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.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.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)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-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.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.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.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.Alginates: Salts of alginic acid that are extracted from marine kelp and used to make dental impressions and as absorbent material for surgical dressings.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.Isocitrate Lyase: A key enzyme in the glyoxylate cycle. It catalyzes the conversion of isocitrate to succinate and glyoxylate. EC 4.1.3.1.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).Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.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)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.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.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.Cytochromes 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)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.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.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.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.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.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.Glycosaminoglycans: 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.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.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)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.Sulfonium Compounds: Sulfur compounds in which the sulfur atom is attached to three organic radicals and an electronegative element or radical.Glycoside HydrolasesDermatan 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)Bacterial Proteins: Proteins found in any species of bacterium.Carbohydrate Sequence: The sequence of carbohydrates within POLYSACCHARIDES; GLYCOPROTEINS; and GLYCOLIPIDS.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.Disaccharides: Oligosaccharides containing two monosaccharide units linked by a glycosidic bond.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.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.Kinetics: The rate dynamics in chemical or physical systems.Pseudomonas: A genus of gram-negative, aerobic, rod-shaped bacteria widely distributed in nature. Some species are pathogenic for humans, animals, and plants.N-Glycosyl Hydrolases: A class of enzymes involved in the hydrolysis of the N-glycosidic bond of nitrogen-linked sugars.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.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)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.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.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)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.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.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.Heparitin Sulfate: A heteropolysaccharide that is similar in structure to HEPARIN. It accumulates in individuals with MUCOPOLYSACCHARIDOSIS.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Biocatalysis: The facilitation of biochemical reactions with the aid of naturally occurring catalysts such as ENZYMES.Catalytic Domain: The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Chromatography, Gel: Chromatography on non-ionic gels without regard to the mechanism of solute discrimination.Isoenzymes: Structurally related forms of an enzyme. Each isoenzyme has the same mechanism and classification, but differs in its chemical, physical, or immunological characteristics.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.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.Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.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.Genes, Bacterial: The functional hereditary units of BACTERIA.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Molecular Weight: The sum of the weight of all the atoms in a molecule.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.Phosphorus-Oxygen Lyases: Enzymes that catalyze the cleavage of a phosphorus-oxygen bond by means other than hydrolysis or oxidation. EC 4.6.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.Bacillus subtilis: A species of gram-positive bacteria that is a common soil and water saprophyte.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).Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.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.Crystallization: The formation of crystalline substances from solutions or melts. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Chromatography, High Pressure Liquid: Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.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.Proteoglycans: Glycoproteins which have a very high polysaccharide content.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.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)Carbon-Sulfur Lyases: Enzymes that catalyze the cleavage of a carbon-sulfur bond by means other than hydrolysis or oxidation. EC 4.4.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.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Protein Structure, Secondary: The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.DNA Repair: The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.Protein Folding: Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.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.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.
  • In this study we have cloned and characterized the genes encoding pyruvate formate-lyase and its activating enzyme of Clostridium pasteurianum. (nih.gov)
  • Tomato strain DC3000 ( 6 ) have both family PL-5 and -7 alginate lyases, although their genes are separately located in the bacterial genomes. (asm.org)
  • Therefore, we propose that A1-II and A1-III encoded by the A1-I gene are the original alginate lyases of families PL-7 and -5, respectively, and that the A1-II and A1-III genes that were derived from the A1-I gene independently evolved into various genes belonging to families PL-7 and -5 through duplication, modification, and translocation. (asm.org)
  • 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)
  • Following assembly and annotation, an orf, annotated as family 8 polysaccharide lyase genes, was identified, encoding an amino acid sequence with a similarity to CS lyases according to NCBI blastX. (springer.com)
  • Several genes related to cell metabolism, including those involved in the metabolisms of cell wall, carbohydrates and antioxidants, light reactions, biotic and abiotic stress responses, as well as genes coding for transcription factors (TFs), protein kinases (PKs) and proteins involved in the abscisic acid (ABA) and ethylene signaling pathways, were differentially regulated by drought stress. (springer.com)
  • The data suggest that the rootstock-induced drought tolerance in sweet orange includes the transcriptional activation of genes related to the cell wall, soluble carbohydrate and antioxidant metabolisms, biotic and abiotic stress responses, TFs, PKs and ABA signaling pathway, and the downregulation of genes involved in the starch metabolism, light reactions and ethylene signaling. (springer.com)
  • The most comprehensive E. coli model to date ( E. coli i JE660a GSM) accounts for 660 genes and includes 627 unique biochemical reactions. (biomedcentral.com)
  • An expanded genome-scale metabolic model of E. coli ( i JR904 GSM/GPR) has been reconstructed which includes 904 genes and 931 unique biochemical reactions. (biomedcentral.com)
  • In the early phase of infection of sugar beet (Beta vulgaris L.) leaves with the phytopathogenic fungus Cercospora beticola, a reduction in the expression of the phenylalanine ammonia lyase (BvPAL) and cinnamic acid 4-hydroxylase (BvC4H) genes was observed. (deepdyve.com)
  • Phosphoenolpyruvate inhibited Escherichia coli NADP-isocitrate dehydrogenase allosterically (K-i of 0.31 mM) and isocitrate lyase uncompetitivelly (K-i' of 0.893 mM). (eurekamag.com)
  • Phosphoenolpyruvate enhances the uncompetitive inhibition of isocitrate lyase by increasing isocitrate, which protects isocitrate dehydrogenase from the inhibition, and contributes to the control through the tricarboxylic acid cycle and glyoxylate shunt. (eurekamag.com)
  • However, since then, many bacteria have been described that do not contain isocitrate lyase, the key enzyme of this pathway. (pnas.org)
  • Isotopically labeled acetate and bicarbonate were transformed to ethylmalonyl-CoA by cell extracts of acetate-grown, isocitrate lyase-negative Rhodobacter sphaeroides as determined by NMR spectroscopy. (pnas.org)
  • For methylotrophic bacteria such as Methylobacterium extorquens , extension of the serine cycle with reactions of the ethylmalonyl-CoA pathway leads to a simplified scheme for isocitrate lyase-independent C 1 assimilation. (pnas.org)
  • Isocitrate lyase, the first key enzyme of the glyoxylate cycle, together with enzymes of the citric acid cycle, is responsible for the oxidation of acetyl-CoA to glyoxylate ( Fig. 1 ). (pnas.org)
  • The citric acid cycle is modified to bypass the two decarboxylation steps by the action of its two key enzymes isocitrate lyase and malate synthase. (pnas.org)
  • However, the glyoxylate cycle cannot be the sole solution for acetyl-CoA assimilation, because several organisms that require such an anaplerotic reaction sequence lack isocitrate lyase activity ( 4 - 8 ) or show a labeling pattern after growth on acetate inconsistent with the operation of the glyoxylate cycle in acetate assimilation ( 9 , 10 ). (pnas.org)
  • In addition, the diverse group of streptomycetes uses an alternate, isocitrate lyase-independent route for acetyl-CoA assimilation, and there appears to be a direct link to antibiotic biosynthesis ( 8 , 14 ). (pnas.org)
  • The glyoxylate cycle is a sequence of anaplerotic reactions catalyzed by the key enzymes isocitrate lyase (ICL) and malate synthase (MLS). (mdpi.com)
  • The N-acetylneuraminate lyase from Clostridium perfringens was expressed in Escherichia coli as a fusion protein with a His-tag and purified to homogeneity using metal chelate affinity and anion exchange chromatography. (nih.gov)
  • O-acetylserine (thiol) lyase is a pyridoxal phosphate-dependent enzyme, and a lysine residue at the N-terminal region of this protein is involved in binding this cofactor (Saito et al. (thefreedictionary.com)
  • These mutations alter a region of the CYP17A1 protein that plays a role in the enzyme's 17,20-lyase function but not its 17α-hydroxylase function. (medlineplus.gov)
  • The three endotype alginate lyases are encoded by a single gene ( 21 ), and precursor protein A1-I is autocatalytically processed into A1-II and A1-III ( 14 ). (asm.org)
  • Recombinant PyAly protein, rPyAly, which was produced with E. coli BL21(DE3) by cold-inducible expression system, drastically decreased the viscosity of alginate solution in the early stage of reaction. (eurekaselect.com)
  • Both cytosolic and mitochondrial reactions generate important molecules that can modulate protein structure and function, regulate enzymatic reactions, and control cell fate and function. (jci.org)
  • Gene to protein to reaction associations (GPR) are now directly included in the model. (biomedcentral.com)
  • Adenylosuccinate lyase and other enzymes involved in purine synthesis form a group of proteins (a protein complex) called the purinosome. (nih.gov)
  • Most of the mutations involved in this condition change single protein building blocks (amino acids) in the adenylosuccinate lyase enzyme. (nih.gov)
  • We use this method to make subunit contact predictions for an additional 36 protein complexes with unknown structures, and present models based on these predictions for the tripartite ATP-independent periplasmic (TRAP) transporter, the tripartite efflux system, the pyruvate formate lyase-activating enzyme complex, and the methionine ABC transporter. (elifesciences.org)
  • It was specific on the pyruvated mannosyl residue in the intact xanthan molecule, but about 50% lyase activity remained when xanthan was partially depyruvated. (hindawi.com)
  • Glycolysis is a series of biochemical reactions by which one molecule of glucose (Glc) is oxidized to two molecules of pyruvic acid (Pyr) and a relatively small amount of the universal energy storage molecule adenosine triphosphate (ATP). (newworldencyclopedia.org)
  • In the preparatory phase (reactions 1-5), 2 ATP are invested in order to prepare the glucose molecule for further catabolism. (newworldencyclopedia.org)
  • In the second half reaction, which is not shown, the aspartate and histidine residues deprotonate a water molecule, and the hydroxide ion thus formed then bounces the N-terminal peptide fragment off the serine, again by nucleophilic attack on the carbonyl group. (uwaterloo.ca)
  • As part of this complex, adenylosuccinate lyase converts a molecule called succinylaminoimidazole carboxamide ribotide (SAICAR) to aminoimidazole carboxamide ribotide (AICAR) and converts succinyladenosine monophosphate (SAMP) to adenosine monophosphate (AMP). (nih.gov)
  • Methylglyoxal is produced naturally as a byproduct of normal biochemistry, but is highly toxic, due to its chemical reactions with proteins, nucleic acids, and other cellular components. (wikipedia.org)
  • Ligases are used in catalysis where two substrates are ligated and the formation of carbon-carbon, carbon-sulfide, carbon-nitrogen, and carbon-oxygen bonds due to condensation reactions. (wikibooks.org)
  • Lyase enzymes have potential to expand the application of biocatalysis in chemical synthesis - they can selectively synthesize molecules with multiple chiral centres, based on the formation of carbon-carbon and carbon-nitrogen bonds. (europa.eu)
  • Phenylalanine and tyrosine ammonia-lyases form cinnamic acid and p -coumaric acid, which are precursors of a wide range of aromatic compounds of biotechnological interest. (asm.org)
  • Lack of highly active and specific tyrosine ammonia-lyases has previously been a limitation in metabolic engineering approaches. (asm.org)
  • The enzymes were also efficient in Saccharomyces cerevisiae , where p -coumaric acid accumulation was improved 5-fold over that in strains expressing previously characterized tyrosine ammonia-lyases. (asm.org)
  • Aromatic amino acid ammonia-lyases and aminomutases. (asm.org)
  • Kinetic analysis of the reactions catalyzed by histidine and phenylalanine ammonia lyases. (biomedsearch.com)
  • Methods: The cDNA encoding an alginate lyase PyAly was cloned and was used for the construction of recombinant PyAly (rPyAly) expression system in Escherichia coli. (eurekaselect.com)
  • We demonstrate this procedure for the genome- scale reconstruction of Escherichia coli and also Saccharomyces cerevisiae wherein compartmentalization of intra-cellular reactions results in a more complex topology of the metabolic network. (biomedcentral.com)
  • Origin and Diversity of Alginate Lyases of Families PL-5 and -7 in Sphingomonas sp. (asm.org)
  • strain A1 has three endotype alginate lyases (A1-I, A1-II [family PL- and A1-III [family PL-, each of which is encoded by a single gene. (asm.org)
  • A large number of alginate lyases, from sources ranging from bacteria to marine animals, have been characterized ( 32 ), although little information on the diversity and evolution of alginate lyases has been accumulated. (asm.org)
  • Most alginate lyases are classified into two families, PL-5 and -7. (asm.org)
  • The bacterium incorporates the macromolecule (alginate) through a "superchannel," consisting of a pit formed on the cell surface and a pit-dependent ABC transporter ( 13 , 22 ), and depolymerizes the polymer into its constituent monosaccharides through concerted reactions catalyzed by three intracellular endotype alginate lyases (A1-I, A1-II, and A1-III) and an exotype alginate lyase (A1-IV) ( 8 , 36 ). (asm.org)
  • As the first step to confirm this hypothesis, we report here the molecular diversity and evolution of alginate lyases in Sphingomonas sp. (asm.org)
  • However, all characterized PL- 7 alginate lyases are from prokaryotic bacteria cells. (eurekaselect.com)
  • The amino-acid sequence of the catalytic domain showed 19-29% identities to those of bacterial characterized alginate lyases classified into family PL-7. (eurekaselect.com)
  • Jafari C, Panzer U, Steinmetz OM, Zahner G, Stahl RA, Harendza S: Enhanced expression of selenocysteine lyase in acute glomerulonephritis and its regulation by AP-1. (hmdb.ca)
  • which is catalyzed by the enzyme selenocysteine lyase. (hmdb.ca)
  • Elisa Lanfranchi, Kerstin Steiner, Anton Glieder, Ivan Hajnal, Roger A. Sheldon, Sander van Pelt and Margit Winkler, "Mini-Review: Recent Developments in Hydroxynitrile Lyases for Industrial Biotechnology", Recent Patents on Biotechnology (2013) 7: 197. (eurekaselect.com)
  • A1WD05_ACISJ Adenylosuccinate lyase OS=Acidovorax sp. (uniprot.org)
  • The ADSL gene provides instructions for making an enzyme called adenylosuccinate lyase. (nih.gov)
  • More than 50 mutations in the ADSL gene have been found to cause adenylosuccinate lyase deficiency. (nih.gov)
  • A reduction of adenylosuccinate lyase function, possibly due to a shortage of purinosomes, leads to buildup of SAICAR and SAMP. (nih.gov)
  • Detection of these substances in body fluids can help with diagnosis of adenylosuccinate lyase deficiency. (nih.gov)
  • damage to brain tissue caused by one or both of these substances likely underlies the neurological problems that occur in adenylosuccinate lyase deficiency. (nih.gov)
  • Studies suggest that the amount of SAICAr relative to S-Ado reflects the severity of adenylosuccinate lyase deficiency. (nih.gov)
  • Biochemical and biophysical analysis of five disease-associated human adenylosuccinate lyase mutants. (nih.gov)
  • Zikanova M, Skopova V, Hnizda A, Krijt J, Kmoch S. Biochemical and structural analysis of 14 mutant adsl enzyme complexes and correlation to phenotypic heterogeneity of adenylosuccinate lyase deficiency. (nih.gov)
  • The purified xanthan lyase has a molecular mass of 110 kDa and a specific activity of 28.2 U/mg that was much higher than that of both Paenibacillus and Bacillus lyases. (hindawi.com)
  • However, xanthan lyase was purified from both Paenibacillus alginolyticus XL-1 and Bacillus sp. (hindawi.com)
  • 5 - 9 )) The three enzymes and one non-enzymic factor involved in the pathway are lipolytic acyl hydrolase(LAH), lipoxygenase, fatty acid hydroperoxide lyase (hydroperoxide lyase) and an isomerization factor (Fig. 1). (springer.com)
  • This led to the proposal of an IMPA biodegradative pathway involving an organophosphate hydrolase catalyzed reaction forming MPA. (osti.gov)
  • When that chemical reaction occurs in a living organism, the catalyst is known as an enzyme. (encyclopedia.com)
  • Every one of those reactions could be made to occur by adding heat, electricity, or some other form of energy - but not within a living organism. (encyclopedia.com)
  • First we identify the metabolites in the metabolic network reconstruction which cannot be produced under any uptake conditions and subsequently we identify the reactions from a customized multi-organism database that restores the connectivity of these metabolites to the parent network using four mechanisms. (biomedcentral.com)
  • This connectivity restoration is hypothesized to take place through four mechanisms: a) reversing the directionality of one or more reactions in the existing model, b) adding reaction from another organism to provide functionality absent in the existing model, c) adding external transport mechanisms to allow for importation of metabolites in the existing model and d) restore flow by adding intracellular transport reactions in multi-compartment models. (biomedcentral.com)
  • The identified gaps can be filled both by making modifications in the existing model and by adding missing reactions by reconciling multi-organism databases of reactions with existing genome-scale models. (biomedcentral.com)
  • The radical S-adenosyl-L-methionine tryptophan lyase NosL converts L-tryptophan into 3-methylindolic acid, which is a precursor in the synthesis of the thiopeptide antibiotic nosiheptide. (univ-grenoble-alpes.fr)
  • In this review, we summarize the current state-of-the-art regarding late transition-metal-catalyzed reactions of acyl fluorides, including their synthesis and transformations. (bioportfolio.com)
  • Any eukaryotic metabolite produced during a metabolic reaction in plants, the kingdom that include flowering plants, conifers and other gymnosperms. (ebi.ac.uk)
  • This includes dynamic models for metabolic networks, which represent the set of chemical processes and reactions occurring in a cell. (royalsocietypublishing.org)
  • For example, hypoxia induces changes in regulatory T cell and macrophage metabolic profiles, including generation of 2-hydroxyglutarate, which inhibits demethylase reactions to modulate cell fate and function. (jci.org)
  • These missing reaction steps may lead to the prediction of erroneous genetic interventions for a targeted overproduction or the elucidation of misleading organizational principles and properties of the metabolic network. (biomedcentral.com)
  • Dozens of mutations in the CYP17A1 gene have been found to cause 17α-hydroxylase/17,20-lyase deficiency. (medlineplus.gov)
  • The principle focus of research effort in KYROBIO was to enable enabling the industrial application of the lyase class of enzymes. (europa.eu)