Enzyme Naming & Classification PDF

# **Naming of Enzymes** - In the early days, enzymes were given names by their discoverers in an arbitrary manner. For example, the names pepsin, trypsin and chymotrypsin convey no information about the function of the enzyme or the nature of the substrate on which they act. - In general, the suff...

# **Naming of Enzymes** - In the early days, enzymes were given names by their discoverers in an arbitrary manner. For example, the names pepsin, trypsin and chymotrypsin convey no information about the function of the enzyme or the nature of the substrate on which they act. - In general, the suffix "-ase" was added to the name of their substrate, e.g. lipase acts on lipids; nuclease on nucleic acids; lactase on lactose etc., or to a word or phrase describing their activity (their function), e.g. Oxidases, decarboxylases, dehydrogenases etc. ## **Some names describe both the substrate and the function.** For example, lactate dehydrogenase oxidizes lactate. A chemical diagram is shown with the following details: - The chemical formula for lactate is shown on the left side of the diagram. - The enzyme “Lactate dehydrogenase” is shown in between an arrow pointing to the left and an arrow pointing to the right. - The chemical formula for pyruvate is shown to the right of the diagram. - The chemicals “NAD+” and “NADH + H+” are shown below and in between the two arrows. # **Enzyme Classification** - In 1961, according to the report of the first Enzyme Commission (EC) of International Union of Pure and Applied Chemistry (IUPAC), Enzymes are classified into 6 major classes based on the reaction they catalyze, and each have (4-13) subclasses. - They were assigned code numbers, prefixed by E.C., which contain four elements separated by points and have the following meaning: | Element | Description | |---|---| | 1st | Enzyme Class (e.g. Oxidoreductase) | | 2nd | Specific Group to which the enzyme acts | | 3rd | General Group to which the enzyme acts | | 4th | Specific Substrate | # **Enzymes Are Classified into six functional Classes (EC number Classification)** based on the types of reactions that they catalyze - **EC 1:** Oxidoreductases - **EC 2:** Transferases - **EC 3:** Hydrolases - **EC 4:** Lyases - **EC 5:** Isomerases - **EC 6:** Ligases # **e.g. EC 2.7.1.1 [ATP:D-hexose-6-phosphotransferase]** ATP + D-Glucose → D-Glucose 6-phosphate + ADP In that: - **2** refers to the class (transferase) - **7** refers to the subclass (phosphotransferase) which transfer a phosphate group. - **1** refers to the sub-subclass (refers that alcohol act like phosphate acceptor). - **1** refers to the enzyme in its sub-subclass. (hexokinase) or to the substrate (hexose). Which is the enzyme that helps in the transferring of phosphate group from ATP to the hydroxyl group on the 6th carbon atom of Glucose? # **The enzyme can be classified into 6 main classes in that order** | Class | Subclass | Action | |---|---|---| | I Oxidoreductases | Dehydrogenases, oxidases, peroxidases, catalase, oxygenases, hydroxylases, reductases | Transfer of electrons (A+B → A+B¯) | | II Transferases | Transaldolase, transketolase, kinases, etc. | Transfer of functional groups (A-B+C → A+B-C) | | III Hydrolases | Esterases, glycosidases, peptidases, phosphatases, thiolases, amidases, etc. | Cleave a bond with water addition (A-B+H₂O →A-H+B-OH) | | IV Lyases | Decarboxylases, aldolases, hydratases, dehydratases synthases | Cleave without water, often forming a double bond (A-BA=B+Z-W) | | V Isomerases | Racemases, epimerases, mutases | Interconvert isomeric structures (A-BA-B) | | VI Ligases | Synthetases, carboxylases | ATP-dependent condensations (A + B → A-B) | # **EC 1. Oxidoreductases** - Oxidation-reduction reactions are very common in biochemical pathways and are catalyzed by a broad class of enzymes called oxidoreductases. - Whenever an oxidation-reduction reaction occurs, at least one substrate gains electrons and becomes reduced, and another substrate loses electrons and becomes oxidized. # **One subset of reactions is catalyzed by dehydrogenases, which accept and donate electrons in the form of hydride ions (H) or hydrogen atoms. Usually, an electron-transferring coenzyme, such as NAD+/NADH, acts as an electron donor or acceptor.** Two chemical diagrams are shown: - The top diagram shows the chemical structures of succinate, fumarate, FAD, and FADH2. - The bottom diagram shows the chemical structures of malate, oxaloacetate, NAD+, and NADH. # **In another subset of reactions, O₂ donates either one or both of its oxygen atoms to an acceptor (e.g. xanthine oxidase). When this occurs, O₂ becomes reduced, and an electron donor is oxidized. Enzymes participating in reactions with O₂ are called hydroxylases and oxidases when one oxygen atom is incorporated into a substrate and the other oxygen atom into water, or both atoms are incorporated into water.** They are called oxygenases when both atoms of oxygen are incorporated into the acceptor. Most hydroxylases and oxidases require metal ions, such as Fe+2, for electron transfer. A chemical diagram is shown with the following details: - The chemical formula for hypoxanthine is shown on the left side of the diagram. - The enzyme “xanthine oxidase” is shown in between an arrow pointing to the left and an arrow pointing to the right. - The chemical formula for xanthine is shown to the right of the diagram. - The chemical “H2O + O2” is shown below the first arrow and the chemical “H2O2” is shown above it. - The chemical “H2O + O2” is shown below the second arrow and the chemical “H2O2” is shown above it. There is a second diagram that shows the same enzyme “xanthine oxidase”. - On the left, it shows the chemical formula for xanthine. - On the right, it shows the chemical formula for uric acid. - The chemical “H2O + O2” is shown below the first arrow and the chemical “H2O2” is shown above it. - The chemical “H2O + O2” is shown below the second arrow and the chemical “H2O2” is shown above it. # **EC 2. Transferases** - Transferases catalyze group transfer reactions-the transfer of a functional group from one molecule to another. If the transferred group is a high-energy phosphate, the enzyme is a kinase; if the transferred group is a carbohydrate residue, the enzyme is a Glycosyltransferase; if it is a fatty acyl group, the enzyme is an acyltransferase. Two chemical diagrams are shown: - The top diagram shows the chemical formulas for glucose and ATP. - The bottom diagram shows the chemical formulas for glucose 6-phosphate and ADP. # **Another subset of group transfer reaction consists of transamination. In this type of reaction, the nitrogen group from an amino acid is donated to an alpha-keto acid, forming a new amino acid and the alpha-keto acid corresponding to the donor amino acid. Enzymes catalyzing this type of reaction are called transaminases or aminotransferases. The coenzyme pyridoxal phosphate is required for all transaminases.** Two chemical diagrams are shown: - The top diagram shows the chemical formulas for alanine, oxoglutarate, pyruvate, and glutamate. - The bottom diagram shows the chemical formulas for aspartate, oxoglutarate, oxaloacetate, and glutamate. The following explanation is provided for the diagrams: - **Alanine aminotransferase (ALT) or Glutamate pyruvate transaminase (GPT):** It escapes in large amounts from dead or dying liver tissue, and GPT may be measured in blood samples for diagnostic purposes. - **Aspartate aminotransferase (AST) or Glutamate oxaloacetate transaminase (GOT):** It escapes in large amounts from dead or dying heart tissues and enters the bloodstream, so GOT is often measured in blood samples for medical diagnostic purposes, such as myocardial infarction. # **EC 3. Hydrolases** - In hydrolysis reactions, C-O, C-N, or C-S bonds cleaved by the addition of H2O in the form of OH- and H⁺ to the atoms forming the bond. - The enzyme class names specify the group being cleaved (e.g. the enzyme commonly named chymotrypsin is a protease, a hydrolase that cleaves peptide bonds in proteins). Two chemical diagrams are shown that represent a hydrolysis reaction with water addition: - The left represents what’s before the reaction. - The right represents what’s after the reaction. # **Other examples for hydrolases** – Protein hydrolyzing enzymes (Proteases or Peptidases) - Carbohydrates hydrolyzing enzymes (Amylase, Maltase, Lactase) - Lipid hydrolyzing enzymes (Lipase) - Phosphate hydrolyzing enzymes (Phosphatases) - Ester hydrolyzing enzymes (Esterases) A chemical diagram shows a hydrolysis reaction with the following description: - Pyrophosphate is shown on the left side of the diagram. - The enzyme “Pyrophosphatase” is shown under the arrow pointing to the right. - Phosphate is shown to the right of the diagram. # **EC 4. Lyases** - Lyases consist of a diverse group of enzymes cleaving C-C, C-O, and C-N bonds by means other than hydrolysis or oxidation. - Some of the enzymes catalyzing C-C bond cleavage are called aldolases, decarboxylases (when carbon dioxide is released from a substrate), and thiolases (when the sulfur-containing nucleophile of cysteine or CoASH is used to break a carbon-carbon bond). A chemical diagram is shown that shows the aldolase reaction. - To the left, the chemical formula for fructose 1,6-bisphosphate is shown. - To the right, the chemical formulas for dihydroxyacetone phosphate and glyceraldehyde 3-phosphate are shown. - The enzyme **Aldolase** is shown above the arrow pointing to the right. # **Lyases also includes dehydratases and many synthases** - **Dehydratases remove water from two adjacent C-C bonds to form a double bond (e.g. Enolase)** - **Synthases when the physiologically important direction of the reaction favors the formation of a C-C bond (e.g. citrate synthase)** Two chemical diagrams are shown: - The first diagram shows the chemical formulas for 2-phosphoglycerate and phosphoenolpyruvate. - The enzyme **Enolase** is shown above the arrow pointing to the right. - The second diagram shows the chemical formulas for acetyl-CoA, oxaloacetate, and citrate. - The enzyme **Citrate synthase** is shown under the arrow pointing to the right. # **EC 5. Isomerases** - Many biochemical reactions simply rearrange the existing atoms of a molecule, that create isomers of the starting material. Enzymes rearranging the bond structure of a compound are called isomerases. - Whereas enzymes catalyzing movement of chemical groups such as phosphate group from one atom to another are called mutases. Two chemical diagrams are shown: - The top diagram shows the chemical formula for citrate on the left and the chemical formula for isocitrate on the right. - The enzyme **Isomerase** is shown below the line between the two chemical formulas. - The bottom diagram shows the chemical formula for 3-Phosphoglycerate on the left and the chemical formula for 2-Phosphoglycerate on the right. - The enzyme **Mutase** is shown above the arrow pointing to the right. # **EC 6. Ligases (Synthetases)** - Catalyze ligation or joining of two substrates. - Require chemical energy (ATP) Three chemical diagrams are shown: - The left diagram shows the chemical formulas for L-glutamate and L-glutamine. - The enzyme **Glutamine synthetase** is shown above the arrow pointing to the right. - The right diagram shows the chemical formulas for glutamate, cysteine, and y-Glutamylcysteine synthetase. The enzyme **y-Glutamylcysteine synthetase** is shown below the arrow pointing to the right. - Another diagram shows the chemical formula for glycine and glutathione synthetase. The enzyme **Glutathione synthetase** is shown below the arrow pointing to the right.