ECOLOGICAL BIOCHEMISTRY - Study Guide - V. M. Isaenko 2005

Appendix 2.

LIST OF CITED ENZYMES AND THE REACTIONS THEY CATALYZE

Adenylyl cyclase (EC 4.6.1.1)—an enzyme of the lyase Class that catalyzes The formation of 3',5-cyclic AMP from ATP. The enzyme is located in Plasma Membranes and is activated by certain Hormones (epinephrine, vasopressin, Glucagon, and corticotropin). The resulting cyclic AMP serves as an important regulator of METABOLISM.

Adenosine triphosphatase (EC 3.6.1.3)—an enzyme of the hydrolase class that catalyzes the Hydrolysis of ATP to ADP. The reaction results from the combined action of Proteins that utilize ATP to power processes such as Muscle contraction, maintenance of concentration gradients, membrane transport, and regulation of ion concentration.

Alcohol dehydrogenase (NAD⁺(P⁺)) (EC 1.1.1.71)—an enzyme of the oxidoreductase class that catalyzes the reversible oxidation of primary or secondary alcohols to aldehydes or ketones, respectively, using NAD⁺ or NADP⁺ as electron acceptors. The enzyme also facilitates the interconversion of retinol and retinal.

Alcohol dehydrogenase (NADP⁺) (EC 1.1.1.2)—an enzyme of the oxidoreductase class that catalyzes the reversible oxidation of primary or secondary alcohols to aldehydes or ketones, using NADP⁺ as an electron acceptor.

Aldehyde oxidase (EC 1.2.3.1)—an enzyme of the oxidoreductase class that catalyzes The oxidation of aldehydes to their corresponding acids with the generation of a peroxide anion. It is a molybdenum flavoprotein that catalyzes the oxidation of various heterocyclic compounds and xenobiotics.

Aminoacyl-tRNA synthetase (EC 6.1.1.7)—any of a group of ligases that catalyze the formation of a bond between an Amino Acid and its tRNA at the expense of ATP energy, leading to the activation of Amino Acids as a step in Protein Synthesis. Individual Enzymes are highly specific for a single amino acid and its cognate tRNA.

Aminoxidase — see L-Amino Acid Oxidase.

Aspartate ammonia-lyase (EC 4.3.1.1)—an enzyme that acts on a substrate (aspartic acid) to release ammonia via elimination, resulting in the formation of a double bond.

Aspartate carbamoyltransferase (EC 2.1.3.2)—an enzyme of the transferase class that catalyzes the formation of carbamoylaspartate from carbamoyl phosphate and aspartate in the committed first step of Pyrimidine Nucleotide Biosynthesis.

Na⁺,K⁺-ATPase (EC 3.6.1.36)—a membrane-bound enzyme located on the secretory surfaces of parietal Cells. It utilizes energy derived from ATP hydrolysis to drive Ion Exchange across The Cell membrane during acid secretion into the gastric lumen. Protons and chloride ions are pumped against a gradient across the apical membrane of activated parietal cells into the gastric lumen in exchange for potassium ions. In the EC nomenclature, it is referred to as H⁺/K⁺-exchanging ATPase.

Na⁺,K⁺-ATPase (EC 3.6.1.37)—an enzyme of the hydrolase class that catalyzes the hydrolysis of ATP to provide the energy required for the operation of the cellular sodium pump. In the EC nomenclature, it is referred to as Na⁺K⁺-exchanging ATPase.

Acetylcholinesterase (EC 3.1.1.7)—an enzyme of the hydrolase class that hydrolyzes acetylcholine into Choline and acetate.

Hexokinase (EC 2.7.1.1)—an enzyme of the transferase class that catalyzes the phosphorylation of hexoses at the C-6 position, marking the initial step in cellular utilization of free hexoses. This enzyme is found in all Tissues and exists in multiple isozyme forms.

Hyaluronidase—any of three enzymes (hyaluronoglucuronidase (EC 4.2.2.1), hyaluronoglucosaminidase (EC 3.2.1.35), and hyaluronate lyase (EC 3.2.1.36)) that catalyze the degradation of hyaluronic acid. These enzymes are found in mammalian Testes, bee and snake venoms, and certain species of Clostridium, Staphylococcus, and Streptococcus.

Hydrolases (EC 3)—a class of enzymes that catalyze the Cleavage of chemical bonds involving the incorporation of Water, such as esterases, glucosidases, lipases, nucleotidases, peptidases, and Phosphatases.

3-Hydroxyacyl-CoA dehydrogenase (β-Keto reductase) (EC 1.1.1.35)—an enzyme of the oxidoreductase class that catalyzes the oxidation at C-3 of L-hydroxyacyl-coenzyme A to form ketoacyl-coenzyme A, using NAD⁺ as an electron acceptor. This reaction constitutes one of the steps in Fatty acid oxidation.

Glutamate-ammonia ligase (EC 6.3.1.2)—an enzyme of the ligase class that catalyzes the ATP-dependent amination of glutamate with ammonium ions.

Glutamate dehydrogenase (NAD⁺(P⁺)) (EC 1.4.1.3)—an enzyme of the oxidoreductase class that catalyzes the Oxidative Deamination of glutamate to form α-ketoglutarate, using NAD⁺ or NADP⁺ as an electron acceptor. The reverse reaction plays a major role in both the Synthesis and Breakdown of glutamic acid, and, via transaminases, of Other Amino Acids as well.

Glutamine Synthetase — see Glutamate-ammonia ligase.

Glucose-6-phosphate dehydrogenase (EC 1.1.1.49)—an enzyme of the oxidoreductase class that catalyzes the oxidation of glucose-6-phosphate to the corresponding lactone, reducing NADP⁺ to NADPH. This reaction represents the first step in the Pentose Phosphate Pathway of glucose metabolism. A genetically determined deficiency of this enzyme causes severe hemolytic crises in affected individuals.

Glucose oxidase (EC 1.1.3.4)—an enzyme of the oxidoreductase class that catalyzes the oxidation of glucose, reducing oxygen to hydrogen peroxide. It is a flavoprotein containing FAD and exhibits high Specificity for β-D-glucose. It possesses antibacterial activity due to the generation of hydrogen peroxide in the catalyzed reaction.

Glucokinase (EC 2.7.1.2)—an enzyme of the transferase class that catalyzes the phosphorylation of D-glucose at the C-6 position. The enzyme is found in invertebrates and microorganisms, and displays exceptionally high specificity for glucose.

β-Galactosidase (EC 3.2.1.23) is a specific group of enzymes belonging to the hydrolase class that catalyzes the cleavage of terminal, β-linked, non-reducing galactose residues from various substrates, including lactosylceramides, lactose, and various Glycoproteins and Oligosaccharides.

β-Glucosidase (EC 3.2.1.21) is any member of the hydrolase class that catalyzes the hydrolysis of terminal, non-reducing β-1,4-glucose residues from glucosides.

β-Glucuronidase (EC 3.2.1.31) is a lysosomal enzyme of the hydrolase class that catalyzes the cleavage of terminal glucuronic acid residues from various β-glucuronides. It plays a vital role in the degradation of various glycosaminoglycans.

Deoxyribonucleases (DNases) are Nucleases that specifically catalyze the cleavage of phosphodiester bonds in Deoxyribonucleic Acids. Deoxyribonucleases are subdivided into those that cleave internal bonds within the molecule (endodeoxyribonucleases) and those that cleave bonds at its ends (exodeoxyribonucleases). These include: deoxyribonuclease I (EC 3.1.21.1, DNase I), an endonuclease that generates di- and oligonucleotides with 5'-phosphate groups (this enzyme is found in the Pancreas and Thymus tissues); and deoxyribonuclease II (EC 3.1.22.1, DNase II), an endonuclease that produces di- and oligonucleotides with 3'-phosphate groups (present in the Liver, pancreas, thymus, and gastric mucosa tissues).

Dxygenase is a term used in the recommended names of oxygenases—enzymes that catalyze the incorporation of both oxygen atoms from O₂ into a single substrate (EC 1.13.11). Most of these enzymes require iron or copper to exhibit activity.

DNA-dependent RNA polymerase (EC 2.7.7.6) is an enzyme of the transferase class that catalyzes template-directed stepwise addition of ribonucleotides to the 3'-end of a growing RNA chain using a single-stranded DNA template. This reaction is essential for the transmission of Genetic information from DNA to proteins. Prokaryotes possess a single such polymerase, whereas eukaryotes have three: type I transcribes most ribosomal RNA genes; type II synthesizes messenger and heterogeneous nuclear RNA molecules; type III transcribes genes for one variety of ribosomal RNA and for Transfer RNA molecules.

Elastase (EC 3.4.21.11) is an enzyme that catalyzes The breakdown of Elastin and other proteins. It primarily cleaves the polypeptide chain at bonds involving the carbonyl group of amino acids with uncharged, non-aromatic side chains. Elastase activity is specifically inhibited by α-antitrypsin.

Endopeptidase (EC 3.4.21-24; 3.4.99) is any peptidase that catalyzes the cleavage of internal peptide bonds within a polypeptide or protein. They are divided into subclasses based on their catalytic mechanism, including Serine Endopeptidases, Cysteine endopeptidases, aspartic endopeptidases, metalloendopeptidases, and other endopeptidases.

Endoribonuclease (EC 3.1.26-27) is any member of two subclasses of hydrolase enzymes that catalyze the hydrolysis of internal ribonucleotide bonds, yielding oligonucleotides or polynucleotides.

Esterases is a term used in the recommended and trivial names of hydrolases acting on ester bonds (EC 3.1) to yield an alcohol and an acid.

Isomerase (EC 5) is a class of enzymes that catalyze geometric or structural changes within a molecule to form a single product. These reactions do not cause any net change in concentration other than for the substrate and the product. The class encompasses epimerases, isomerases, Mutases, and racemases.

Isocitrate dehydrogenase (NADP⁺) (EC 1.1.1.42) is an oxidoreductase enzyme that catalyzes The oxidative decarboxylation of isocitrate to α-ketoglutarate, utilizing NADP⁺ as an electron acceptor. The enzyme exists in two isoforms (cytoplasmic and mitochondrial), requires Mg²⁺ or Mn²⁺ ions, and is present in all tissues. This reaction serves to maintain the pool of reducing equivalents within the cell.

Carboxypeptidase (EC 3.4.15-18) is any exopeptidase of the hydrolase class that catalyzes the hydrolytic Cleavage of the terminal or penultimate peptide bond at the C-terminus of a peptide or polypeptide.

Carboxypeptidase B (EC 3.4.17.2) is a hydrolase enzyme that catalyzes the removal of C-terminal Arginine or Lysine residues from Polypeptides. It is a zinc-containing metalloenzyme found in pancreatic juice.

Catalase (EC 1.11.1.6) is a hemoprotein enzyme of the oxidoreductase class that catalyzes The conversion of hydrogen peroxide into water and oxygen, thereby protecting cells. It is found in almost all animal cells, with the exception of certain obligate anaerobic Bacteria.

Catechol-O-methyltransferase (EC 2.1.1.6) is a transferase enzyme that catalyzes The transfer of methyl groups from S-adenosylmethionine to a catechol or catecholamine, such as dopa, dopamine, epinephrine, or norepinephrine. The enzyme is found in the Cytoplasm, notably in the Kidneys, liver, and Central Nervous system.

Kinase is a term used in the recommended and common names of phosphotransferases and diphosphotransferases belonging to the transferase class (EC 2.7.16), which catalyze the transfer of a high-energy phosphate group from a donor compound (e.g., ATP or GTP) to an acceptor compound (such as a hydroxyl, carboxyl, nitrogen, or another phosphate group).

Collagenases are enzymes that catalyze the hydrolysis of peptide bonds in the triple-helical regions of Collagen. The most common are: 1) interstitial collagenase (EC 3.4.24.7), a group of hydrolase enzymes that catalyzes the cleavage of native collagen, typically at Glycine-leucine or glycine-isoleucine bonds. The best-studied are those enzyme groups that cleave fibrillar collagens into a large N-terminal (75%) fragment and a small C-terminal (25%) fragment. These enzymes require zinc. They are widespread in vertebrates and participate in collagen breakdown during tissue remodeling or embryonic and prenatal development; 2) microbial collagenase (EC 3.4.24.3), any of numerous collagenases isolated from various microorganisms, particularly Clostridium histolyticum. They selectively cleave collagen at the N-terminal side of glycine residues and occur in several classes with varying specificity.

Xanthine oxidase (EC 1.1.3.22) is an oxidoreductase enzyme that catalyzes the oxidation of hypoxanthine to xanthine and of xanthine to uric acid, representing the final stages of purine degradation. It is an iron-molybdenum flavoprotein containing FAD. Enzyme deficiency, an autosomal recessive trait, causes xanthinuria.

Lysophospholipase (EC 3.1.1.5) is a hydrolase enzyme that catalyzes the hydrolysis of the acyl group of 2-lysophospholipid, representing a step in the degradation of dietary and intracellular Phospholipids.

Lipase (EC 3.1) is any enzyme that hydrolytically cleaves fatty acid anions from triglycerides or phospholipids (see triacylglycerol lipase).

Luciferase is the name of various Monooxygenases that catalyze reactions producing Bioluminescence in certain marine crustaceans, fish, bacteria, and insects (EC 1.13.12.5-8, 1.14.14.3, 1.14.99.21). The enzyme is a flavoprotein that oxidizes luciferin into an electron-excited compound which emits energy in the form of light.

Methyltransferase (EC 2.1.1) is any member of the subclass of transferase enzymes that catalyzes the transfer of methyl groups from one compound to another.

Monooxygenase is a term used in the recommended names of certain oxidoreductase enzymes. It refers to any enzyme that catalyzes the incorporation of one atom from molecular oxygen into a compound while reducing the other oxygen atom to water. This includes enzymes in which the oxygen acceptor also serves as a hydrogen donor (EC 1.13.12), as well as those in which Other Compounds act as hydrogen Donors in a coupled reaction (EC 1.14.13 to 1.14.18 and 1.14.99).

5'-Nucleotidase (EC 3.1.3.5) is a membrane-bound cytoplasmic nucleotidase that specifically cleaves the phosphate from the 5'-position of NUCLEOTIDES to yield nucleosides. The enzyme acts on a wide range of 5'-nucleotides, and this reaction forms part of the primary pathway of nucleotide degradation.

H⁺-transporting ATP synthase (EC 3.6.1.34) is an inner mitochondrial membrane enzyme complex that catalyzes the phosphorylation of ADP to form ATP. The energy required for ATP synthesis during Oxidative Phosphorylation—which is coupled with electron transport—is derived from the transmembrane transfer of protons and electrons, resulting in the generation of a hydrogen ion Electrochemical Potential gradient.

Nitrate reductase (EC 1.9.6.1) is an enzyme that catalyzes the reduction of nitrates to nitrites. This reaction enables plants to utilize nitrate nitrogen for PROTEIN SYNTHESIS AND, under certain conditions, allows specific bacteria to use nitrate as a terminal electron acceptor during Respiration.

Nitrite reductase (EC 1.7.2.1) is a copper-containing oxidoreductase enzyme that catalyzes the oxidation of nitrogen compounds (such as nitric oxide) using cytochrome as an electron acceptor.

Nucleosidase (EC 3.2.2) is a term used in the recommended names of certain glycosidases that hydrolyze N-glycosidic bonds, specifically denoting enzymes that catalyze the cleavage of a nucleoside into a purine or pyrimidine base and a sugar.

Oxidase (EC 1.4.3) is a term used in the recommended names of certain oxidoreductases to designate those in which molecular oxygen serves as the hydrogen acceptor.

L-amino acid oxidase (EC 1.4.3.2) is an oxidoreductase enzyme that catalyzes the oxidative deamination of L-amino acids to yield 2-keto acids, producing hydrogen peroxide as a byproduct. This flavoprotein acts on all natural monocarboxylic L-amino acids except Serine and Threonine.

Oxidoreductases (EC 1) comprise a class of enzymes that catalyze the reversible transfer of electrons from a substrate that becomes oxidized to one that becomes reduced. This class includes dehydrogenases, hydroxylases, oxidases, oxygenases, peroxidases, and reductases.

Pancreatic Ribonuclease (EC 3.1.27.5) is an endoribonuclease derived from the pancreas of ruminants, widely used in The Study of enzymatic mechanisms and molecular biology research. It specifically catalyzes the cleavage of terminal pyrimidine nucleotide 3'-phosphate residues. It is also known as ribonuclease I.

Peroxidase (EC 1.11.1.7) is a term used in the recommended names of oxidoreductase enzymes that catalyze the oxidation of organic substrates by hydrogen peroxide, which is reduced to water. These Hemoproteins are widespread in plants and occasionally found in animal tissues.

Pyruvate decarboxylase (EC 4.1.1.1; now referred to as pyruvate-lippamide dehydrogenase) is a lyase enzyme that catalyzes the decarboxylation of 2-keto acids to form aldehydes, acting as part of the anaerobic enzymatic pathway that converts glucose into ethanol and CO₂. Found in Yeast, this enzyme requires pyrophosphate as a cofactor.

Pyruvate kinase (EC 2.7.1.40) is a transferase enzyme that catalyzes the transfer of a high-energy phosphate group from phosphoenolpyruvate to ADP, yielding ATP and pyruvate. This represents one of the two ATP-generating steps in the Embden–Meyerhof pathway and serves as a major regulatory point within it. The enzyme exists in three distinct isozymes. An autosomal recessive deficiency of pyruvate kinase in erythrocytes leads to hemolytic anemia.

Protease — see endopeptidase.

Protein kinase (EC 2.7.1.37) is a transferase enzyme that catalyzes the phosphorylation of the OH groups of serine, threonine, or Tyrosine residues in enzymes and other proteins, utilizing ATP as a phosphate donor. Specific protein Kinases, typically named after their substrates, are regulated by phosphorylation enzymes, thereby catalyzing key reactions in processes such as Glycogen Metabolism, Cholesterol Biosynthesis, and amino acid transformation. Other kinases generate caseins secreted in milk.

Ribonucleases (EC 3.1) are hydrolase-class nucleases that specifically catalyze the cleavage of phosphodiester bonds in ribonucleic

acids. Ribonucleases are subdivided into those that cleave internal bonds (endoribonucleases) and those that cleave terminal bonds (exoribonucleases). The term "ribonuclease" is sometimes used specifically to designate pancreatic ribonuclease (see pancreatic ribonuclease).

RNA-dependent RNA polymerase (EC 2.7.7.48) is a transferase enzyme that catalyzes the template-directed addition of ribonucleotides to the 3' end of a growing RNA chain using a single-stranded RNA template. This reaction is essential for Transcription and, in some cases, RNA Replication in most RNA Viruses, with the exception of Retroviruses.

RNA polymerase is a general term denoting any enzyme that catalyzes the template-directed assembly of ribonucleotides into an RNA chain (see DNA-dependent RNA polymerase and RNA-dependent RNA polymerase).

Ca²⁺-ATPase (EC 3.6.1.38) is a membrane-bound enzyme that hydrolyzes ATP to supply the energy required for the operation of the cellular calcium pump. In the EC nomenclature, it is referred to as a calcium-transporting ATPase.

Transferases (EC 2) comprise a class of enzymes that transfer chemical groups from one compound (the donor) to another (the acceptor). Systematic names are formed According to the scheme: donor:acceptor group-transferase. Recommended names are usually structured as acceptor group-transferase or donor group-transferase. In many cases, the donor is a cofactor (coenzyme) that carries the transferred group.

Triacylglycerol lipase (EC 3.1.1.3) is a hydrolase enzyme that catalyzes the removal of two outer acyl groups from triglycerides during dietary fat Digestion. Individual enzymes are often named after the tissues with which they are associated. The term is sometimes used specifically to denote pancreatic lipase, the primary intestinal lipase that digests ingested fats into Fatty acids and monoglycerides (this enzymatic activity requires Bile salts and colipase).

Phosphatase (EC 3.1.3) is a term used in the recommended names of certain hydrolase enzymes—specifically phosphoric monoester hydrolases—that catalyze the removal of inorganic phosphate from phosphoric esters.

Acid phosphatase (EC 3.1.3.2) is a hydrolase enzyme that catalyzes the cleavage of orthophosphates from orthophosphoric acid monoesters in an acidic environment. The enzyme is present in the liver, Spleen, Bone Marrow, plasma, formed Blood elements, and the Prostate Gland of mammals.

Alkaline phosphatase (EC 3.1.3.1) is a hydrolase enzyme that catalyzes the removal of orthophosphate from an orthophosphoric monoester under alkaline conditions. Various Forms of the enzyme occur in normal and malignant tissues. Reduced alkaline phosphatase activity in bones, inherited as an autosomal recessive trait, causes hypophosphatasia.

Phosphoglucomutase (EC 5.4.2.2) is an isomerase enzyme that requires the presence of an intermediate, glucose 1,6-bisphosphate, to catalyze the interconversion of glucose 1-phosphate and glucose 6-phosphate, a key step in glycogen synthesis and utilization. It also catalyzes the interconversion of ribose 1-phosphate and ribose 5-phosphate isomers.

Phosphodiesterase is a term used in the recommended names of certain phosphoric diester hydrolases (EC 3.1.4) belonging to the hydrolase class, which catalyze the hydrolysis of one of the two ester bonds in a phosphodiester compound.

Phospholipase is any enzyme of the hydrolase class that catalyzes the hydrolysis of specific ester bonds in phospholipids. Individual enzymes are grouped based on the bonds they hydrolyze, and further divided into categories: carboxylic esterases (phospholipase A₂) or phosphodiesterases (phospholipase C, phospholipase D).

Phospholipase A₂ (EC 3.1.1.4) is an esterase that catalyzes the hydrolysis of the central acyl group of a membrane phospholipid, yielding a free Fatty acid and a lysophospholipid. This reaction is crucial during the assimilation of dietary phospholipids, as it releases arachidonic acid for various processes, including platelet activation. The enzyme is found in various forms across all mammalian tissues, as well as in snake and bee venoms.

6-Phosphofructokinase (EC 2.7.1.11) is a transferase enzyme that catalyzes the phosphorylation of fructose-6-phosphate by means of ATP to yield fructose-1,6-bisphosphate. This irreversible reaction is a vital step and the primary regulatory site of Glucose metabolism in the Embden–Meyerhof pathway.

6-Phosphofructo-2-kinase (EC 2.7.1.105) is a transferase enzyme that catalyzes the phosphorylation of fructose 6-phosphate using ATP to form fructose 2,6-bisphosphate. In the liver, it participates in the REGULATION OF CARBOHYDRATE Metabolism.

Fructose-1,6-bisphosphatase (EC 3.1.3.11) is a hydrolase enzyme that catalyzes the hydrolysis of fructose-1,6-diphosphate to form fructose-6-phosphate. This reaction is part of The Gluconeogenesis pathway that takes place in The Liver and kidneys. In the EC nomenclature, it is referred to as fructose-bisphosphatase.

Fructose-2,6-bisphosphatase (EC 3.1.3.46) is an enzyme that catalyzes the hydrolysis of fructose-2,6-diphosphate to yield fructose-6-phosphate. In the liver, it participates in The regulation of Carbohydrate Metabolism.

Cholinesterase (EC 3.1.1.8) is a hydrolase enzyme that catalyzes the cleavage of acyl groups from various choline esters, including acetylcholine and related compounds. The enzyme is primarily found in blood serum, the liver, and the pancreas; the determination of its activity is used to test liver function, assess sensitivity to succinylcholine, and diagnose organophosphate insecticide poisoning.

Cytochrome oxidase — see cytochrome c oxidase.

Cytochrome c oxidase (EC 1.9.3.1) is a multimeric enzyme complex of The inner mitochondrial membrane that catalyzes the transfer of electrons from cytochrome c to oxygen, resulting in the oxidation of the former and the reduction of the latter at the terminal stage of the Electron Transport Chain, where oxygen is utilized for substrate oxidation. The enzyme contains Cytochromes a and a₃, two copper atoms, and is associated with proton translocation and, consequently, ATP synthesis. Iron (Fe²⁺) has a high affinity for CO; in its Fe³⁺ state, it binds CN^-, S^2-, and N₃. The binding of these agents inactivates the enzyme, which accounts for their extreme toxicity to all aerobic organisms.