Oxygen: An element with atomic symbol O, atomic number 8, and atomic weight [15.99903; 15.99977]. It is the most abundant element on earth and essential for respiration.Carbon: A nonmetallic element with atomic symbol C, atomic number 6, and atomic weight [12.0096; 12.0116]. It may occur as several different allotropes including DIAMOND; CHARCOAL; and GRAPHITE; and as SOOT from incompletely burned fuel.Lyases: A class of enzymes that catalyze the cleavage of C-C, C-O, and C-N, and other bonds by other means than by hydrolysis or oxidation. (Enzyme Nomenclature, 1992) EC 4.Chondroitin Lyases: Enzymes which catalyze the elimination of delta-4,5-D-glucuronate residues from polysaccharides containing 1,4-beta-hexosaminyl and 1,3-beta-D-glucuronosyl or 1,3-alpha-L-iduronosyl linkages thereby bringing about depolymerization. EC 4.2.2.4 acts on chondroitin sulfate A and C as well as on dermatan sulfate and slowly on hyaluronate. EC 4.2.2.5 acts on chondroitin sulfate A and C.Carbon Dioxide: A colorless, odorless gas that can be formed by the body and is necessary for the respiration cycle of plants and animals.Oxygen Consumption: The rate at which oxygen is used by a tissue; microliters of oxygen STPD used per milligram of tissue per hour; the rate at which oxygen enters the blood from alveolar gas, equal in the steady state to the consumption of oxygen by tissue metabolism throughout the body. (Stedman, 25th ed, p346)Reactive Oxygen Species: Molecules or ions formed by the incomplete one-electron reduction of oxygen. These reactive oxygen intermediates include SINGLET OXYGEN; SUPEROXIDES; PEROXIDES; HYDROXYL RADICAL; and HYPOCHLOROUS ACID. They contribute to the microbicidal activity of PHAGOCYTES, regulation of signal transduction and gene expression, and the oxidative damage to NUCLEIC ACIDS; PROTEINS; and LIPIDS.Carbon Monoxide: Carbon monoxide (CO). A poisonous colorless, odorless, tasteless gas. It combines with hemoglobin to form carboxyhemoglobin, which has no oxygen carrying capacity. The resultant oxygen deprivation causes headache, dizziness, decreased pulse and respiratory rates, unconsciousness, and death. (From Merck Index, 11th ed)Nanotubes, Carbon: Nanometer-sized tubes composed mainly of CARBON. Such nanotubes are used as probes for high-resolution structural and chemical imaging of biomolecules with ATOMIC FORCE MICROSCOPY.Pectobacterium chrysanthemi: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria that causes vascular wilts on a wide range of plant species. It was formerly named Erwinia chrysanthemi.Chondroitinases and Chondroitin Lyases: Enzymes which catalyze the elimination of glucuronate residues from chondroitin A,B, and C or which catalyze the hydrolysis of sulfate groups of the 2-acetamido-2-deoxy-D-galactose 6-sulfate units of chondroitin sulfate. EC 4.2.2.-.Pectins: High molecular weight polysaccharides present in the cell walls of all plants. Pectins cement cell walls together. They are used as emulsifiers and stabilizers in the food industry. They have been tried for a variety of therapeutic uses including as antidiarrheals, where they are now generally considered ineffective, and in the treatment of hypercholesterolemia.Phycobiliproteins: Light harvesting proteins found in phycobilisomes.Carbon Monoxide Poisoning: Toxic asphyxiation due to the displacement of oxygen from oxyhemoglobin by carbon monoxide.Chicory: A thick-rooted perennial (Cichorium intybus) native to Europe but widely grown for its young leaves used as salad greens and for its roots, dried and ground-roasted, used to flavor or adulterate coffee. (From Webster, 3d ed)Oxygen Inhalation Therapy: Inhalation of oxygen aimed at restoring toward normal any pathophysiologic alterations of gas exchange in the cardiopulmonary system, as by the use of a respirator, nasal catheter, tent, chamber, or mask. (From Dorland, 27th ed & Stedman, 25th ed)Aldehyde-Lyases: Enzymes that catalyze a reverse aldol condensation. A molecule containing a hydroxyl group and a carbonyl group is cleaved at a C-C bond to produce two smaller molecules (ALDEHYDES or KETONES). EC 4.1.2.Carbon Isotopes: Stable carbon atoms that have the same atomic number as the element carbon, but differ in atomic weight. C-13 is a stable carbon isotope.Singlet Oxygen: An excited state of molecular oxygen generated photochemically or chemically. Singlet oxygen reacts with a variety of biological molecules such as NUCLEIC ACIDS; PROTEINS; and LIPIDS; causing oxidative damages.Carbon-Oxygen Lyases: Enzymes that catalyze the cleavage of a carbon-oxygen bond by means other than hydrolysis or oxidation. EC 4.2.Erwinia: A genus of gram-negative, facultatively anaerobic, rod-shaped bacteria whose organisms are associated with plants as pathogens, saprophytes, or as constituents of the epiphytic flora.Oxo-Acid-Lyases: Enzymes that catalyze the cleavage of a carbon-carbon bond of a 3-hydroxy acid. (Dorland, 28th ed) EC 4.1.3.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Heparin Lyase: An enzyme of the isomerase class that catalyzes the eliminative cleavage of polysaccharides containing 1,4-linked D-glucuronate or L-iduronate residues and 1,4-alpha-linked 2-sulfoamino-2-deoxy-6-sulfo-D-glucose residues to give oligosaccharides with terminal 4-deoxy-alpha-D-gluc-4-enuronosyl groups at their non-reducing ends. (From Enzyme Nomenclature, 1992) EC 4.2.2.7.Carbon Tetrachloride: A solvent for oils, fats, lacquers, varnishes, rubber waxes, and resins, and a starting material in the manufacturing of organic compounds. Poisoning by inhalation, ingestion or skin absorption is possible and may be fatal. (Merck Index, 11th ed)Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Polygalacturonase: A cell wall-degrading enzyme found in microorganisms and higher plants. It catalyzes the random hydrolysis of 1,4-alpha-D-galactosiduronic linkages in pectate and other galacturonans. EC 3.2.1.15.Carbon Sequestration: Any of several processes for the permanent or long-term artificial or natural capture or removal and storage of carbon dioxide and other forms of carbon, through biological, chemical or physical processes, in a manner that prevents it from being released into the atmosphere.Alginates: Salts of alginic acid that are extracted from marine kelp and used to make dental impressions and as absorbent material for surgical dressings.Oxygen Isotopes: Stable oxygen atoms that have the same atomic number as the element oxygen, but differ in atomic weight. O-17 and 18 are stable oxygen isotopes.Carbon Disulfide: A colorless, flammable, poisonous liquid, CS2. It is used as a solvent, and is a counterirritant and has local anesthetic properties but is not used as such. It is highly toxic with pronounced CNS, hematologic, and dermatologic effects.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Hexuronic Acids: Term used to designate tetrahydroxy aldehydic acids obtained by oxidation of hexose sugars, i.e. glucuronic acid, galacturonic acid, etc. Historically, the name hexuronic acid was originally given to ascorbic acid.Rhodophyta: Plants of the division Rhodophyta, commonly known as red algae, in which the red pigment (PHYCOERYTHRIN) predominates. However, if this pigment is destroyed, the algae can appear purple, brown, green, or yellow. Two important substances found in the cell walls of red algae are AGAR and CARRAGEENAN. Some rhodophyta are notable SEAWEED (macroalgae).Kinetics: The rate dynamics in chemical or physical systems.Sphingomonas: A genus of gram-negative, aerobic, rod-shaped bacteria characterized by an outer membrane that contains glycosphingolipids but lacks lipopolysaccharide. They have the ability to degrade a broad range of substituted aromatic compounds.Isocitrate Lyase: A key enzyme in the glyoxylate cycle. It catalyzes the conversion of isocitrate to succinate and glyoxylate. EC 4.1.3.1.Partial Pressure: The pressure that would be exerted by one component of a mixture of gases if it were present alone in a container. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Hydrogen-Ion Concentration: The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Phycobilins: Open chain tetrapyrroles that function as light harvesting chromophores in PHYCOBILIPROTEINS.Chondroitin ABC Lyase: An enzyme that catalyzes the eliminative degradation of polysaccharides containing 1,4-beta-D-hexosaminyl and 1,3-beta-D-glucuronosyl or 1,3-alpha-L-iduronosyl linkages to disaccharides containing 4-deoxy-beta-D-gluc-4-enuronosyl groups. (Enzyme Nomenclature, 1992)Oxidation-Reduction: A chemical reaction in which an electron is transferred from one molecule to another. The electron-donating molecule is the reducing agent or reductant; the electron-accepting molecule is the oxidizing agent or oxidant. Reducing and oxidizing agents function as conjugate reductant-oxidant pairs or redox pairs (Lehninger, Principles of Biochemistry, 1982, p471).Bacterial Proteins: Proteins found in any species of bacterium.Hyperbaric Oxygenation: The therapeutic intermittent administration of oxygen in a chamber at greater than sea-level atmospheric pressures (three atmospheres). It is considered effective treatment for air and gas embolisms, smoke inhalation, acute carbon monoxide poisoning, caisson disease, clostridial gangrene, etc. (From Segen, Dictionary of Modern Medicine, 1992). The list of treatment modalities includes stroke.Carbon Tetrachloride PoisoningCytochromes c1: The 30-kDa membrane-bound c-type cytochrome protein of mitochondria that functions as an electron donor to CYTOCHROME C GROUP in the mitochondrial and bacterial RESPIRATORY CHAIN. (From Enzyme Nomenclature, 1992, p545)Pseudomonas: A genus of gram-negative, aerobic, rod-shaped bacteria widely distributed in nature. Some species are pathogenic for humans, animals, and plants.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Flavobacterium: A genus of gram-negative, aerobic, rod-shaped bacteria widely distributed in SOIL and WATER. Its organisms are also found in raw meats, MILK and other FOOD, hospital environments, and human clinical specimens. Some species are pathogenic in humans.Glucuronic Acid: A sugar acid formed by the oxidation of the C-6 carbon of GLUCOSE. In addition to being a key intermediate metabolite of the uronic acid pathway, glucuronic acid also plays a role in the detoxification of certain drugs and toxins by conjugating with them to form GLUCURONIDES.Bacteroides: A genus of gram-negative, anaerobic, rod-shaped bacteria. Its organisms are normal inhabitants of the oral, respiratory, intestinal, and urogenital cavities of humans, animals, and insects. Some species may be pathogenic.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Adenylosuccinate Lyase: An enzyme that, in the course of purine ribonucleotide biosynthesis, catalyzes the conversion of 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole to 5'-phosphoribosyl-4-carboxamide-5-aminoimidazole and the conversion of adenylosuccinic acid to AMP. EC 4.3.2.2.Streptococcus anginosus: A species of gram-positive bacteria in the STREPTOCOCCUS MILLERI GROUP. It is the most frequently seen isolate of that group, has a proclivity for abscess formation, and is most often isolated from the blood, gastrointestinal, and urogenital tract.Hevea: A plant genus of the family EUPHORBIACEAE, order Euphorbiales, subclass Rosidae. Commercial natural RUBBER is mainly obtained from Hevea brasiliensis but also from some other plants.Anoxia: Relatively complete absence of oxygen in one or more tissues.Nitrogen: An element with the atomic symbol N, atomic number 7, and atomic weight [14.00643; 14.00728]. Nitrogen exists as a diatomic gas and makes up about 78% of the earth's atmosphere by volume. It is a constituent of proteins and nucleic acids and found in all living cells.Hydrogen Peroxide: A strong oxidizing agent used in aqueous solution as a ripening agent, bleach, and topical anti-infective. It is relatively unstable and solutions deteriorate over time unless stabilized by the addition of acetanilide or similar organic materials.Oxidative Stress: A disturbance in the prooxidant-antioxidant balance in favor of the former, leading to potential damage. Indicators of oxidative stress include damaged DNA bases, protein oxidation products, and lipid peroxidation products (Sies, Oxidative Stress, 1991, pxv-xvi).Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.Aerobiosis: Life or metabolic reactions occurring in an environment containing oxygen.Carbon Footprint: A measure of the total greenhouse gas emissions produced by an individual, organization, event, or product. It is measured in units of equivalent kilograms of CARBON DIOXIDE generated in a given time frame.Oximetry: The determination of oxygen-hemoglobin saturation of blood either by withdrawing a sample and passing it through a classical photoelectric oximeter or by electrodes attached to some translucent part of the body like finger, earlobe, or skin fold. It includes non-invasive oxygen monitoring by pulse oximetry.Anaerobiosis: The complete absence, or (loosely) the paucity, of gaseous or dissolved elemental oxygen in a given place or environment. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Glycoside HydrolasesGlycosaminoglycans: Heteropolysaccharides which contain an N-acetylated hexosamine in a characteristic repeating disaccharide unit. The repeating structure of each disaccharide involves alternate 1,4- and 1,3-linkages consisting of either N-acetylglucosamine or N-acetylgalactosamine.Proteus vulgaris: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria that occurs in soil, fecal matter, and sewage. It is an opportunistic pathogen and causes cystitis and pyelonephritis.Uronic Acids: Acids derived from monosaccharides by the oxidation of the terminal (-CH2OH) group farthest removed from the carbonyl group to a (-COOH) group. (From Stedmans, 26th ed)Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Carbon Radioisotopes: Unstable isotopes of carbon that decay or disintegrate emitting radiation. C atoms with atomic weights 10, 11, and 14-16 are radioactive carbon isotopes.CarboxyhemoglobinCatalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.Disaccharides: Oligosaccharides containing two monosaccharide units linked by a glycosidic bond.Atmosphere: The gaseous envelope surrounding a planet or similar body. (From Random House Unabridged Dictionary, 2d ed)Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Sulfonium Compounds: Sulfur compounds in which the sulfur atom is attached to three organic radicals and an electronegative element or radical.Chondroitin Sulfates: Derivatives of chondroitin which have a sulfate moiety esterified to the galactosamine moiety of chondroitin. Chondroitin sulfate A, or chondroitin 4-sulfate, and chondroitin sulfate C, or chondroitin 6-sulfate, have the sulfate esterified in the 4- and 6-positions, respectively. Chondroitin sulfate B (beta heparin; DERMATAN SULFATE) is a misnomer and this compound is not a true chondroitin sulfate.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Biomass: Total mass of all the organisms of a given type and/or in a given area. (From Concise Dictionary of Biology, 1990) It includes the yield of vegetative mass produced from any given crop.Glucose: A primary source of energy for living organisms. It is naturally occurring and is found in fruits and other parts of plants in its free state. It is used therapeutically in fluid and nutrient replacement.Carbohydrate Sequence: The sequence of carbohydrates within POLYSACCHARIDES; GLYCOPROTEINS; and GLYCOLIPIDS.Carbon-Carbon Lyases: Enzymes that catalyze the cleavage of a carbon-carbon bond by means other than hydrolysis or oxidation. This subclass contains the DECARBOXYLASES, the ALDEHYDE-LYASES, and the OXO-ACID-LYASES. EC 4.1.Fungi: A kingdom of eukaryotic, heterotrophic organisms that live parasitically as saprobes, including MUSHROOMS; YEASTS; smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi, commonly known as molds, refer to those that grow as multicellular colonies.DNA-(Apurinic or Apyrimidinic Site) Lyase: A DNA repair enzyme that catalyses the excision of ribose residues at apurinic and apyrimidinic DNA sites that can result from the action of DNA GLYCOSYLASES. The enzyme catalyzes a beta-elimination reaction in which the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. This enzyme was previously listed under EC 3.1.25.2.Carbon-Nitrogen Lyases: Enzymes that catalyze the cleavage of a carbon-nitrogen bond by means other than hydrolysis or oxidation. Subclasses are the AMMONIA-LYASES, the AMIDINE-LYASES, the amine-lyases, and other carbon-nitrogen lyases. EC 4.3.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Genes, Bacterial: The functional hereditary units of BACTERIA.Dermatan Sulfate: A naturally occurring glycosaminoglycan found mostly in the skin and in connective tissue. It differs from CHONDROITIN SULFATE A (see CHONDROITIN SULFATES) by containing IDURONIC ACID in place of glucuronic acid, its epimer, at carbon atom 5. (from Merck, 12th ed)Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Hemoglobins: The oxygen-carrying proteins of ERYTHROCYTES. They are found in all vertebrates and some invertebrates. The number of globin subunits in the hemoglobin quaternary structure differs between species. Structures range from monomeric to a variety of multimeric arrangements.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Blood Gas Analysis: Measurement of oxygen and carbon dioxide in the blood.Photosynthesis: The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide using energy obtained from light rather than from the oxidation of chemical compounds. Photosynthesis comprises two separate processes: the light reactions and the dark reactions. In higher plants; GREEN ALGAE; and CYANOBACTERIA; NADPH and ATP formed by the light reactions drive the dark reactions which result in the fixation of carbon dioxide. (from Oxford Dictionary of Biochemistry and Molecular Biology, 2001)Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Plants: Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.Culture Media: Any liquid or solid preparation made specifically for the growth, storage, or transport of microorganisms or other types of cells. The variety of media that exist allow for the culturing of specific microorganisms and cell types, such as differential media, selective media, test media, and defined media. Solid media consist of liquid media that have been solidified with an agent such as AGAR or GELATIN.Oxyhemoglobins: A compound formed by the combination of hemoglobin and oxygen. It is a complex in which the oxygen is bound directly to the iron without causing a change from the ferrous to the ferric state.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Antioxidants: Naturally occurring or synthetic substances that inhibit or retard the oxidation of a substance to which it is added. They counteract the harmful and damaging effects of oxidation in animal tissues.N-Glycosyl Hydrolases: A class of enzymes involved in the hydrolysis of the N-glycosidic bond of nitrogen-linked sugars.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Soot: A dark powdery deposit of unburned fuel residues, composed mainly of amorphous CARBON and some HYDROCARBONS, that accumulates in chimneys, automobile mufflers and other surfaces exposed to smoke. It is the product of incomplete combustion of carbon-rich organic fuels in low oxygen conditions. It is sometimes called lampblack or carbon black and is used in INK, in rubber tires, and to prepare CARBON NANOTUBES.Bacillus: A genus of BACILLACEAE that are spore-forming, rod-shaped cells. Most species are saprophytic soil forms with only a few species being pathogenic.Free Radicals: Highly reactive molecules with an unsatisfied electron valence pair. Free radicals are produced in both normal and pathological processes. They are proven or suspected agents of tissue damage in a wide variety of circumstances including radiation, damage from environment chemicals, and aging. Natural and pharmacological prevention of free radical damage is being actively investigated.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Biocatalysis: The facilitation of biochemical reactions with the aid of naturally occurring catalysts such as ENZYMES.Mitochondria: Semiautonomous, self-reproducing organelles that occur in the cytoplasm of all cells of most, but not all, eukaryotes. Each mitochondrion is surrounded by a double limiting membrane. The inner membrane is highly invaginated, and its projections are called cristae. Mitochondria are the sites of the reactions of oxidative phosphorylation, which result in the formation of ATP. They contain distinctive RIBOSOMES, transfer RNAs (RNA, TRANSFER); AMINO ACYL T RNA SYNTHETASES; and elongation and termination factors. Mitochondria depend upon genes within the nucleus of the cells in which they reside for many essential messenger RNAs (RNA, MESSENGER). Mitochondria are believed to have arisen from aerobic bacteria that established a symbiotic relationship with primitive protoeukaryotes. (King & Stansfield, A Dictionary of Genetics, 4th ed)Catalytic Domain: The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.Biodegradation, Environmental: Elimination of ENVIRONMENTAL POLLUTANTS; PESTICIDES and other waste using living organisms, usually involving intervention of environmental or sanitation engineers.Isoenzymes: Structurally related forms of an enzyme. Each isoenzyme has the same mechanism and classification, but differs in its chemical, physical, or immunological characteristics.Pulmonary Gas Exchange: The exchange of OXYGEN and CARBON DIOXIDE between alveolar air and pulmonary capillary blood that occurs across the BLOOD-AIR BARRIER.Superoxide Dismutase: An oxidoreductase that catalyzes the reaction between superoxide anions and hydrogen to yield molecular oxygen and hydrogen peroxide. The enzyme protects the cell against dangerous levels of superoxide. EC 1.15.1.1.Respiration: The act of breathing with the LUNGS, consisting of INHALATION, or the taking into the lungs of the ambient air, and of EXHALATION, or the expelling of the modified air which contains more CARBON DIOXIDE than the air taken in (Blakiston's Gould Medical Dictionary, 4th ed.). This does not include tissue respiration (= OXYGEN CONSUMPTION) or cell respiration (= CELL RESPIRATION).Catalase: An oxidoreductase that catalyzes the conversion of HYDROGEN PEROXIDE to water and oxygen. It is present in many animal cells. A deficiency of this enzyme results in ACATALASIA.Acetates: Derivatives of ACETIC ACID. Included under this heading are a broad variety of acid forms, salts, esters, and amides that contain the carboxymethane structure.Chromatography, High Pressure Liquid: Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.Carbohydrate Conformation: The characteristic 3-dimensional shape of a carbohydrate.DNA Glycosylases: A family of DNA repair enzymes that recognize damaged nucleotide bases and remove them by hydrolyzing the N-glycosidic bond that attaches them to the sugar backbone of the DNA molecule. The process called BASE EXCISION REPAIR can be completed by a DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE which excises the remaining RIBOSE sugar from the DNA.Electrodes: Electric conductors through which electric currents enter or leave a medium, whether it be an electrolytic solution, solid, molten mass, gas, or vacuum.Protein Conformation: The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).Free Radical Scavengers: Substances that influence the course of a chemical reaction by ready combination with free radicals. Among other effects, this combining activity protects pancreatic islets against damage by cytokines and prevents myocardial and pulmonary perfusion injuries.Carbohydrate Metabolism: Cellular processes in biosynthesis (anabolism) and degradation (catabolism) of CARBOHYDRATES.Hyperoxia: An abnormal increase in the amount of oxygen in the tissues and organs.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.Cell Hypoxia: A condition of decreased oxygen content at the cellular level.Blood Gas Monitoring, Transcutaneous: The noninvasive measurement or determination of the partial pressure (tension) of oxygen and/or carbon dioxide locally in the capillaries of a tissue by the application to the skin of a special set of electrodes. These electrodes contain photoelectric sensors capable of picking up the specific wavelengths of radiation emitted by oxygenated versus reduced hemoglobin.Chromatography, Gel: Chromatography on non-ionic gels without regard to the mechanism of solute discrimination.Graphite: An allotropic form of carbon that is used in pencils, as a lubricant, and in matches and explosives. It is obtained by mining and its dust can cause lung irritation.Intramolecular Lyases: Enzymes of the isomerase class that catalyze reactions in which a group can be regarded as eliminated from one part of a molecule, leaving a double bond, while remaining covalently attached to the molecule. (From Enzyme Nomenclature, 1992) EC 5.5.Soil: The unconsolidated mineral or organic matter on the surface of the earth that serves as a natural medium for the growth of land plants.NADPH Oxidase: A flavoprotein enzyme that catalyzes the univalent reduction of OXYGEN using NADPH as an electron donor to create SUPEROXIDE ANION. The enzyme is dependent on a variety of CYTOCHROMES. Defects in the production of superoxide ions by enzymes such as NADPH oxidase result in GRANULOMATOUS DISEASE, CHRONIC.Energy Metabolism: The chemical reactions involved in the production and utilization of various forms of energy in cells.Chromatography: Techniques used to separate mixtures of substances based on differences in the relative affinities of the substances for mobile and stationary phases. A mobile phase (fluid or gas) passes through a column containing a stationary phase of porous solid or liquid coated on a solid support. Usage is both analytical for small amounts and preparative for bulk amounts.Molecular Weight: The sum of the weight of all the atoms in a molecule.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Water: A clear, odorless, tasteless liquid that is essential for most animal and plant life and is an excellent solvent for many substances. The chemical formula is hydrogen oxide (H2O). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Superoxides: Highly reactive compounds produced when oxygen is reduced by a single electron. In biological systems, they may be generated during the normal catalytic function of a number of enzymes and during the oxidation of hemoglobin to METHEMOGLOBIN. In living organisms, SUPEROXIDE DISMUTASE protects the cell from the deleterious effects of superoxides.Magnetic Resonance Spectroscopy: Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).Heparitin Sulfate: A heteropolysaccharide that is similar in structure to HEPARIN. It accumulates in individuals with MUCOPOLYSACCHARIDOSIS.Enzyme Stability: The extent to which an enzyme retains its structural conformation or its activity when subjected to storage, isolation, and purification or various other physical or chemical manipulations, including proteolytic enzymes and heat.Oligosaccharides: Carbohydrates consisting of between two (DISACCHARIDES) and ten MONOSACCHARIDES connected by either an alpha- or beta-glycosidic link. They are found throughout nature in both the free and bound form.Bacillus subtilis: A species of gram-positive bacteria that is a common soil and water saprophyte.Methane: The simplest saturated hydrocarbon. It is a colorless, flammable gas, slightly soluble in water. It is one of the chief constituents of natural gas and is formed in the decomposition of organic matter. (Grant & Hackh's Chemical Dictionary, 5th ed)Gene Expression Regulation, Enzymologic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.Oxidoreductases: The class of all enzymes catalyzing oxidoreduction reactions. The substrate that is oxidized is regarded as a hydrogen donor. The systematic name is based on donor:acceptor oxidoreductase. The recommended name will be dehydrogenase, wherever this is possible; as an alternative, reductase can be used. Oxidase is only used in cases where O2 is the acceptor. (Enzyme Nomenclature, 1992, p9)Carbon Compounds, Inorganic: Inorganic compounds that contain carbon as an integral part of the molecule but are not derived from hydrocarbons.Cell Wall: The outermost layer of a cell in most PLANTS; BACTERIA; FUNGI; and ALGAE. The cell wall is usually a rigid structure that lies external to the CELL MEMBRANE, and provides a protective barrier against physical or chemical agents.Polarography: An electrochemical technique for measuring the current that flows in solution as a function of an applied voltage. The observed polarographic wave, resulting from the electrochemical response, depends on the way voltage is applied (linear sweep or differential pulse) and the type of electrode used. Usually a mercury drop electrode is used.Heme Oxygenase (Decyclizing): A mixed function oxidase enzyme which during hemoglobin catabolism catalyzes the degradation of heme to ferrous iron, carbon monoxide and biliverdin in the presence of molecular oxygen and reduced NADPH. The enzyme is induced by metals, particularly cobalt. EC 1.14.99.3.Trees: Woody, usually tall, perennial higher plants (Angiosperms, Gymnosperms, and some Pterophyta) having usually a main stem and numerous branches.Crystallization: The formation of crystalline substances from solutions or melts. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Ecosystem: A functional system which includes the organisms of a natural community together with their environment. (McGraw Hill Dictionary of Scientific and Technical Terms, 4th ed)Gases: The vapor state of matter; nonelastic fluids in which the molecules are in free movement and their mean positions far apart. Gases tend to expand indefinitely, to diffuse and mix readily with other gases, to have definite relations of volume, temperature, and pressure, and to condense or liquefy at low temperatures or under sufficient pressure. (Grant & Hackh's Chemical Dictionary, 5th ed)Lactic Acid: A normal intermediate in the fermentation (oxidation, metabolism) of sugar. The concentrated form is used internally to prevent gastrointestinal fermentation. (From Stedman, 26th ed)Citric Acid Cycle: A series of oxidative reactions in the breakdown of acetyl units derived from GLUCOSE; FATTY ACIDS; or AMINO ACIDS by means of tricarboxylic acid intermediates. The end products are CARBON DIOXIDE, water, and energy in the form of phosphate bonds.Electron Transport: The process by which ELECTRONS are transported from a reduced substrate to molecular OXYGEN. (From Bennington, Saunders Dictionary and Encyclopedia of Laboratory Medicine and Technology, 1984, p270)Luminescent Measurements: Techniques used for determining the values of photometric parameters of light resulting from LUMINESCENCE.Seawater: The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.Air: The mixture of gases present in the earth's atmosphere consisting of oxygen, nitrogen, carbon dioxide, and small amounts of other gases.Nitric Oxide: A free radical gas produced endogenously by a variety of mammalian cells, synthesized from ARGININE by NITRIC OXIDE SYNTHASE. Nitric oxide is one of the ENDOTHELIUM-DEPENDENT RELAXING FACTORS released by the vascular endothelium and mediates VASODILATION. It also inhibits platelet aggregation, induces disaggregation of aggregated platelets, and inhibits platelet adhesion to the vascular endothelium. Nitric oxide activates cytosolic GUANYLATE CYCLASE and thus elevates intracellular levels of CYCLIC GMP.Spectrophotometry: The art or process of comparing photometrically the relative intensities of the light in different parts of the spectrum.Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.Lactates: Salts or esters of LACTIC ACID containing the general formula CH3CHOHCOOR.Autotrophic Processes: The processes by which organisms use simple inorganic substances such as gaseous or dissolved carbon dioxide and inorganic nitrogen as nutrient sources. Contrasts with heterotrophic processes which make use of organic materials as the nutrient supply source. Autotrophs can be either chemoautotrophs (or chemolithotrophs), largely ARCHAEA and BACTERIA, which also use simple inorganic substances for their metabolic energy reguirements; or photoautotrophs (or photolithotrophs), such as PLANTS and CYANOBACTERIA, which derive their energy from light. Depending on environmental conditions some organisms can switch between different nutritional modes (autotrophy; HETEROTROPHY; chemotrophy; or PHOTOTROPHY) to utilize different sources to meet their nutrient and energy requirements.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Chromatography, Ion Exchange: Separation technique in which the stationary phase consists of ion exchange resins. The resins contain loosely held small ions that easily exchange places with other small ions of like charge present in solutions washed over the resins.Plant Diseases: Diseases of plants.Fermentation: Anaerobic degradation of GLUCOSE or other organic nutrients to gain energy in the form of ATP. End products vary depending on organisms, substrates, and enzymatic pathways. Common fermentation products include ETHANOL and LACTIC ACID.Light: That portion of the electromagnetic spectrum in the visible, ultraviolet, and infrared range.Plant Leaves: Expanded structures, usually green, of vascular plants, characteristically consisting of a bladelike expansion attached to a stem, and functioning as the principal organ of photosynthesis and transpiration. (American Heritage Dictionary, 2d ed)Electrochemistry: The study of chemical changes resulting from electrical action and electrical activity resulting from chemical changes.Succinic Acid: A water-soluble, colorless crystal with an acid taste that is used as a chemical intermediate, in medicine, the manufacture of lacquers, and to make perfume esters. It is also used in foods as a sequestrant, buffer, and a neutralizing agent. (Hawley's Condensed Chemical Dictionary, 12th ed, p1099; McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1851)Alkanes: The generic name for the group of aliphatic hydrocarbons Cn-H2n+2. They are denoted by the suffix -ane. (Grant & Hackh's Chemical Dictionary, 5th ed)Hydrogen: The first chemical element in the periodic table. It has the atomic symbol H, atomic number 1, and atomic weight [1.00784; 1.00811]. It exists, under normal conditions, as a colorless, odorless, tasteless, diatomic gas. Hydrogen ions are PROTONS. Besides the common H1 isotope, hydrogen exists as the stable isotope DEUTERIUM and the unstable, radioactive isotope TRITIUM.Glutathione: A tripeptide with many roles in cells. It conjugates to drugs to make them more soluble for excretion, is a cofactor for some enzymes, is involved in protein disulfide bond rearrangement and reduces peroxides.Nitrates: Inorganic or organic salts and esters of nitric acid. These compounds contain the NO3- radical.Electron Spin Resonance Spectroscopy: A technique applicable to the wide variety of substances which exhibit paramagnetism because of the magnetic moments of unpaired electrons. The spectra are useful for detection and identification, for determination of electron structure, for study of interactions between molecules, and for measurement of nuclear spins and moments. (From McGraw-Hill Encyclopedia of Science and Technology, 7th edition) Electron nuclear double resonance (ENDOR) spectroscopy is a variant of the technique which can give enhanced resolution. Electron spin resonance analysis can now be used in vivo, including imaging applications such as MAGNETIC RESONANCE IMAGING.Lung: Either of the pair of organs occupying the cavity of the thorax that effect the aeration of the blood.Geologic Sediments: A mass of organic or inorganic solid fragmented material, or the solid fragment itself, that comes from the weathering of rock and is carried by, suspended in, or dropped by air, water, or ice. It refers also to a mass that is accumulated by any other natural agent and that forms in layers on the earth's surface, such as sand, gravel, silt, mud, fill, or loess. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1689)Blood Substitutes: Substances that are used in place of blood, for example, as an alternative to BLOOD TRANSFUSIONS after blood loss to restore BLOOD VOLUME and oxygen-carrying capacity to the blood circulation, or to perfuse isolated organs.Molecular Structure: The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.Rats, Sprague-Dawley: A strain of albino rat used widely for experimental purposes because of its calmness and ease of handling. It was developed by the Sprague-Dawley Animal Company.Heme: The color-furnishing portion of hemoglobin. It is found free in tissues and as the prosthetic group in many hemeproteins.Oxidants: Electron-accepting molecules in chemical reactions in which electrons are transferred from one molecule to another (OXIDATION-REDUCTION).Phosphorus-Oxygen Lyases: Enzymes that catalyze the cleavage of a phosphorus-oxygen bond by means other than hydrolysis or oxidation. EC 4.6.Myoglobin: A conjugated protein which is the oxygen-transporting pigment of muscle. It is made up of one globin polypeptide chain and one heme group.Oceans and Seas: A great expanse of continuous bodies of salt water which together cover more than 70 percent of the earth's surface. Seas may be partially or entirely enclosed by land, and are smaller than the five oceans (Atlantic, Pacific, Indian, Arctic, and Antarctic).Cerebrovascular Circulation: The circulation of blood through the BLOOD VESSELS of the BRAIN.Fatty Acids: Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated (FATTY ACIDS, UNSATURATED). (Grant & Hackh's Chemical Dictionary, 5th ed)Exercise Test: Controlled physical activity which is performed in order to allow assessment of physiological functions, particularly cardiovascular and pulmonary, but also aerobic capacity. Maximal (most intense) exercise is usually required but submaximal exercise is also used.Hemodynamics: The movement and the forces involved in the movement of the blood through the CARDIOVASCULAR SYSTEM.Carbonates: Salts or ions of the theoretical carbonic acid, containing the radical CO2(3-). Carbonates are readily decomposed by acids. The carbonates of the alkali metals are water-soluble; all others are insoluble. (From Grant & Hackh's Chemical Dictionary, 5th ed)Soil Microbiology: The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.Oxygen Radioisotopes: Unstable isotopes of oxygen that decay or disintegrate emitting radiation. O atoms with atomic weights 13, 14, 15, 19, and 20 are radioactive oxygen isotopes.Helium: Helium. A noble gas with the atomic symbol He, atomic number 2, and atomic weight 4.003. It is a colorless, odorless, tasteless gas that is not combustible and does not support combustion. It was first detected in the sun and is now obtained from natural gas. Medically it is used as a diluent for other gases, being especially useful with oxygen in the treatment of certain cases of respiratory obstruction, and as a vehicle for general anesthetics. (Dorland, 27th ed)Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.Signal Transduction: The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.

The Saccharomyces cerevisiae ETH1 gene, an inducible homolog of exonuclease III that provides resistance to DNA-damaging agents and limits spontaneous mutagenesis. (1/349)

The recently sequenced Saccharomyces cerevisiae genome was searched for a gene with homology to the gene encoding the major human AP endonuclease, a component of the highly conserved DNA base excision repair pathway. An open reading frame was found to encode a putative protein (34% identical to the Schizosaccharomyces pombe eth1(+) [open reading frame SPBC3D6.10] gene product) with a 347-residue segment homologous to the exonuclease III family of AP endonucleases. Synthesis of mRNA from ETH1 in wild-type cells was induced sixfold relative to that in untreated cells after exposure to the alkylating agent methyl methanesulfonate (MMS). To investigate the function of ETH1, deletions of the open reading frame were made in a wild-type strain and a strain deficient in the known yeast AP endonuclease encoded by APN1. eth1 strains were not more sensitive to killing by MMS, hydrogen peroxide, or phleomycin D1, whereas apn1 strains were approximately 3-fold more sensitive to MMS and approximately 10-fold more sensitive to hydrogen peroxide than was the wild type. Double-mutant strains (apn1 eth1) were approximately 15-fold more sensitive to MMS and approximately 2- to 3-fold more sensitive to hydrogen peroxide and phleomycin D1 than were apn1 strains. Elimination of ETH1 in apn1 strains also increased spontaneous mutation rates 9- or 31-fold compared to the wild type as determined by reversion to adenine or lysine prototrophy, respectively. Transformation of apn1 eth1 cells with an expression vector containing ETH1 reversed the hypersensitivity to MMS and limited the rate of spontaneous mutagenesis. Expression of ETH1 in a dut-1 xthA3 Escherichia coli strain demonstrated that the gene product functionally complements the missing AP endonuclease activity. Thus, in apn1 cells where the major AP endonuclease activity is missing, ETH1 offers an alternate capacity for repair of spontaneous or induced damage to DNA that is normally repaired by Apn1 protein.  (+info)

Phosphorylation of the DNA repair protein APE/REF-1 by CKII affects redox regulation of AP-1. (2/349)

The DNA repair protein apurinic endonuclease (APE/Ref-1) exerts several physiological functions such as cleavage of apurinic/apyrimidinic sites and redox regulation of the transcription factor AP-1, whose activation is part of the cellular response to DNA damaging treatments. Here we demonstrate that APE/Ref-1 is phosphorylated by casein kinase II (CKII). This was shown for both the recombinant APE/Ref-1 protein (Km=0.55 mM) and for APE/Ref-1 expressed in COS cells. Phosphorylation of APE/Ref-1 did not alter the repair activity of the enzyme, whereas it stimulated its redox capability towards AP-1, thus promoting DNA binding activity of AP-1. Inhibition of CKII mediated phosphorylation of APE/Ref-1 blocked mutagen-stimulated increase in AP-1 binding. It also abrogated the induction of c-Jun protein and rendered cells more sensitive to induced DNA damage. Thus, phosphorylation of APE/Ref-1 appears to be involved in regulating the different physiological activities of the enzyme. CKII mediated phosphorylation of APE/Ref-1 and concomitant increase in AP-1 binding activity appears to be a novel mechanism of cellular stress response, forcing transcription of AP-1 target gene(s) the product(s) of which may exert protective function.  (+info)

Metabolic engineering of a 1,2-propanediol pathway in Escherichia coli. (3/349)

1,2-Propanediol (1,2-PD) is a major commodity chemical that is currently derived from propylene, a nonrenewable resource. A goal of our research is to develop fermentation routes to 1,2-PD from renewable resources. Here we report the production of enantiomerically pure R-1,2-PD from glucose in Escherichia coli expressing NADH-linked glycerol dehydrogenase genes (E. coli gldA or Klebsiella pneumoniae dhaD). We also show that E. coli overexpressing the E. coli methylglyoxal synthase gene (mgs) produced 1,2-PD. The expression of either glycerol dehydrogenase or methylglyoxal synthase resulted in the anaerobic production of approximately 0.25 g of 1,2-PD per liter. R-1,2-PD production was further improved to 0.7 g of 1,2-PD per liter when methylglyoxal synthase and glycerol dehydrogenase (gldA) were coexpressed. In vitro studies indicated that the route to R-1,2-PD involved the reduction of methylglyoxal to R-lactaldehyde by the recombinant glycerol dehydrogenase and the reduction of R-lactaldehyde to R-1, 2-PD by a native E. coli activity. We expect that R-1,2-PD production can be significantly improved through further metabolic and bioprocess engineering.  (+info)

The catalytic mechanism of a pyrimidine dimer-specific glycosylase (pdg)/abasic lyase, Chlorella virus-pdg. (4/349)

The repair of UV light-induced cyclobutane pyrimidine dimers can proceed via the base excision repair pathway, in which the initial step is catalyzed by DNA glycosylase/abasic (AP) lyases. The prototypical enzyme studied for this pathway is endonuclease V from the bacteriophage T4 (T4 bacteriophage pyrimidine dimer glycosylase (T4-pdg)). The first homologue for T4-pdg has been found in a strain of Chlorella virus (strain Paramecium bursaria Chlorella virus-1), which contains a gene that predicts an amino acid sequence homology of 41% with T4-pdg. Because both the structure and critical catalytic residues are known for T4-pdg, homology modeling of the Chlorella virus pyrimidine dimer glycosylase (cv-pdg) predicted that a conserved glutamic acid residue (Glu-23) would be important for catalysis at pyrimidine dimers and abasic sites. Site-directed mutations were constructed at Glu-23 to assess the necessity of a negatively charged residue at that position (Gln-23) and the importance of the length of the negatively charged side chain (Asp-23). E23Q lost glycosylase activity completely but retained low levels of AP lyase activity. In contrast, E23D retained near wild type glycosylase and AP lyase activities on cis-syn dimers but completely lost its activity on the trans-syn II dimer, which is very efficiently cleaved by the wild type cv-pdg. As has been shown for other glyscosylases, the wild type cv-pdg catalyzes the cleavage at dimers or AP sites via formation of an imino intermediate, as evidenced by the ability of the enzyme to be covalently trapped on substrate DNA when the reactions are carried out in the presence of a strong reducing agent; in contrast, E23D was very poorly trapped on cis-syn dimers but was readily trapped on DNA containing AP sites. It is proposed that Glu-23 protonates the sugar ring, so that the imino intermediate can be formed.  (+info)

Pokeweed antiviral protein cleaves double-stranded supercoiled DNA using the same active site required to depurinate rRNA. (5/349)

Ribosome-inactivating proteins (RIPs) are N-glycosylases that remove a specific adenine from the sarcin/ricin loop of the large rRNA in a manner analogous to N-glycosylases that are involved in DNA repair. Some RIPs have been reported to remove adenines from single-stranded DNA and cleave double-stranded supercoiled DNA. The molecular basis for the activity of RIPs on double-stranded DNA is not known. Pokeweed antiviral protein (PAP), a single-chain RIP from Phytolacca americana, cleaves supercoiled DNA into relaxed and linear forms. Double-stranded DNA treated with PAP contains apurinic/apyrimidinic (AP) sites due to the removal of adenine. Using an active-site mutant of PAP (PAPx) which does not depurinate rRNA, we present evidence that double-stranded DNA treated with PAPx does not contain AP sites and is not cleaved. These results demonstrate for the first time that PAP cleaves supercoiled double-stranded DNA using the same active site that is required for depurination of rRNA.  (+info)

Age-associated increase in 8-oxo-deoxyguanosine glycosylase/AP lyase activity in rat mitochondria. (6/349)

The mitochondrial theory of aging postulates that organisms age due to the accumulation of DNA damage and mutations in the multiple mitochondrial genomes, leading to mitochondrial dysfunction. Among the wide variety of DNA damage, 8-oxo-deoxyguanosine (8-oxo-dG) has received the most attention due to its mutagenicity and because of the possible correlation between its accumulation and pathological processes like cancer, degenerative diseases and aging. Although still controversial, many studies show that 8-oxo-dG accumulates with age in the mitochondrial (mt) DNA. However, little is known about the processing of this lesion and no study has yet examined whether mtDNA repair changes with age. Here, we report the first study on age-related changes in mtDNA repair, accomplished by assessing the cleavage activity of mitochondrial extracts towards an 8-oxo-dG-containing substrate. In this study, mitochondria obtained from rat heart and liver were used. We find that this enzymatic activity is higher in 12 and 23 month-old rats than in 6 month-old rats, in both liver and heart extracts. These mitochondrial extracts also cleave oligonucleotides containing a U:A mismatch, at the uracil position, reflecting the combined action of mitochondrial uracil DNA glycosylase (mtUDG) and mitochondrial apurinic/apyrimidinic (AP) endonucleases. The mtUDG activity did not change with age in liver mitochondria, but there was a small increase in activity from 6 to 23 months in rat heart extracts, after normalization to citrate synthase activity. Endonuclease G activity, measured by a plasmid relaxation assay, did not show any age-associated change in liver, but there was a significant decrease from 6 to 23 months in heart mitochondria. Our results suggest that the mitochondrial capacity to repair 8-oxo-dG, the main oxidative base damage suggested to accumulate with age in mtDNA, does not decrease, but rather increases with age. The specific increase in 8-oxo-dG endonuclease activity, rather than a general up-regulation of DNA repair in mitochondria, suggests an induction of the 8-oxo-dG-specific repair pathway with age.  (+info)

Overexpression of the human HAP1 protein sensitizes cells to the lethal effect of bioreductive drugs. (7/349)

Abasic sites (AP sites) are generated in DNA either directly by DNA-damaging agents or by DNA glycosylases acting during base excision repair. These sites are repaired in human cells by the HAP1 protein, which, besides its AP-endonuclease activity, also possesses a redox function. To investigate the ability of HAP1 protein to modulate cell resistance to DNA-damaging agents, CHO cells were transfected with HAP1 cDNA, resulting in stable expression of the protein in the cell nuclei. The sensitivity of the transfected cells to the toxic effect of various agents, e.g. methylmethane sulfonate, bleomycin and H2O2, was not modified. However, the transfected cells became more sensitive to killing by mitomycin C, porfiromycin, daunorubicin and aziridinyl benzoquinone, drugs that are activated by reduction. To test whether the redox function of HAP1 protein was involved in this increased cytotoxicity, we have constructed a mutated HAP1 protein endowed with normal AP-endonuclease activity but deleted for redox function. When this mutated protein was expressed in the cells, elevated AP-endonuclease activity was measured, but sensitization to the lethal effects of compounds requiring bioreduction was no longer observed. These results suggest that HAP1 protein, besides its involvement in DNA repair, is able to activate bioreduction of alkylating drugs used in cancer chemotherapy.  (+info)

Prokaryotic expression and characterization of human AP DNA endonuclease. (8/349)

The expression of major human apurinic/apyrimidinic DNA endonuclease (APEX) from its cDNA in E. coli (DH5 alpha) was attempted in order to obtain a biologically active recombinant APEX. E. coli cells were transformed by a prokaryotic translation vector (pGEX-4T-3) harboring APEX cDNA. GST-APEX fusion protein with a molecular weight of 6.3 KDa was induced by IPTG (1.0 mM) treatment. Western blot immunodetection identified the induced protein as the GST-APEX fusion protein. The survival rate of E. coli cells (DH5 alpha) transformed with pGEX-4T-3-APEX increased when the cells were treated with N-diethyl-N-nitrosamine (DENA) or 3'-methyl-4-monomethylaminoazobenzene (3'-MeMAB), indicating that APEX expression had a protective effect on the cytotoxicity of these carcinogens. The fusion protein extracted from E. coli cells and purified by GSH-agarose gel affinity chromatography exhibited APEX activity. Treatment of thrombin to the GST-APEX fusion protein and affinity purification followed by Sephacryl S-100 gel filtration resulted in APEX peptide with MW 36 KDa, which exhibited AP DNA repair activity (8,7000 EU/mg protein). N-ethylmaleimide (0.1 mM) or AMP (0.98 mM) inhibited APEX activity by 50% and kinetic analysis indicated that the recombinant APEX (rAPEX) had a Km value of 0.022 microM (AP sites for AP DNA) and the Ki value was 0.48 mM for AMP. These results indicated that E. coli cells expressing biologically active GST-APEX were resistant to the cell damage caused by chemical carcinogens and that rAPEX purified from E. coli cells transformed with APEX cDNA-inserted translation vector was similar to native APEX in some properties.  (+info)

SWISS-MODEL Template Library (SMTL) entry for 1egh.1. STRUCTURE OF METHYLGLYOXAL SYNTHASE COMPLEXED WITH THE COMPETITIVE INHIBITOR 2-PHOSPHOGLYCOLATE
Definition of O-succinylhomoserine (thiol)-lyase. Provided by Stedmans medical dictionary and Drugs.com. Includes medical terms and definitions.
Threonine biosynthesis is a general feature of prokaryotes, eukaryotic microorganisms, and higher plants. Since mammals lack the appropriate synthetic machinery, instead obtaining the amino acid through their diet, the pathway is a potential focus for the development of novel antibiotics, antifungal agents, and herbicides. Threonine synthase (TS), a pyridoxal-5-phosphate-dependent enzyme, catalyzes the final step in the pathway, in which L-homoserine phosphate and water are converted into threonine and inorganic phosphate. In the present publication, we report structural and functional studies of Mycobacterium tuberculosis TS, the product of the rv1295 (thrC) gene. The structure gives new insights into the catalytic mechanism of TSs in general, specifically by suggesting the direct involvement of the phosphate moiety of the cofactor, rather than the inorganic phosphate product, in transferring a proton from C4 to C(gamma) in the formation of the alphabeta-unsaturated aldimine. It further ...
See what Mety Listiani (listianimety) has discovered on Pinterest, the worlds biggest collection of everybodys favorite things.
AIMS: Human AP endonuclease 1 (HAP1) plays a major role in the repair of apurinic/apyrimidinic (AP) sites in cellular DNA by catalysing hydrolytic cleavage of the phosphodiester backbone 5 to the site. HAP1 is also known to be a potent reduction-oxidation (redox) factor, regulating the binding activity of a number of transcription factors. The purpose of the present study was to examine the expression of HAP-1 in a wide range of human tissues. METHODS AND RESULTS: Using a recently developed specific rabbit polyclonal antibody, we performed immunohistochemistry on paraffin-embedded tissue material. Nuclear staining was detected in crypt cells of the small and large intestine, epithelial cells of breast ducts, basal cells of the skin, alveolar cells of the lung, lymphocytes of the marginal zone of the spleen, in the surface epithelium and stromal cells of the ovary and the transitional epithelium of the bladder. Unexpectedly for a presumed nuclear protein, the staining pattern in some cell ...
Activation-induced cytidine deaminase (AID) initiates a process generating DNA mutations and breaks in germinal center (GC) B cells that are necessary for somatic hypermutation and class-switch recombination. GC B cells can "tolerate" DNA damage while rapidly proliferating because of partial suppression of the DNA damage response by BCL6. In this study, we develop a model to study the response of mouse GC B cells to endogenous DNA damage. We show that the base excision repair protein apurinic/apyrimidinic endonuclease (APE) 2 protects activated B cells from oxidative damage in vitro. APE2-deficient mice have smaller GCs and reduced Ab responses compared with wild-type mice. DNA double-strand breaks are increased in the rapidly dividing GC centroblasts of APE2-deficient mice, which activate a p53-independent cell cycle checkpoint and a p53-dependent apoptotic response. Proliferative and/or oxidative damage and AID-dependent damage are additive stresses that correlate inversely with GC size in ...
1E9N: Two Divalent Metal Ions in the Active Site of a New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, Ape1: Implications for the Catalytic Mechanism
In the process of cell metabolism, genomic DNA is harmed by free radicals, mutagens, and ionizing radiation. The damage in DNA results in carcinogenesis, aging, and cell death. Apurinic/apyrimidinic (AP) sites, which arise by hydrolysis of N-glycos
Apurinic/apyrimidinic endonuclease 1 (APE1)/redox effector factor (Ref-1) is a key regulator of cellular response to oxidative stress. It is a multifunctional protein involved in both transcriptional regulation of gene expression during adaptive cellular response to oxidative stress, and in base excision repair pathway of DNA lesions generated as a consequence of oxidant-induced base damages. In the latter, APE1/Ref-1 contributes to the maintenance of the genome stability. APE1 normally resides in the nucleus and this is consistent with its established role in base excision repair and redox regulation of transcription factors [Tell et al 2009]. However, in some cancers, abnormal re-distribution of APE1 to the cytoplasm or its presence in both the nucleus and the cytoplasm without losing its ability to repair abasic DNA has been observed and these have baffled many researchers [Tell et al 2005]. We have recently identified APE1/Ref-1 as an endoribonuclease that cleaves c-myc mRNA in vitro and ...
DNA-(apurinic or apyrimidinic site) lyase (APE-1) antibody | P27695 | APEX nuclease (APEN), Apurinic-apyrimidinic endonuclease 1 (AP endonuclease 1), (APE-1), REF-1, Redox factor-1, APEX1, APE, APE1, APEX, APX, HAP1, REF1
References for Abcams Recombinant Human AP2 alpha protein (ab114726). Please let us know if you have used this product in your publication
Buy our Recombinant Human AP180 protein. Ab160702 is a protein fragment produced in Wheat germ and has been validated in WB, ELISA. Abcam provides free…
In this study, we aim at evaluation the role of the Asp148Glu (rs1130409) variant at apurinic/apyrimidinic endonuclease (APE) gene in renal cell carcinoma (RCC) risk and the contribution of different genotypes to its transcriptional mRNA levels. In the case-control study, 92 RCC patients and 580 cancer-free patients matched by age and gender were recruited. The apurinic/APE genotyping work was con...
DNA with an abasic site is a cyto-toxic intermediate in the base excision repair (BER) pathway that is handled by the enzyme Apuridinic/Apyrimidinic endonuclease (APE1) [99, 56, 168, 90]. Several kinetics and thermodynamics aspects of the mechanism by which the APE1 enzyme processes its abasic DNA substrate have been discussed in this thesis. APE1 is an endonuclease that is it cleaves the DNA backbone at a non-terminal site, here at the abasic site. To obtain eminent insight about the catalytic role of amino acid residues and magnesium ions which are representatively recognized in active sites of endonuclease enzymes, quantum mechanical calculations of reaction pathways based on various cluster models mimicking such active sites of endonuclease enzymes have been performed and subsequently discussed in section 4. In this light our results underline the importance of an enzymatic active site architecture in the catalytic reaction, given the substrate is properly positioned. As a side-effect, we ...
The graph shows the array of tests that a study did of human samples [clustering together in the lime green] vs chimpanzee samples [clustering together in blue]. Obviously human variation is nothing like chimp variation from the human. We aint chimps, much as we act like them sometimes. The red cluster is for some neanderthal samples. FAR closer to us than the chimps, yet still cleanly separate. When the laboratory results are shown for the alleged Bigfoot/Human hybrid mDNA, the cluster from those results COULD end up on either side of the neanderthal cluster, but if it is on the right side then the argument that Bigfoot is a "hybrid" will have to be made on much more specific grounds [something like some mDNA areas are human-identical, and shouldnt be, and some mDNA areas are more like ape mDNA. Such a claim will surprise me at least until I hear the argument, because, as you remember, the mDNA comes not from "mixing" but from the mother alone. Ultimately mDNA is mixed in humans due to a lot ...
Methods Expression of APE1 was evaluated by immunohistochemistry in a series of 55 RBs and in retina. In tumours, APE1 expression was analysed in cytoplasm and nucleus independently and correlated with histopathological features, including invasion, differentiation and International Intraocular Retinoblastoma Classification groups. Relative APE1 mRNA and protein expressions were evaluated by real-time PCR and western blot. The expression of APE1 in tumour groups was compared with retinal tissue.. ...
Meadows K.L., Song B., Doetsch P.W.. Saccharomyces cerevisiae possesses two Escherichia coli endonuclease III homologs, NTG1 and NTG2, whose gene products function in the base excision repair pathway and initiate removal of a variety of oxidized pyrimidines from DNA. Although the glycosylase activity of these proteins has been well studied, the in vivo importance of the AP lyase activity has not been determined. Previous genetic studies have suggested that the AP lyase activities of Ntg1p and Ntg2p may be major contributors in the initial processing of abasic sites. We conducted a biochemical characterization of the AP lyase activities of Ntg1p and Ntg2p via a series of kinetic experiments. Such studies were designed to determine if Ntg1p and Ntg2p prefer specific bases located opposite abasic sites and whether these lesions are processed with a catalytic efficiency similar to Apn1p, the major hydrolytic AP endonuclease of yeast. Our results indicate that Ntg1p and Ntg2p are equally effective in ...
Histones and polyamines nick the phosphodiester bond 3′ to AP (apurinic/apyrimidinic) sites in DNA by inducing a beta-elimination reaction, which can be followed by delta-elimination. These beta- and delta-elimination reactions might be important for the repair of AP sites in chromatin DNA in either of two ways. In one pathway, after the phosphodiester bond 5′ to the AP site has been hydrolysed with an AP endonuclease, the 5′-terminal base-free sugar 5′-phosphate is released by beta-elimination. The one-nucleotide gap limited by 3′-OH and 5′-phosphate ends is then closed by DNA polymerase-beta and DNA ligase. We have shown in vitro that such a repair is possible. In the other pathway, the nicking 3′ to the AP site by beta-elimination occurs first. We have shown that the 3′-terminal base-free sugar so produced cannot be released by the chromatin AP endonuclease from rat liver. But it can be released by delta-elimination, leaving a gap limited by 3′-phosphate and 5′-phosphate. ...
The sperm and egg fuse in the process of fertilization to form a fertilized egg, or zygote.[12] This undergoes a period of divisions to form a ball or sheet of similar cells called a blastula or blastoderm. These cell divisions are usually rapid with no growth so the daughter cells are half the size of the mother cell and the whole embryo stays about the same size. They are called cleavage divisions. Mouse epiblast primordial germ cells (see Figure: "The initial stages of human embryogenesis") undergo extensive epigenetic reprogramming.[13] This process involves genome-wide DNA demethylation, chromatin reorganization and epigenetic imprint erasure leading to totipotency.[13] DNA demethylation is carried out by a process that utilizes the DNA base excision repair pathway.[14] Morphogenetic movements convert the cell mass into a three layered structure consisting of multicellular sheets called ectoderm, mesoderm and endoderm, which are known as germ layers. This is the process of gastrulation. ...
FUNCTION: DNA repair enzyme that cleaves apurinic/apyrimidinic (AP) sites and removes 3-blocking groups present at single strand breaks of damaged DNA. APN1 accounts for > 97% of both apurinic/ apyrimidinic (AP) lyase and DNA 3-repair diesterase activities ...
Objective Quantitative real-time PCR (qPCR) is usually routinely performed for experiments designed to identify the molecular mechanisms involved in the pathogenesis of dental care fluorosis. samples. Results Probably the most stably indicated genes relating to geNorm were and and were and and and is a component of major histocompatibility complex (MHC) class 1 and a cell surface marker for those nucleated cells 48 is definitely a member of the family of TATA-box transcription factors 49 is definitely a glycolytic enzyme 50 Hprt is definitely portion of purine synthesis in the salvage pathway 51 and functions in the translational machinery.52 The data presented here will facilitate accurate and reproducible transcript profiling MP-470 studies in fluoride treated rats and in enamel organ-derived LS8 cells. 2 Materials and MP-470 Methods 2.1 Animals All animals were treated humanely. Sprague-Dawley rats (6-week-old) were purchased from Charles River Laboratories (Wilmington MA). Animals were ...
Looking for online definition of SPVC or what SPVC stands for? SPVC is listed in the Worlds largest and most authoritative dictionary database of abbreviations and acronyms
PERFECT TIMING - CAR WASH - WHEN IS THE MOST PERFECT TIME TO WASH YOUR CAR? UNDER THE RAIN? HAHAHA. WHY USE A HOSE TO CLEAN IF YOU CAN CLEAN WITH RAINWATER? THIS GUY IS FUNNY. MORE FU... ...
Residues 187-311 are 76% similar to a (CYSTEINE SYNTHASE O-ACETYLSERINE LYASE SULFHYDRYLASE) protein domain (PD001075) which is seen in Q9CKD0_PASMU ...
Frataxin deficiency results in mitochondrial dysfunction and oxidative stress and it is the cause of the hereditary neurodegenerative disease Friedreich ataxia (FA). Here, we present evidence that one of the pleiotropic effects of oxidative stress in frataxin-deficient yeast cells (Δyfh1 mutant) is damage to nuclear DNA and that repair requires the Apn1 AP-endonuclease of the base excision repair pathway.. Read More: Apn1 AP-endonuclease is essential for the repair of oxidatively damaged DNA bases in yeast frataxin-deficient cells. ...
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Sulfur Assimilation and Abiotic Stress in Plants und Buchbewertungen gibt es auf ReadRate.com. Bücher können hier direkt online erworben werden.
Rabbit monoclonal antibody raised against a human AP2S1 peptide using ARM Technology. A synthetic peptide of human AP2S1 is used for rabbit immunization.Customer or Abnova will decide on the preferred peptide sequence. (H00001175-K) - Products - Abnova
Le kit éthanol biocarburant flexfuel KIA 4 cylindres REF-44002 Starflex, adapte votre moteur au biocarburant éthanol, votre boitier est préréglé pour votre moteur !
ITC analysis of the interaction between substrate, OAS (O-acetylserine) and OASS. Data is plotted as heat signal (μJ/sec) versus time (min) in the upper panel
Looking for online definition of cystathionine gamma-lyase in the Medical Dictionary? cystathionine gamma-lyase explanation free. What is cystathionine gamma-lyase? Meaning of cystathionine gamma-lyase medical term. What does cystathionine gamma-lyase mean?
1783 Ape1 is the major human apurinic/apyrimidinic (AP) endonuclease, with significant functions in the repair of 3-oxidative DNA damages, such as phosphoglycolates, as well as 3-non-conventional ends. We have recently shown that besides processing AP and strand break damages in the context of duplex oligonucleotide substrates, Ape1 also cleaves efficiently at AP sites in single-stranded (ss) DNA regions. This includes the incision of AP sites in the ss portion of bubble- and fork-like DNA conformations. We are presently examining the role of DNA secondary structure on Ape1 incision efficiency of ss AP site-containing oligonucleotides. In addition, we are exploring the impact of the ss DNA binding protein RPA and the Cockayne syndrome B protein (CSB) on regulating Ape1 activity on ss and bubble-containing AP substrates. The biological ramifications of Ape1s ability to incise alternative DNA structural forms, particularly in the context of replication- or transcription-coupled repair, will be ...
hyaluronate lyase (EC 4.2.2.1); chondroitin AC lyase (EC 4.2.2.5); xanthan lyase (EC 4.2.2.12); chondroitin ABC lyase (EC 4.2.2.20 ...
APEX1, 0.1 mg. Apurinic/apyrimidinic (AP) sites occur frequently in DNA molecules by spontaneous hydrolysis, by DNA damaging agents or by DNA glycosylases that remove specific abnormal bases.
mmh mmh. any advice on how to stop them from getting rowdy THE MINUTE I enter the house from work. Theyre both sleeping, I come in, take my shoes off, gove them some love (is that my mistake?) and then as soon as I go on to my business they start playing roughly. I guess I get them excited? But Im not consciously encouraging them to get it roughing up, except that maybe theyre seeking attention cause they know Ill stop them eventually ...
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Cysteine occupies a central position in plant metabolism due to its biochemical functions. Arabidopsis thaliana cells contain different O-acetylserine(thiol)lyase (OASTL) enzymes that catalyze the biosynthesis of cysteine. Because they are localized in the cytosol, plastids and mitochondria, this results in multiple subcellular cysteine pools. Much progress has been made on the most abundant OASTL enzymes; however, information on the less abundant OASTL-like proteins has been scarce. To unequivocally establish the enzymatic reaction catalyzed by the minor cytosolic OASTL isoform CS-LIKE (AT5G28030), we expressed this enzyme in bacteria and characterized the purified recombinant protein. Our results demonstrate that CS-LIKE catalyzes the desulfuration of L-cysteine to sulfide plus ammonia and pyruvate. Thus, CS-LIKE is a novel L-cysteine desulfhydrase (EC 4.4.1.1), and we propose to designate it DES1. The impact and functionality of DES1 in cysteine metabolism was revealed by the phenotype of the T-DNA
Elliott, R, Astley, S, Southon, S and Archer, D (2000) The development of DNA repair assays which show that dietary carrots stimulate DNA repair activity In: 3rd Conference on Food and Cancer Prevention, 1999-09-05 - 1999-09-08, UNIV E ANGLIA, NORWICH, ENGLAND. Full text not available from this repository ...
Im probably not saying this right because I really dont understand all the different pathways and their effect on the body, but Im wondering if...
Catalyzes the conversion of O-acetylserine to cysteine. Also acts as a sensor of cysteine availability in the signal transduction pathway modulating CymR activity. When cysteine is present, the pool of O-acetylserine (OAS) is low, which leads to the formation of a CymR-CysK complex and transcriptional repression of the CymR regulon occurs. In the absence of cysteine, the OAS pool is high and the CymR-CysK complex is mostly dissociated, leading to a faster dissociation of CymR from its DNA targets and the lifting of CymR-dependent repression ...
Ref-1: Tsuyuki et al., Arch Intern Med 2001; 161: 2337-42. Ref-2: Demissei et al., Int J Cardiol 2016; 204: 164-171. Ref-3: Arrigo et al., Eur J Heart Fail 2017 Feb; 19(2): 201-208. doi: 10.1002/ejhf.682. Epub 2016 Oct 28. Ref-4: Alba et al. Am J Med 2016;129 (1): 96-104 e7. Ref-5: Maisel et al., Eur J Heart Fail 2012; 14: 278-86. ...
Production of purified recombinant human aP2 protein, Recombinant human aP2 protein is produced by standard recombinant DNA technology. In the typical case, aP2 is produced by heterologous expression in E. coli strain BL21(D53) transformed with pET11a vector containing the full length human aP2 cDNA (Baxa, C. A., Sha, R. S., Buelt, M. K., Smith, A. J., Matarese, V., Chinander, L. L., Boundy, K. L., and Bernlohr, D. A. (1989). Human adipocyte lipid-binding protein: purification of the protein and cloning of its complementary DNA. Biochemistry 28: 8683-8690 and Xu, Z., Buelt, M. K., Banaszak, L. J., and Bernlohr, D. A. (1991). Expression, purification and crystallization of the adipocyte lipid binding protein. J. Biol. Chem. 266: 14367-14370). Purification of aP2 from E. coli is conducted as described by Xu, yielding essentially homogeneous aP2 protein with molecular weight ˜14600 daltons and free of endogenous fatty acids. The purified aP2 is capable of binding up to one mole of free fatty acid ...
1N8P: Determinants of Enzymatic Specificity in the Cys-Met-Metabolism PLP-Dependent Enzymes Family: Crystal Structure of Cystathionine gamma-lyase from Yeast and Intrafamiliar Structural Comparison
Complete information for APEX2 gene (Protein Coding), Apurinic/Apyrimidinic Endodeoxyribonuclease 2, including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene Compendium
Venemas latter posts in the series discuss evidence that could count as weak, or circumstantial, evidence for common descent -- evidence such as high levels of human / ape genetic similarities. At most, however, this evidence shows circumstantial evidence for common ancestry. It says nothing about the information-generative abilities of random mutation and natural selection. Venema would have done well to heed Behes advice in The Edge of Evolution that modern Darwinists point to evidence of common descent and erroneously assume it to be evidence of the power of random mutation. In fact, if we factor into the analysis the possibility of common design of functional genetic programs, Venemas evidence doesnt even strongly point to common descent. But Venema ignores the possibility of common design ...
Venemas latter posts in the series discuss evidence that could count as weak, or circumstantial, evidence for common descent -- evidence such as high levels of human / ape genetic similarities. At most, however, this evidence shows circumstantial evidence for common ancestry. It says nothing about the information-generative abilities of random mutation and natural selection. Venema would have done well to heed Behes advice in The Edge of Evolution that modern Darwinists point to evidence of common descent and erroneously assume it to be evidence of the power of random mutation. In fact, if we factor into the analysis the possibility of common design of functional genetic programs, Venemas evidence doesnt even strongly point to common descent. But Venema ignores the possibility of common design ...
Immunofluorescence assessment of Ref-1 response in cardiac tissue after 4 months following implantation of cardiac stem cells. (A-D) Control and (E-H) the L
Material: SUS #1 Thickness: 1mm #2 Thickness: 0.8mm. #1 Product Size: 1060x380x830mmH. #2 Product Size: 950x350x815mmH. Capacity: 48Lx3. Weight: 42kg ...
TY - JOUR. T1 - Apurinic DNA endonuclease activities in repair-deficient human cell lines. AU - Moses, Robb. AU - Beaudet, Arthur L.. PY - 1978/2. Y1 - 1978/2. N2 - Several autosomal recessive diseases are associated with apparent DNA repair defects in cell culture. It seemed likely that a defect in excision repair reported for ataxia telangiectasia cells might reflect a lack of apurinic endonuclease activity. We report here normal levels of apurinic endonuclease activity in extracts of cell lines derived from patients with ataxia telangiectasia, xeroderma pigmentosum (complementation group D), Cockayne dwarfism, Fanconi anemia and Bloom syndrome.. AB - Several autosomal recessive diseases are associated with apparent DNA repair defects in cell culture. It seemed likely that a defect in excision repair reported for ataxia telangiectasia cells might reflect a lack of apurinic endonuclease activity. We report here normal levels of apurinic endonuclease activity in extracts of cell lines derived ...
Experiences with the local application of a synthetic tar-corticoid preparation Positional memory in vertebrate limb development and regeneration. Molecular clones of Borrelia burgdorferi, aetiologic agent of Lyme borreliosis, were isolated and analysed by DNA sequence determination. Thus, our data demonstrate that Atf6 is required for alcoholic FLD and epistatically interacts with fasn to cause this disease, suggesting triglyceride biogenesis as the mechanism of UPR induced cialis prices FLD. Differential expression of hepatic apurinic/apyrimidinic endonuclease 1, a DNA repair enzyme, in chronic hepatitis. Knowledge of the nerves that supply the dura mater of the skull and their pathways is important to the clinician who treats headache and to the neurosurgeon who operates in this region. c-MET is a receptor tyrosine kinase whose phosphorylation activates important proliferation pathways. Detailed Audiological Evaluation of a Patient with Xeroderma Pigmentosum with Neural Degeneration. ...
One of the most frequent lesions formed in cellular DNA are abasic (apurinic/apyrimidinic, AP) sites that are both cytotoxic and mutagenic, and must be removed efficiently to maintain genetic stability. It is generally believed that the repair of AP
To develop an effective therapeutic technique for cardiac regeneration using bone tissue marrow mesenchymal stem cells (BM-MSCs) the principal mouse BM-MSCs (1st BM-MSCs) and 5th passing BM-MSCs from β-galactosidase transgenic mice were respectively intramyocardially transplanted in to the acute myocardial infarction (AMI) style of outdoors type mice. higher differentiation potentials towards cardiomocytes or vascular endothelial cells is a conventional method of getting a large numbers of BM-MSCs as needed by transplantation. Nevertheless through the sub-culture control BM-MSCs gradually reduce their differentiation strength towards cardiomyocytes and vascular endothelial cells which will probably result in much less adequate improvement in cardiac efficiency [13]. Previous research suggest that natural properties of BM-MSCs arent everlasting features and their proliferation and differentiation properties decrease along with passaging procedure [13] [14]. How exactly to obtain sufficient ...
Allinson, Sarah L. and Dianov, Grigory L. (2002) Co-ordination of base excision repair. In: Recent research development in repair and mutagenesis. Research Signpost. Full text not available from this repository ...
kulmburg at aug.ukl.uni-freiburg.de (Peter.Kulmburg at AUG.UKL.UNI-FREIBURG.DE) wrote: : Dear collegues, : I do not adhere to your list, however, Iwould like to get some infos. : Please reply to my private address and not to the list. Thank you in : advance. : 8 of 20 amino acids are known to be essential for human beings, any book of : biology tells us. But none told me yet, which (key) enzymes lack in humans : or mice for the production of the respective amino acid. : I have been asked by my students today and could not answer. Can anybody : help me? I am especially interested in the biosynthesis of methionine. : Thank you very much for your help Peter Kulmburg I dont know the answer, but there are some nice metabolism databases available on the net. With them and SwissProt (or another protein database), your students should be able to figure things out for themselves (it would make a nice assignment for a university student or even a team of high schoolers). I had an assignment like this in ...
Acylation is the term given to substituting an acyl group such as CH-3CO- into another molecule. An acyl group is a hydrocarbon group attached to a carbon-oxygen double bond ...
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on polysaccharides. The systematic ... name of this enzyme class is 2,1-beta-D-fructan lyase (alpha-D-fructofuranose-beta-D-fructofuranose-1,2':2,3'-dianhydride- ...
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on phosphates. The systematic name ... of this enzyme class is geranyl-diphosphate diphosphate-lyase [cyclizing, (−)-endo-fenchol-forming]. Other names in common use ...
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on phosphates. The systematic name ... and geranyldiphosphate diphosphate lyase [(+)-(R)-limonene-forming]. This enzyme participates in monoterpenoid biosynthesis. ... of this enzyme class is geranyl-diphosphate diphosphate-lyase [cyclizing, (+)-(4R)-limonene-forming]. Other names in common use ...
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on phosphates. The systematic name ... of this enzyme class is trans,trans-farnesyl-diphosphate diphosphate-lyase (cyclizing, vetispiradiene-forming). Other names in ...
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on phosphates. The systematic name ... of this enzyme class is 2-trans,6-trans-farnesyl-diphosphate diphosphate-lyase (cyclizing, pentalenene-forming). This enzyme is ...
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on phosphates. The systematic name ... trans-farnesyl diphosphate aristolochene-lyase, trans,trans-farnesyl-diphosphate diphosphate-lyase (cyclizing,, and ... of this enzyme class is 2-trans,6-trans-farnesyl-diphosphate diphosphate-lyase (cyclizing, aristolochene-forming). Other names ...
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on phosphates. The systematic name ... and glycerone-phosphate phospho-lyase. This enzyme participates in pyruvate metabolism and is constitutively expressed. As of ... of this enzyme class is glycerone-phosphate phosphate-lyase (methylglyoxal-forming). Other names in common use include ...
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on phosphates. The systematic name ... and geranylgeranyl-diphosphate diphosphate-lyase (cyclizing). This enzyme participates in diterpenoid biosynthesis. Moesta P, ... of this enzyme class is geranylgeranyl-diphosphate diphosphate-lyase (cyclizing, casbene-forming). Other names in common use ...
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on phosphates. The systematic name ... Other names in common use include geranylgeranyl-diphosphate diphosphate-lyase (cyclizing,, and taxadiene-forming). This enzyme ... of this enzyme class is geranylgeranyl-diphosphate diphosphate-lyase (cyclizing, taxa-4,11-diene-forming). ...
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on phosphates. The systematic name ... and O-phospho-L-homoserine phospho-lyase (adding water). This enzyme participates in glycine, serine and threonine metabolism ... of this enzyme class is O-phospho-L-homoserine phosphate-lyase (adding water L-threonine-forming). Other names in common use ...
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on phosphates. The systematic name ... of this enzyme class is geranyl-diphosphate diphosphate-lyase [(3R)-linalool-forming]. Other names in common use include (3R)- ...
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on phosphates. The systematic name ... of this enzyme class is dimethylallyl-pyrophosphate pyrophosphate-lyase (isoprene-forming). Other names in common use include ...
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on phosphates. The systematic name ... 3-phosphoshikimate phosphate-lyase. This enzyme participates in phenylalanine, tyrosine and tryptophan biosynthesis. Chorismate ... of this enzyme class is 5-O-(1-carboxyvinyl)-3-phosphoshikimate phosphate-lyase (chorismate-forming). This enzyme is also ...
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on phosphates. The systematic name ... 6-trans-farnesyl-diphosphate diphosphate-lyase, and (germacrene-A-forming). Wallaart TE; Kodde, J; Verstappen, FW; Altug, IG; ... of this enzyme class is 2-trans,6-trans-farnesyl-diphosphate diphosphate-lyase [(+)-(R)-germacrene-A-forming]. Other names in ...
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on phosphates. The systematic name ... of this enzyme class is geranyl-diphosphate diphosphate-lyase (cyclizing, sabinene-hydrate-forming). This enzyme is also called ...
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on phosphates. The systematic name ... trans-farnesyl-diphosphate sesquiterpenoid-lyase. This enzyme participates in terpenoid biosynthesis. As of late 2007, 9 ... of this enzyme class is trans,trans-farnesyl-diphosphate diphosphate-lyase (cyclizing, trichodiene-forming). Other names in ...
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on phosphates. The systematic name ... ent-copalyl-diphosphate diphosphate-lyase, and (cyclizing). This enzyme participates in diterpenoid biosynthesis. Fall RR, West ... of this enzyme class is ent-copalyl-diphosphate diphosphate-lyase (cyclizing, ent-kaurene-forming). Other names in common use ...
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on phosphates. The systematic name ... of this enzyme class is 2-trans,6-trans-farnesyl-diphosphate diphosphate-lyase (amorpha-4,11-diene-forming). This enzyme is ...
It belongs to the family of lyases, specifically the hydro-lyases, which cleave carbon-oxygen bonds. The systematic name of ... This enzyme belongs to the family of lyases, specifically the hydro-lyases, which cleave carbon-oxygen bonds. This enzyme ... 5-dehydroquinate hydro-lyase, and 3-dehydroquinate hydro-lyase. The aromatic amino acids produced by the shikimate acid pathway ... this enzyme class is 3-dehydroquinate hydro-lyase (3-dehydroshikimate-forming). This enzyme is one of the few examples of ...
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on phosphates. The systematic name ... This enzyme is also called copalyl-diphosphate diphosphate-lyase (cyclizing). This enzyme participates in diterpenoid ... of this enzyme class is (+)-copalyl-diphosphate diphosphate-lyase [cyclizing (−)-abietadiene-forming]. ...
This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting on phosphates. The systematic name ... of this enzyme class is geranyl-diphosphate diphosphate-lyase (myrcene-forming). This enzyme participates in monoterpenoid ...
This enzyme belongs to the family of lyases, specifically the hydro-lyases, which cleave carbon-oxygen bonds. The systematic ... tartrate hydro-lyase. This enzyme participates in glyoxylate and dicarboxylate metabolism. It has 2 cofactors: iron, and Thiol ... name of this enzyme class is (R,R)-tartrate hydro-lyase (oxaloacetate-forming). Other names in common use include tartrate ...
This enzyme belongs to the family of lyases, specifically the hydro-lyases, which cleave carbon-oxygen bonds. The systematic ... and 4a-hydroxytetrahydrobiopterin hydro-lyase. As of late 2007, 3 structures have been solved for this class of enzymes, with ... name of this enzyme class is (6R)-6-(L-erythro-1,2-dihydroxypropyl)-5,6,7,8-tetrahydro-4a-hydroxy pterin hydro-lyase [(6R)-6-(L ...
This enzyme belongs to the family of lyases, specifically the hydro-lyases, which cleave carbon-oxygen bonds. The systematic ... and 16alpha-hydroxyprogesterone hydro-lyase. Glass TL, Lamppa RS (1985). "Purification and properties of 16 alpha- ... name of this enzyme class is 16alpha-hydroxyprogesterone hydro-lyase (16,17-didehydroprogesterone-forming). Other names in ...
This enzyme belongs to the family of lyases, specifically the hydro-lyases, which cleave carbon-oxygen bonds. The systematic ... THE PURIFICATION AND PROPERTIES OF BETA-ISOHEXENYLGLUTACONYL-COA-HYDRATASE AND BETA-HYDROXY-BETA-ISOHEXENYLGLUTARYL-COA-LYASE ... glutaryl-CoA hydro-lyase. SEUBERT W, FASS E (1964). "[STUDIES ON THE BACTERIAL DEGRADATION OF ISOPRENOIDS. IV. ... name of this enzyme class is 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA hydro-lyase [3-(4-methylpent-3-en-1-yl)pent-2- ...
52 The role of active oxygen in the response of plants to water deficit and desiccation". The New Phytologist. 125: 27-58. doi: ... SOD2 knockout or null mutations cause growth inhibition on respiratory carbon sources in addition to decreased post-diauxic ... EC4 Lyases (list). *EC5 Isomerases (list). *EC6 Ligases (list). *EC7 Translocases (list) ... Thus, SOD is an important antioxidant defense in nearly all living cells exposed to oxygen. One exception is Lactobacillus ...
Carbon-oxygen lyases (EC 4.2) (primarily dehydratases). 4.2.1: Hydro-Lyases. *Carbonic anhydrase ... 5-phosphonooxy-L-lysine phospho-lyase (EC 4.2.3.134, 5-phosphohydroxy-L-lysine ammoniophospholyase, AGXT2L2 (gene)) is an ... Purification of the phospho-lyase". J. Biol. Chem. 249: 5784-5789. PMID 4412716.. ... 5-phosphonooxy-L-lysine phospho-lyase at the US National Library of Medicine Medical Subject Headings (MeSH) ...
Lyases [EC 4]. ⌊Carbon-Oxygen Lyases [EC 4.2]. ⌊Hydro-Lyases [EC 4.2.1]. ⌊colneleate synthase ... In enzyme science, colneleate synthase as a hydro-lyase reaction reaction is a lyase enzyme. * ...
Lyases [EC 4]. ⌊Carbon-Oxygen Lyases [EC 4.2]. ⌊Hydro-Lyases [EC 4.2.1]. ⌊Isohexenylglutaconyl-CoA hydratase ... In biochemistry, Isohexenylglutaconyl-CoA hydratase as a hydro-lyase reaction is a lyase enzyme. * ...
Carbon-Oxygen Lyases / genetics * Cell Cycle / genetics * Cysteine Synthase * DNA-Binding Proteins / metabolism* ...
CARBON-OXYGEN LYASE * Deposited: 1994-04-27 Released: 1995-04-27 *Deposition author(s): Wedekind, J.E., Reed, G.H., Rayment, I. ...
Classification: CARBON-OXYGEN LYASE. *Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ...
Lyases;. Carbon-oxygen lyases;. Acting on phosphates. Sysname. (2E,6E)-farnesyl-diphosphate diphosphate-lase (cyclizing, gamma- ...
Lyases;. Carbon-oxygen lyases;. Acting on polysaccharides. Sysname. alginate beta-D-mannuronate---uronate lyase. ... alginate lyase I;. alginate lyase;. alginase I;. alginase II;. alginase;. poly(beta-D-1,4-mannuronide) lyase;. poly(beta-D- ... mannuronate) lyase;. aly (gene name) (ambiguous);. poly[(1-,4)-beta-D-mannuronide] lyase. ...
Lyases;. Carbon-oxygen lyases;. Acting on polysaccharides. Sysname. (1-,4)-alpha-D-galacturonan lyase. ... pectic acid lyase;. pectic lyase;. alpha-1,4-D-endopolygalacturonic acid lyase;. PGA lyase;. PPase-N;. endo-alpha-1,4- ... pectate lyase;. polygalacturonic transeliminase;. pectic acid transeliminase;. polygalacturonate lyase;. endopectin ... polygalacturonic acid lyase;. polygalacturonic acid lyase;. pectin trans-eliminase;. Polygalacturonic acid trans-eliminase. ...
Lyases;. Carbon-oxygen lyases;. Hydro-lyases. Sysname. 4-hydroxy-2-oxohexanoate hydro-lyase [(2Z,4Z)-2-hydroxyhexa-2,4-dienoate ...
Lyases;. Carbon-oxygen lyases;. Acting on phosphates. Sysname. geranyl-diphosphate diphosphate-lyase (cyclizing, 1,8-cineole- ... The oxygen atom is derived from water. The reaction proceeds via linalyl diphosphate and alpha-terpineol, the stereochemistry ...
pectate trisaccharide-lyase;. exopectate-lyase;. pectate lyase A;. PelA. Class. Lyases;. Carbon-oxygen lyases;. Acting on ... Differs in specificity from EC 4.2.2.9, pectate disaccharide-lyase, as the predominant action is removal of a trisaccharide ... Molecular and biochemical characterization of the thermoactive family 1 pectate lyase from the hyperthermophilic bacterium ...
Lyases;. Carbon-oxygen lyases;. Acting on phosphates. Sysname. (2E,6E)-farnesyl-diphosphate diphosphate-lyase (alpha- ...
Lyases;. Carbon-oxygen lyases;. Acting on phosphates. Sysname. all-trans-heptaprenyl-diphosphate diphosphate-lyase (cyclizing, ...
Lyases;. Carbon-oxygen lyases;. Acting on phosphates. Sysname. (2E,6E)-farnesyl-diphosphate diphosphate-lyase (beta-eudesmol- ...
Lyases;. Carbon-oxygen lyases;. Acting on phosphates. Sysname. (2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, beta- ...
Lyases;. Carbon-oxygen lyases;. Hydro-lyases. Sysname. (R)-10-hydroxystearate 10-hydro-lyase (oleate-forming). ...
Carbon-oxygen Lyases. Enzymes that catalyze the cleavage of a carbon-oxygen bond by means other than hydrolysis or oxidation. ... Phosphorus-oxygen Lyases. Enzymes that catalyze the cleavage of a phosphorus-oxygen bond by means other than hydrolysis or ... Oxygen Radical Absorbance Capacity. A measure of the ability of a substance, such as a food, to quench oxygen free radicals in ... A protocol for three-component reactions of cyclic ethers, α-diazo esters, and weak nitrogen, oxygen, carbon, and sulfur ...
Lyases;. Carbon-oxygen lyases;. Acting on polysaccharides. Sysname. chondroitin B lyase. Reaction(IUBMB). Eliminative cleavage ... This is the only lyase that is known to be specific for dermatan sulfate as substrate. The minimum substrate length required ... The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic ... Purification, characterization and specificity of chondroitin lyases and glycuronidase from Flavobacterium heparinum. ...
Lyases;. Carbon-oxygen lyases;. Hydro-lyases. Sysname. UDP-N-acetyl-alpha-D-glucosamine hydro-lyase (inverting; UDP-2-acetamido ... UDP-N-acetylglucosamine hydro-lyase (inverting;. UDP-2-acetamido-2,6-dideoxy-beta-L-arabino-hex-4-ulose-forming). ...
Lyases;. Carbon-oxygen lyases;. Acting on phosphates. Sysname. geranyl-diphosphate diphosphate-lyase [cyclizing; (S)-limonene- ... geranyldiphosphate diphosphate lyase [cyclizing, (4S)-limonene-forming];. geranyl-diphosphate diphosphate-lyase [cyclizing;. ...
4. Lyases. 4.2 Carbon-oxygen lyases. 4.2.1 Hydro-lyases. 4.2.1.17 enoyl-CoA hydratase. EC042_2581 (fadJ). 5. Isomerases. 5.1 ...
4. Lyases. 4.2 Carbon-oxygen lyases. 4.2.1 Hydro-lyases. 4.2.1.17 enoyl-CoA hydratase. YPN_0198. 5. Isomerases. 5.1 Racemases ...
4. Lyases. 4.2 Carbon-oxygen lyases. 4.2.1 Hydro-lyases. 4.2.1.17 enoyl-CoA hydratase. XNC1_3875 (fadB). 5. Isomerases. 5.1 ...
4. Lyases. 4.2 Carbon-oxygen lyases. 4.2.1 Hydro-lyases. 4.2.1.17 enoyl-CoA hydratase. A3UG_21950 (fadB). 5. Isomerases. 5.1 ...
  • Since DNA AP lyase is a class of structures who have numerous target genes that encode for different variations of the enzyme, there is no one single enzyme structure that can be used as an example that encompasses all versions of the enzyme. (wikipedia.org)
  • Xanthan lyase is produced by bacteria that degrade this polysaccharide, such as Bacillus, Corynebacterium and Paenibacillus species. (wikipedia.org)
  • The three-dimensional crystal structure of the catalytic module of a "family PL-10" polysaccharide lyase, Pel10Acm from Cellvibrio japonicus , solved at a resolution of 1.3 Å, reveals a new polysaccharide lyase fold and is the first example of a polygalacturonic acid lyase that does not exhibit the "parallel β-helix" topology. (pnas.org)
  • Common coordination of the −1 and +1 subsite saccharide carboxylate groups by a protein-liganded Ca 2+ ion, the positioning of an arginine catalytic base in close proximity to the α-carbon hydrogen and numerous other conserved enzyme-substrate interactions, considered in light of mutagenesis data for both families, suggest a generic polysaccharide anti -β-elimination mechanism. (pnas.org)
  • Polysaccharide lyases (EC 4.2.2.x) are carbon-oxygen lyases that harness β-elimination chemistry (reviewed in ref. 1 ) to bring about degradation of C5 uronic acid containing pyranoside substrates such as polygalacturonates, alginates, hyaluronan, and chondroitin. (pnas.org)
  • In contrast to the 87 sequence-derived families of glycoside hydrolases, polysaccharide lyases have been classified into just 12 families on the basis of amino acid sequence similarities ( 5 ), reflecting the requirement for substrate uronic acid groups in the elimination mechanism. (pnas.org)
  • Polysaccharide Lyases (EC 4.2.2. (cazy.org)
  • Subfamily information is provided throughout the ensemble of the polysaccharide lyase families described so far. (cazy.org)
  • 1 ] Lombard V, Bernard T, Rancurel C, Brumer H, Coutinho PM, Henrissat B (2010) A hierarchical classification of polysaccharide lyases for glycogenomics. (cazy.org)
  • Based on the analysis of a large panel of experimentally characterized polysaccharide lyases, we examined the correlation of various enzyme properties with the three levels of the classification: fold, family and subfamily. (biochemj.org)
  • PLs (polysaccharide lyases) are a group of enzymes (EC 4.2.2. (biochemj.org)
  • Here we report the 1.3-Å resolution three-dimensional structure of the competent catalytic module of the polygalacturonic acid lyase Pel10A (Pel10Acm), from Cellvibrio japonicus, together with analysis of the activity of wild-type and mutant enzymes. (pnas.org)
  • The "Michaelis" complex of an inactive mutant in association with the substrate trigalacturonate/Ca 2+ reveals the catalytic machinery harnessed by this polygalacturonate lyase, which displays a stunning resemblance, presumably through convergent evolution, to the tetragalacturonic acid complex observed for a structurally unrelated polygalacturonate lyase from family PL-1. (pnas.org)
  • A catalytic mechanism featuring proton abstraction from C5 of the +1 subsite sugar residue, termed the α-carbon, and proton donation to the glycosidic oxygen, with the elimination of the leaving group from C4, termed the β-carbon ( 1 , 6 ) seems the most plausible. (pnas.org)
  • He covers chiral discrimination in the active site of oxidoreductases, transferases and chiral discrimination, the influence of chirality on the hydrolysis reactions within the active site of hydrolases, the influence of chirality on the reactions in the active site of lyases , and chiral discrimination in the active site of ligases. (thefreedictionary.com)
  • These enzymes are grouped into six classes: hydrolases (including proteases, amylases and lipases that break down the main nutrients - fats, carbohydrates and proteins), isomerases, ligases, lyases , oxidoreductases and transferases. (thefreedictionary.com)
  • The systematic name of this enzyme class is (3R)-3-hydroxybutanoyl-[acyl-carrier-protein] hydro-lyase (but-2-enoyl-[acyl-carrier protein]-forming). (wikipedia.org)
  • APE1 is a gene that codes for DNA AP lyase in humans which binds to AP DNA loops into both the DNA major and minor grooves and binds a flipped-out AP site in a pocket that excludes DNA bases and racemized-anomer AP sites. (wikipedia.org)
  • Other names in common use include: fumarase L-malate hydro-lyase (S)-malate hydro-lyase The FH gene is localized to the chromosomal position 1q42.3-q43. (wikipedia.org)
  • Escherichia coli N-acetylneuraminate lyase (EC 4.1.3.3) (gene nanA), which catalyses the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate. (embl-heidelberg.de)
  • Pectin lyases are significant compared to that of PG and PE in capability to undergo [beta]-elimination mechanism to degrade highly esterified pectins (present in fruits) into small molecules without producing methanol (7). (thefreedictionary.com)
  • Pectin lyases are the only known pectinases capable of degrading highly esterified pectins (like those found in fruits) into small molecules via [beta]-elimination mechanism without producing methanol. (thefreedictionary.com)
  • Pectin lyases are the only known pectinases capable of degrading highly esterified pectins (like those found in fruits) into small molecules via β-elimination mechanism without producing methanol (which is toxic), in contrast with the combination of PG and PE, which are normally found in commercial products. (wikipedia.org)
  • In the April 21 issue of the journal Science Signaling , a University of Chicago-based research team describes the precise mechanism that cells in the carotid bodies use to detect oxygen levels in the blood as it flows toward the brain. (uchicagomedicine.org)
  • In E. coli, DNA AP lyase (endonuclease III) helps repair oxidative damage to DNA bases by catalyzing the excision of the damaged pyrimidines and purines from ring saturation or opening from the DNA backbone. (wikipedia.org)
  • DNA AP lyase activity is documented to have similar function in both E. Coli and in humans. (wikipedia.org)
  • Bacteriophage T4 and Micrococcus luteus UV endonucleases were actually shown not to be under the class of "endonuclease," but rather were β-elimination catalysts for reactions at AP sites at the C3'-O-P bond-thus, classifying them as AP lyases. (wikipedia.org)