stains from the common food additive guar gum.[114]
Brewing industry Amylase, glucanases, proteases Split polysaccharides and proteins in the malt.[115]: 150–9 
Betaglucanases
Improve the wort and beer filtration characteristics.[115]: 545 
Amyloglucosidase and pullulanases
Make low-calorie beer and adjust fermentability.[115]: 575 
Acetolactate decarboxylase (ALDC) Increase fermentation efficiency by reducing diacetyl formation.[116]
Culinary uses Papain
Tenderize meat for cooking.[117]
Dairy industry Rennin
Hydrolyze protein in the manufacture of cheese.[118]
Lipases Produce
Camembert cheese and blue cheeses such as Roquefort.[119]
Food processing Amylases Produce sugars from starch, such as in making high-fructose corn syrup.[120]
Proteases Lower the protein level of flour, as in biscuit-making.[121]
Trypsin Manufacture hypoallergenic baby foods.[121]
Cellulases, pectinases Clarify
fruit juices.[122]
Molecular biology Nucleases, DNA ligase and polymerases Use restriction digestion and the polymerase chain reaction to create recombinant DNA.[1]: 6.2 
Paper industry
hemicellulases and lignin peroxidases
Remove
kraft pulp.[123]
Personal care
Proteases Remove proteins on contact lenses to prevent infections.[124]
Starch industry Amylases Convert starch into glucose and various syrups.[125]

See also

Enzyme databases

References

  1. ^
  2. .
  3. .
  4. .
  5. .
  6. .
  7. ^ de Réaumur RA (1752). "Observations sur la digestion des oiseaux". Histoire de l'Académie Royale des Sciences. 1752: 266, 461.
  8. ^ Williams HS (1904). A History of Science: in Five Volumes. Volume IV: Modern Development of the Chemical and Biological Sciences. Harper and Brothers.
  9. ^ Payen A, Persoz JF (1833). "Mémoire sur la diastase, les principaux produits de ses réactions et leurs applications aux arts industriels" [Memoir on diastase, the principal products of its reactions, and their applications to the industrial arts]. Annales de chimie et de physique. 2nd (in French). 53: 73–92.
  10. PMID 8595136
    .
  11. ^ Kühne coined the word "enzyme" in: Kühne W (1877). "Über das Verhalten verschiedener organisirter und sog. ungeformter Fermente" [On the behavior of various organized and so-called unformed ferments]. Verhandlungen des Naturhistorisch-medicinischen Vereins zu Heidelberg. new series (in German). 1 (3): 190–193. Relevant passage on page 190: "Um Missverständnissen vorzubeugen und lästige Umschreibungen zu vermeiden schlägt Vortragender vor, die ungeformten oder nicht organisirten Fermente, deren Wirkung ohne Anwesenheit von Organismen und ausserhalb derselben erfolgen kann, als Enzyme zu bezeichnen." (Translation: In order to obviate misunderstandings and avoid cumbersome periphrases, [the author, a university lecturer] suggests designating as "enzymes" the unformed or not organized ferments, whose action can occur without the presence of organisms and outside of the same.)
  12. .
  13. ^ "Eduard Buchner". Nobel Laureate Biography. Nobelprize.org. Retrieved 23 February 2015.
  14. ^ "Eduard Buchner – Nobel Lecture: Cell-Free Fermentation". Nobelprize.org. 1907. Retrieved 23 February 2015.
  15. ^ The naming of enzymes by adding the suffix "-ase" to the substrate on which the enzyme acts, has been traced to French scientist Émile Duclaux (1840–1904), who intended to honor the discoverers of diastase – the first enzyme to be isolated – by introducing this practice in his book Duclaux E (1899). Traité de microbiologie: Diastases, toxines et venins [Microbiology Treatise: diastases, toxins and venoms] (in French). Paris, France: Masson and Co. See Chapter 1, especially page 9.
  16. PMID 10801479
    .
  17. ^ "Nobel Prizes and Laureates: The Nobel Prize in Chemistry 1946". Nobelprize.org. Retrieved 23 February 2015.
  18. S2CID 4161467
    .
  19. .
  20. ^ Moss GP. "Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes by the Reactions they Catalyse". International Union of Biochemistry and Molecular Biology. Retrieved 28 August 2021.
  21. ^ Nomenclature Committee. "EC 2.7.1.1". International Union of Biochemistry and Molecular Biology (NC-IUBMB). School of Biological and Chemical Sciences, Queen Mary, University of London. Archived from the original on 1 December 2014. Retrieved 6 March 2015.
  22. .
  23. .
  24. .
  25. .
  26. .
  27. .
  28. .
  29. ^ "The Catalytic Site Atlas". The European Bioinformatics Institute. Archived from the original on 27 September 2018. Retrieved 4 April 2007.
  30. ^ .
  31. .
  32. .
  33. .
  34. .
  35. .
  36. .
  37. .
  38. .
  39. . From page 2992: "Um ein Bild zu gebrauchen, will ich sagen, dass Enzym und Glucosid wie Schloss und Schlüssel zu einander passen müssen, um eine chemische Wirkung auf einander ausüben zu können." (To use an image, I will say that an enzyme and a glucoside [i.e., glucose derivative] must fit like a lock and key, in order to be able to exert a chemical effect on each other.)
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  44. .
  45. .
  46. .
  47. .
  48. .
  49. .
  50. .
  51. .
  52. .
  53. .
  54. .
  55. ^ de Bolster MW (1997). "Glossary of Terms Used in Bioinorganic Chemistry: Cofactor". International Union of Pure and Applied Chemistry. Archived from the original on 21 January 2017. Retrieved 30 October 2007.
  56. .
  57. .
  58. .
  59. ^ .
  60. ^ "BRENDA The Comprehensive Enzyme Information System". Technische Universität Braunschweig. Retrieved 23 February 2015.
  61. PMID 19073922
    .
  62. .
  63. .
  64. .
  65. .
  66. .
  67. .
  68. .
  69. .
  70. ^ .
  71. .
  72. .
  73. .
  74. .
  75. .
  76. .
  77. ^ .
  78. .
  79. .
  80. .
  81. .
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  84. .
  85. .
  86. .
  87. .
  88. ^ .
  89. .
  90. .
  91. .
  92. .
  93. .
  94. .
  95. .
  96. .
  97. .
  98. .
  99. ^ "Learning About Tay–Sachs Disease". U.S. National Human Genome Research Institute. Retrieved 1 March 2015.
  100. PMID 10527663
    .
  101. .
  102. ^ "Phenylketonuria". Genes and Disease [Internet]. Bethesda (MD): National Center for Biotechnology Information (US). 1998–2015.
  103. ^ "Pseudocholinesterase deficiency". U.S. National Library of Medicine. Retrieved 5 September 2013.
  104. PMID 21753892
    .
  105. .
  106. .
  107. .
  108. .
  109. .
  110. .
  111. .
  112. .
  113. ^ .
  114. ^ .
  115. ^ .
  116. .
  117. .
  118. ^ "Chymosin – GMO Database". GMO Compass. European Union. 10 July 2010. Archived from the original on 26 March 2015. Retrieved 1 March 2015.
  119. .
  120. .
  121. ^ a b "Protease – GMO Database". GMO Compass. European Union. 10 July 2010. Archived from the original on 24 February 2015. Retrieved 28 February 2015.
  122. .
  123. .
  124. .
  125. .

Further reading

External links

  • Media related to Enzymes at Wikimedia Commons