1.
BRENDA
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BRENDA is an information system representing one of the most comprehensive enzyme repositories. It is a resource that comprises molecular and biochemical information on enzymes that have been classified by the IUBMB. Every classified enzyme is characterized with respect to its catalyzed biochemical reaction, kinetic properties of the corresponding reactants are described in detail. BRENDA contains enzyme-specific data manually extracted from scientific literature and additional data derived from automatic information retrieval methods such as text mining. It provides a user interface that allows a convenient and sophisticated access to the data. BRENDA was founded in 1987 at the former German National Research Centre for Biotechnology in Braunschweig and was published as a series of books. Its name was originally an acronym for the Braunschweig Enzyme Database, from 1996 to 2007, BRENDA was located at the University of Cologne. There, BRENDA developed into a publicly accessible enzyme information system, in 2007, BRENDA returned to Braunschweig. Currently, BRENDA is maintained and further developed at the Department of Bioinformatics, a major update of the data in BRENDA is performed twice a year. Besides the upgrade of its content, improvements of the interface are also incorporated into the BRENDA database. The latest update was performed in January 2015, Database, The database contains more than 40 data fields with enzyme-specific information on more than 7000 EC numbers that are classified according to the IUBMB. Currently, BRENDA contains manually annotated data from over 140,000 different scientific articles, each enzyme entry is clearly linked to at least one literature reference, to its source organism, and, where available, to the protein sequence of the enzyme. An important part of BRENDA represent the more than 110,000 enzyme ligands, the term ligand is used in this context to all low molecular weight compounds which interact with enzymes. These include not only metabolites of primary metabolism, co-substrates or cofactors, the origin of these molecules ranges from naturally occurring antibiotics to synthetic compounds that have been synthesized for the development of drugs or pesticides. Furthermore, cross-references to external resources such as sequence and 3D-structure databases. Extensions, Since 2006, the data in BRENDA is supplemented with information extracted from the literature by a co-occurrence based text mining approach. For this purpose, four text-mining repositories FRENDA, AMENDA, DRENDA and KENDA were introduced and these text-mining results were derived from the titles and abstracts of all articles in the literature database PubMed. Data access, There are several tools to access to the data in BRENDA
2.
MetaCyc
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The MetaCyc database contains extensive information on metabolic pathways and enzymes from many organisms. MetaCyc is also used in engineering and metabolomics research. MetaCyc contains extensive data on individual enzymes, describing their subunit structure, cofactors, activators and inhibitors, substrate specificity, MetaCyc data on reactions includes predicted atom mappings that describe the correspondence between atoms in the reactant compounds and the product compounds. It also provides enzyme mini-reviews and literature references, MetaCyc data on metabolites includes chemical structures, predicted Gibbs free energies of formation, and links to external databases
3.
Protein Data Bank
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The Protein Data Bank is a crystallographic database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The PDB is overseen by a called the Worldwide Protein Data Bank. The PDB is a key resource in areas of structural biology, most major scientific journals, and some funding agencies, now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB, for example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology. By 1971, one of Meyers programs, SEARCH, enabled researchers to access information from the database to study protein structures offline. SEARCH was instrumental in enabling networking, thus marking the beginning of the PDB. Upon Hamiltons death in 1973, Tom Koeztle took over direction of the PDB for the subsequent 20 years, in January 1994, Joel Sussman of Israels Weizmann Institute of Science was appointed head of the PDB. In October 1998, the PDB was transferred to the Research Collaboratory for Structural Bioinformatics, the new director was Helen M. Berman of Rutgers University. In 2003, with the formation of the wwPDB, the PDB became an international organization, the founding members are PDBe, RCSB, and PDBj. Each of the four members of wwPDB can act as deposition, data processing, the data processing refers to the fact that wwPDB staff review and annotate each submitted entry. The data are automatically checked for plausibility. The PDB database is updated weekly, likewise, the PDB holdings list is also updated weekly. As of 14 March 2017, the breakdown of current holdings is as follows,103,514 structures in the PDB have a structure factor file,9,057 structures have an NMR restraint file. 2,826 structures in the PDB have a chemical shifts file, therefore, the final conformation of the protein is obtained, in the latter case, by solving a distance geometry problem. A few proteins are determined by cryo-electron microscopy, the significance of the structure factor files, mentioned above, is that, for PDB structures determined by X-ray diffraction that have a structure file, the electron density map may be viewed. The data of such structures is stored on the electron density server, however, since 2007, the rate of accumulation of new protein structures appears to have plateaued. The file format used by the PDB was called the PDB file format. This original format was restricted by the width of computer punch cards to 80 characters per line, around 1996, the macromolecular Crystallographic Information file format, mmCIF, which is an extension of the CIF format started to be phased in
4.
PubMed
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PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval, from 1971 to 1997, MEDLINE online access to the MEDLARS Online computerized database primarily had been through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home-, the PubMed system was offered free to the public in June 1997, when MEDLINE searches via the Web were demonstrated, in a ceremony, by Vice President Al Gore. Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog. As of 5 January 2017, PubMed has more than 26.8 million records going back to 1966, selectively to the year 1865, and very selectively to 1809, about 500,000 new records are added each year. As of the date,13.1 million of PubMeds records are listed with their abstracts. In 2016, NLM changed the system so that publishers will be able to directly correct typos. Simple searches on PubMed can be carried out by entering key aspects of a subject into PubMeds search window, when a journal article is indexed, numerous article parameters are extracted and stored as structured information. Such parameters are, Article Type, Secondary identifiers, Language, publication type parameter enables many special features. As these clinical girish can generate small sets of robust studies with considerable precision, since July 2005, the MEDLINE article indexing process extracts important identifiers from the article abstract and puts those in a field called Secondary Identifier. The secondary identifier field is to store numbers to various databases of molecular sequence data, gene expression or chemical compounds. For clinical trials, PubMed extracts trial IDs for the two largest trial registries, ClinicalTrials. gov and the International Standard Randomized Controlled Trial Number Register, a reference which is judged particularly relevant can be marked and related articles can be identified. If relevant, several studies can be selected and related articles to all of them can be generated using the Find related data option, the related articles are then listed in order of relatedness. To create these lists of related articles, PubMed compares words from the title and abstract of each citation, as well as the MeSH headings assigned, using a powerful word-weighted algorithm. The related articles function has been judged to be so precise that some researchers suggest it can be used instead of a full search, a strong feature of PubMed is its ability to automatically link to MeSH terms and subheadings. Examples would be, bad breath links to halitosis, heart attack to myocardial infarction, where appropriate, these MeSH terms are automatically expanded, that is, include more specific terms. Terms like nursing are automatically linked to Nursing or Nursing and this important feature makes PubMed searches automatically more sensitive and avoids false-negative hits by compensating for the diversity of medical terminology. The My NCBI area can be accessed from any computer with web-access, an earlier version of My NCBI was called PubMed Cubby
5.
National Center for Biotechnology Information
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The National Center for Biotechnology Information is part of the United States National Library of Medicine, a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper, the NCBI houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Major databases include GenBank for DNA sequences and PubMed, a database for the biomedical literature. Other databases include the NCBI Epigenomics database, all these databases are available online through the Entrez search engine. NCBI is directed by David Lipman, one of the authors of the BLAST sequence alignment program. He also leads a research program, including groups led by Stephen Altschul, David Landsman, Eugene Koonin, John Wilbur, Teresa Przytycka. NCBI is listed in the Registry of Research Data Repositories re3data. org, NCBI has had responsibility for making available the GenBank DNA sequence database since 1992. GenBank coordinates with individual laboratories and other databases such as those of the European Molecular Biology Laboratory. Since 1992, NCBI has grown to other databases in addition to GenBank. The NCBI assigns a unique identifier to each species of organism, the NCBI has software tools that are available by WWW browsing or by FTP. For example, BLAST is a sequence similarity searching program, BLAST can do sequence comparisons against the GenBank DNA database in less than 15 seconds. RAG2/IL2RG The NCBI Bookshelf is a collection of freely accessible, downloadable, some of the books are online versions of previously published books, while others, such as Coffee Break, are written and edited by NCBI staff. BLAST is a used for calculating sequence similarity between biological sequences such as nucleotide sequences of DNA and amino acid sequences of proteins. BLAST is a tool for finding sequences similar to the query sequence within the same organism or in different organisms. It searches the query sequence on NCBI databases and servers and post the results back to the browser in chosen format. Input sequences to the BLAST are mostly in FASTA or Genbank format while output could be delivered in variety of such as HTML, XML formatting. HTML is the output format for NCBIs web-page. Entrez is both indexing and retrieval system having data from sources for biomedical research
6.
Enzyme
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Enzymes /ˈɛnzaɪmz/ are macromolecular biological catalysts. Enzymes accelerate, or catalyze, chemical reactions, the molecules at the beginning of the process upon which enzymes may act are called substrates and the enzyme converts these into different molecules, called products. Almost all metabolic processes in the cell need enzymes in order to occur at rates fast enough to sustain life, the set of enzymes made in a cell determines which metabolic pathways occur in that cell. The study of enzymes is called enzymology, enzymes are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are proteins, although a few are catalytic RNA molecules, enzymes specificity comes from their unique three-dimensional structures. Like all catalysts, enzymes increase the rate of a reaction by lowering its activation energy, some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example is orotidine 5-phosphate decarboxylase, which allows a reaction that would take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules, inhibitors are molecules that decrease enzyme activity, many drugs and poisons are enzyme inhibitors. An enzymes activity decreases markedly outside its optimal temperature and pH, some enzymes are used commercially, for example, in the synthesis of antibiotics. French chemist Anselme Payen was the first to discover an enzyme, diastase and he wrote that alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells. In 1877, German physiologist Wilhelm Kühne first used the term enzyme, the word enzyme was used later to refer to nonliving substances such as pepsin, and the word ferment was used to refer to chemical activity produced by living organisms. Eduard Buchner submitted his first paper on the study of yeast extracts in 1897, in a series of experiments at the University of Berlin, he found that sugar was fermented by yeast extracts even when there were no living yeast cells in the mixture. He named the enzyme that brought about the fermentation of sucrose zymase, in 1907, he received the Nobel Prize in Chemistry for his discovery of cell-free fermentation. Following Buchners example, enzymes are usually named according to the reaction they carry out, the biochemical identity of enzymes was still unknown in the early 1900s. Sumner showed that the enzyme urease was a protein and crystallized it. These three scientists were awarded the 1946 Nobel Prize in Chemistry, the discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography. This high-resolution structure of lysozyme marked the beginning of the field of structural biology, an enzymes name is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase
7.
Catalysis
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Catalysis is the increase in the rate of a chemical reaction due to the participation of an additional substance called a catalyst. In most cases, reactions occur faster with a catalyst because they require less activation energy, furthermore, since they are not consumed in the catalyzed reaction, catalysts can continue to act repeatedly. Often only tiny amounts are required in principle, in the presence of a catalyst, less free energy is required to reach the transition state, but the total free energy from reactants to products does not change. A catalyst may participate in multiple chemical transformations, the effect of a catalyst may vary due to the presence of other substances known as inhibitors or poisons or promoters. Catalyzed reactions have an activation energy than the corresponding uncatalyzed reaction, resulting in a higher reaction rate at the same temperature. However, the mechanics of catalysis is complex. Usually, the catalyst participates in this slowest step, and rates are limited by amount of catalyst, in heterogeneous catalysis, the diffusion of reagents to the surface and diffusion of products from the surface can be rate determining. A nanomaterial-based catalyst is an example of a heterogeneous catalyst, analogous events associated with substrate binding and product dissociation apply to homogeneous catalysts. Although catalysts are not consumed by the reaction itself, they may be inhibited, deactivated, in heterogeneous catalysis, typical secondary processes include coking where the catalyst becomes covered by polymeric side products. Additionally, heterogeneous catalysts can dissolve into the solution in a system or sublimate in a solid–gas system. The production of most industrially important chemicals involves catalysis, similarly, most biochemically significant processes are catalysed. Research into catalysis is a field in applied science and involves many areas of chemistry, notably organometallic chemistry. Catalysis is relevant to aspects of environmental science, e. g. the catalytic converter in automobiles. Many transition metals and transition metal complexes are used in catalysis as well, Catalysts called enzymes are important in biology. A catalyst works by providing a reaction pathway to the reaction product. The rate of the reaction is increased as this route has a lower activation energy than the reaction route not mediated by the catalyst. The disproportionation of hydrogen peroxide creates water and oxygen, as shown below,2 H2O2 →2 H2O + O2 This reaction is preferable in the sense that the reaction products are more stable than the starting material, though the uncatalysed reaction is slow. In fact, the decomposition of hydrogen peroxide is so slow that hydrogen peroxide solutions are commercially available and this reaction is strongly affected by catalysts such as manganese dioxide, or the enzyme peroxidase in organisms
8.
Chemical reaction
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A chemical reaction is a process that leads to the transformation of one set of chemical substances to another. Nuclear chemistry is a sub-discipline of chemistry that involves the reactions of unstable. The substance initially involved in a reaction are called reactants or reagents. Chemical reactions are characterized by a chemical change, and they yield one or more products. Reactions often consist of a sequence of individual sub-steps, the elementary reactions. Chemical reactions are described with chemical equations, which present the starting materials, end products. Chemical reactions happen at a characteristic reaction rate at a given temperature, typically, reaction rates increase with increasing temperature because there is more thermal energy available to reach the activation energy necessary for breaking bonds between atoms. Reactions may proceed in the forward or reverse direction until they go to completion or reach equilibrium, Reactions that proceed in the forward direction to approach equilibrium are often described as spontaneous, requiring no input of free energy to go forward. Non-spontaneous reactions require input of energy to go forward. Different chemical reactions are used in combinations during chemical synthesis in order to obtain a desired product, in biochemistry, a consecutive series of chemical reactions form metabolic pathways. These reactions are catalyzed by protein enzymes. Chemical reactions such as combustion in fire, fermentation and the reduction of ores to metals were known since antiquity, in the Middle Ages, chemical transformations were studied by Alchemists. They attempted, in particular, to lead into gold, for which purpose they used reactions of lead. The process involved heating of sulfate and nitrate minerals such as sulfate, alum. In the 17th century, Johann Rudolph Glauber produced hydrochloric acid and sodium sulfate by reacting sulfuric acid, further optimization of sulfuric acid technology resulted in the contact process in the 1880s, and the Haber process was developed in 1909–1910 for ammonia synthesis. From the 16th century, researchers including Jan Baptist van Helmont, Robert Boyle, the phlogiston theory was proposed in 1667 by Johann Joachim Becher. It postulated the existence of an element called phlogiston, which was contained within combustible bodies. This proved to be false in 1785 by Antoine Lavoisier who found the explanation of the combustion as reaction with oxygen from the air
9.
Product (chemistry)
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Products are the species formed from chemical reactions. During a chemical reaction reactants are transformed into products after passing through an energy transition state. This process results in the consumption of the reactants, when represented in chemical equations products are by convention drawn on the right-hand side, even in the case of reversible reactions. The properties of such as their energies help determine several characteristics of a chemical reaction such as whether the reaction is exergonic or endergonic. Additionally the properties of a product can make it easier to extract and purify following a chemical reaction, reactants are molecular materials used to create chemical reactions. The atoms arent created or destroyed, the materials are reactive and reactants are rearranging during a chemical reaction. Here is an example of reactants, CH4 + O2, a non-example is CO2 + H2O or energy. Much of chemistry research is focused on the synthesis and characterization of beneficial products, as well as the detection, other fields include natural product chemists who isolate products created by living organisms and then characterize and study these products. The products of a chemical reaction influence several aspects of the reaction, if the products are lower in energy than the reactants, then the reaction will give off excess energy making it an exergonic reaction. Such reactions are thermodynamically favorable and tend to happen on their own, if the kinetics of the reaction are high enough, however, then the reaction may occur too slowly to be observed, or not even occur at all. If the products are higher in energy than the reactants then the reaction will require energy to be performed and is therefore an endergonic reaction. Additionally if the product is less stable than a reactant, then Lefflers assumption holds that the state will more closely resemble the product than the reactant. Ever since the mid nineteenth century chemists have been preoccupied with synthesizing chemical products. Much of synthetic chemistry is concerned with the synthesis of new chemicals as occurs in the design and creation of new drugs, in biochemistry, enzymes act as biological catalysts to convert substrate to product. For example, the products of the enzyme lactase are galactose and glucose, S + E → P + E Where S is substrate, P is product and E is enzyme. Some enzymes display a form of promiscuity where they convert a single substrate into multiple different products and it occurs when the reaction occurs via a high energy transition state that can be resolved into a variety of different chemical products. Some enzymes are inhibited by the product of their reaction binds to the enzyme and this can be important in the regulation of metabolism as a form of negative feedback controlling metabolic pathways. Product inhibition is also an important topic in biotechnology, as overcoming this effect can increase the yield of a product, Chemical reaction Substrate Reagent Precursor Catalyst Enzyme Product Derivative Chemical equilibrium Second law of thermodynamics
10.
Propionate
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The propionate or propanoate ion is C2H5COO−. A propionic or propanoic compound is a salt or ester of propionic acid. In these compounds, propionate is often written in shorthand, as CH3CH2CO2 or simply EtCO2, propionates should not be confused with propenoates, the ions/salts/esters of propenoic acid. Sodium propionate, NaC2H5CO2 Methyl propionate, Calcium propionate, Ca2 Potassium propionate, KC2H5CO2 Fluticasone propionate, C25H31F3O5S
11.
Pyruvate
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Pyruvic acid is the simplest of the alpha-keto acids, with a carboxylic acid and a ketone functional group. Pyruvate, the base, CH3COCOO−, is a key intermediate in several metabolic pathways. Pyruvic acid can be made from glucose through glycolysis, converted back to carbohydrates via gluconeogenesis and it can also be used to construct the amino acid alanine and can be converted into ethanol or lactic acid via fermentation. Pyruvic acid supplies energy to cells through the citric acid cycle when oxygen is present, pyruvic acid is a colorless liquid with a smell similar to that of acetic acid and is miscible with water. It is the output of the metabolism of known as glycolysis. One molecule of glucose breaks down into two molecules of pyruvate, which are used to provide further energy, in one of two ways. Pyruvate is converted into acetyl-coenzyme A, which is the input for a series of reactions known as the Krebs cycle. Pyruvate is also converted to oxaloacetate by an reaction, which replenishes Krebs cycle intermediates, also. These reactions are named after Hans Adolf Krebs, the biochemist awarded the 1953 Nobel Prize for physiology, jointly with Fritz Lipmann, for research into metabolic processes. The cycle is known as the citric acid cycle or tricarboxylic acid cycle. If insufficient oxygen is available, the acid is broken down anaerobically, creating lactate in animals and ethanol in plants, Pyruvate is a key intersection in the network of metabolic pathways. Pyruvate can be converted into carbohydrates via gluconeogenesis, to fatty acids or energy through acetyl-CoA, to the amino acid alanine, therefore, it unites several key metabolic processes. In glycolysis, phosphoenolpyruvate is converted to pyruvate by pyruvate kinase and this reaction is strongly exergonic and irreversible, in gluconeogenesis, it takes two enzymes, pyruvate carboxylase and PEP carboxykinase, to catalyze the reverse transformation of pyruvate to PEP. Compound C00074 at KEGG Pathway Database, enzyme 2.7.1.40 at KEGG Pathway Database. Compound C00022 at KEGG Pathway Database, click on genes, proteins and metabolites below to link to respective articles. Pyruvate decarboxylation by the pyruvate dehydrogenase complex produces acetyl-CoA, carboxylation by pyruvate carboxylase produces oxaloacetate. Transamination by alanine transaminase produces alanine, reduction by lactate dehydrogenase produces lactate. Pyruvate is sold as a supplement, though evidence supporting this use is lacking
12.
PubMed Identifier
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PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval, from 1971 to 1997, MEDLINE online access to the MEDLARS Online computerized database primarily had been through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home-, the PubMed system was offered free to the public in June 1997, when MEDLINE searches via the Web were demonstrated, in a ceremony, by Vice President Al Gore. Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog. As of 5 January 2017, PubMed has more than 26.8 million records going back to 1966, selectively to the year 1865, and very selectively to 1809, about 500,000 new records are added each year. As of the date,13.1 million of PubMeds records are listed with their abstracts. In 2016, NLM changed the system so that publishers will be able to directly correct typos. Simple searches on PubMed can be carried out by entering key aspects of a subject into PubMeds search window, when a journal article is indexed, numerous article parameters are extracted and stored as structured information. Such parameters are, Article Type, Secondary identifiers, Language, publication type parameter enables many special features. As these clinical girish can generate small sets of robust studies with considerable precision, since July 2005, the MEDLINE article indexing process extracts important identifiers from the article abstract and puts those in a field called Secondary Identifier. The secondary identifier field is to store numbers to various databases of molecular sequence data, gene expression or chemical compounds. For clinical trials, PubMed extracts trial IDs for the two largest trial registries, ClinicalTrials. gov and the International Standard Randomized Controlled Trial Number Register, a reference which is judged particularly relevant can be marked and related articles can be identified. If relevant, several studies can be selected and related articles to all of them can be generated using the Find related data option, the related articles are then listed in order of relatedness. To create these lists of related articles, PubMed compares words from the title and abstract of each citation, as well as the MeSH headings assigned, using a powerful word-weighted algorithm. The related articles function has been judged to be so precise that some researchers suggest it can be used instead of a full search, a strong feature of PubMed is its ability to automatically link to MeSH terms and subheadings. Examples would be, bad breath links to halitosis, heart attack to myocardial infarction, where appropriate, these MeSH terms are automatically expanded, that is, include more specific terms. Terms like nursing are automatically linked to Nursing or Nursing and this important feature makes PubMed searches automatically more sensitive and avoids false-negative hits by compensating for the diversity of medical terminology. The My NCBI area can be accessed from any computer with web-access, an earlier version of My NCBI was called PubMed Cubby
13.
Acetoacetate decarboxylase
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Acetoacetate decarboxylase is an enzyme involved in both the ketone body production pathway in humans and other mammals, and solventogenesis in bacteria. Acetoacetate decarboxylase plays a key role in solvent production by catalyzing the decarboxylation of acetoacetate, yielding acetone and this enzyme has been of particular interest because it is a classic example of how pKa values of ionizable groups in the enzyme active site can be significantly perturbed. Specifically, the pKa value of lysine 115 in the site is unusually low, allowing for the formation of a Schiff base intermediate. Acetoacetate decarboxylase is an enzyme with major implications, specifically in World War I. During the war the Allies needed pure acetone as a solvent for nitro-cellulose, Weizmann was able to harness the organism’s ability to yield acetone from starch in order to mass-produce explosives during the war. This led the American and British governments to install the process devised by Chaim Weizmann in several plants in England, France, Canada. Through Weizmann’s scientific contributions in World War I, he became close with influential British leaders educating them of his Zionist beliefs, one of them was Arthur Balfour, the man after whom the Balfour Declaration—the first document pronouncing British support in the establishment of a Jewish homeland—was named. The production of acetone by acetoacetate decarboxylase-containing or clostridial bacteria was utilized in industrial syntheses in the first half of the twentieth century. In the 1960s, the industry replaced this process with less expensive, however, there has been a growing interest in acetone production that is more environmentally friendly, causing a resurgence in utilizing acetoacetate decarboxylase-containing bacteria. Similarly, isopropanol and butanol fermentation using clostridial species is becoming popular. Acetoacetate decarboxylase is a 365 kDa complex with a homododecameric structure, the overall structure consists of antiparallel β-sheets and a central seven-stranded cone-shaped β-barrel. The core of this β-barrel surrounds the site in each protomer of the enzyme. The active site, consisting of such as Phe27, Met97. However, the site does contain two charged residues, Arg29 and Glu76. Arg29 is thought to play a role in binding, while Glu76 is thought to play a role in the orienting the active site for catalysis. The overall hydrophobic environment of the site plays a critical role in favoring the neutral amine form of Lys115. Another important lysine residue, Lys116, is thought to play an important role in the positioning of Lys115 in the active site, through hydrogen bonds with Ser16 and Met210, Lys116 positions Lys115 in the hydrophobic pocket of the active site to favor the neutral amine form. Acetoacetate decarboxylase from Clostridium acetobutylicum catalyzes the decarboxylation of acetoacetate to yield acetone, the reaction mechanism proceeds via the formation of a Schiff base intermediate, which is covalently attached to lysine 115 in the active site
14.
Aromatic L-amino acid decarboxylase
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Aromatic L-amino acid decarboxylase, also known as DOPA decarboxylase, tryptophan decarboxylase, and 5-hydroxytryptophan decarboxylase, is a lyase enzyme. In normal dopamine and serotonin neurotransmitter synthesis, AADC is not the rate-limiting step in either reaction, however, AADC becomes the rate-limiting step of dopamine synthesis in patients treated with L-DOPA, and the rate-limiting step of serotonin synthesis in people treated with 5-HTP. AADC is inhibited by Carbidopa outside of the blood brain barrier to inhibit the conversion of L-DOPA to dopamine in the treatment of Parkinsons. In humans, AADC is also the rate-limiting enzyme in the formation of trace amines, deficiency of AADC is associated with various symptoms as severe developmental delay, oculogyric crises and autonomic dysfunction. The molecular and clinical spectrum of AAAC deficiency is heterogeneous, the first case of AADC deficiency was described in twin brothers 1990. Patients can be treated with dopamine agonists, MAO inhibitors, clinical phenotype and response to treatment is variable and the long-term and functional outcome is unknown. The gene encoding the enzyme is referred to as DDC and located on chromosome 7 in humans, no direct correlation between gene variation and autism was found. Aromatic amino acids Histidine decarboxylase Aromatic-L-Amino-Acid Decarboxylases at the US National Library of Medicine Medical Subject Headings
15.
Glutamate decarboxylase
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Glutamate decarboxylase or glutamic acid decarboxylase is an enzyme that catalyzes the decarboxylation of glutamate to GABA and CO2. GAD uses PLP as a cofactor, the reaction proceeds as follows, HOOC-CH2-CH2-CH-COOH → CO2 + HOOC-CH2-CH2-CH2NH2 In mammals, GAD exists in two isoforms encoded by two different genes - GAD1 and GAD2. These isoforms are GAD67 and GAD65 with molecular weights of 67 and 65 kDa, GAD1 and GAD2 are expressed in the brain where GABA is used as a neurotransmitter, GAD2 is also expressed in the pancreas. At least two forms, GAD25 and GAD44 are described in the developing brain. They are coded by the alternative transcripts of GAD1, I-80 and I-86, GAD65 and GAD67 synthesize GABA at different locations in the cell, at different developmental times, and for functionally different purposes. GAD67 is spread throughout the cell while GAD65 is localized to nerve terminals. This difference is thought to reflect a difference, GAD67 synthesizes GABA for neuron activity unrelated to neurotransmission, such as synaptogenesis. This function requires widespread, ubiquitous presence of GABA, GAD65, however, synthesizes GABA for neurotransmission, and therefore is only necessary at nerve terminals and synapses. GAD67 is transcribed during early development, while GAD65 is not transcribed until later in life, GAD67 and GAD65 are also regulated differently post-translationally. Both GAD65 and GAD67 are regulated via phosphorylation, but the regulation of these isoforms differs, GAD67 is phosphorylated at threonine 91 by protein kinase A, while GAD65 is phosphorylated, and therefore regulated by, protein kinase C. Both GAD67 and GAD65 are also regulated post-translationally by Pyridoxal 5’-phosphate, GAD is activated when bound to PLP, majority of GAD67 is bound to PLP at any given time, whereas GAD65 binds PLP when GABA is needed for neurotransmission. Both GAD67 and GAD65 are targets of autoantibodies in people who later develop type 1 diabetes mellitus or latent autoimmune diabetes, injections with GAD65 has been shown to preserve some insulin production for 30 months in humans with type 1 diabetes. High titers of autoantibodies to glutamic acid decarboxylase are well documented in association with stiff person syndrome, glutamic acid decarboxylase is the rate-limiting enzyme in the synthesis of γ-aminobutyric acid, and impaired function of GABAergic neurons has been implicated in the pathogenesis of SPS. Autoantibodies to GAD might be the agent or a disease marker. Substantial dysregulation of GAD mRNA expression, coupled with downregulation of reelin, is observed in schizophrenia, the most pronounced downregulation of GAD67 was found in hippocampal stratum oriens layer in both disorders and in other layers and structures of hippocampus with varying degrees. The mechanism underlying the levels of GAD67 in people with schizophrenia remains unclear. Intracerebellar administration of GAD autoantibodies to animals increases the excitability of motoneurons and impairs the production of nitric oxide, epitope recognition contributes to cerebellar involvement. Reduced GABA levels increase glutamate levels as a consequence of inhibition of subtypes of GABA receptors
16.
Histidine decarboxylase
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Histidine decarboxylase is an enzyme responsible for catalyzing the decarboxylation of histidine to form histamine. In mammals, histamine is an important biogenic amine with regulatory roles in neurotransmission, gastric acid secretion, Histidine decarboxylase is the sole member of the histamine synthesis pathway, producing histamine in a one-step reaction. Histamine cannot be generated by any known enzyme. HDC is therefore the source of histamine in most mammals. The enzyme employs a pyridoxal 5-phosphate cofactor, in similarity to many amino acid decarboxylases, eukaryotes, as well as gram-negative bacteria share a common HDC, while gram-positive bacteria employ an evolutionarily unrelated pyruvoyl-dependent HDC. In humans, histidine decarboxylase is encoded by the HDC gene, Histidine decarboxylase is a group II pyridoxal-dependent decarboxylase, along with aromatic-L-amino-acid decarboxylase, and tyrosine decarboxylase. HDC is expressed as a 74 kDa polypeptide which is not enzymatically functional, only after post-translational processing does the enzyme become active. This processing consists of truncating much of the proteins C-terminal chain, Histidine decarboxylase exists as a homodimer, with several amino acids from the respective opposing chain stabilizing the HDC active site. HDC contains several regions that are sequentially and structurally similar to those in a number of other pyridoxal-dependent decarboxylases and this is particularly evident in the vicinity of the active site lysine 305. HDC decarboxylates histidine through the use of a PLP cofactor initially bound in a Schiff base to lysine 305, Histidine initiates the reaction by displacing lysine 305 and forming a aldimine with PLP. Histidines carboxyl group then leaves, forming carbon dioxide, finally, PLP re-forms its original Schiff base at lysine 305, and histamine is released. This mechanism is similar to those employed by other pyridoxal-dependent decarboxylases. In particular, the intermediate is a common feature of all known PLP-dependent decarboxylases. HDC is highly specific for its histidine substrate, Histidine decarboxylase is the primary biological source of histamine. Histamine is an important biogenic amine that moderates numerous physiologic processes, there are four different histamine receptors, H1, H2, H3, and H4, each of which carries a different biological significance. H1 modulates several functions of the central and peripheral nervous system, including rhythm, body temperature. H2 activation results in gastric acid secretion and smooth muscle relaxation, H3 controls histamine turnover by feedback inhibition of histamine synthesis and release. Finally, H4 plays roles in mast cell chemotaxis and cytokine production, in humans, HDC is primarily expressed in mast cells and basophil granulocytes
17.
Malonyl-CoA decarboxylase
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Malonyl-CoA decarboxylase is found from bacteria to humans, has important roles in regulating fatty acid metabolism and food intake, and it is an attractive target for drug discovery. It is an associated with Malonyl-CoA decarboxylase deficiency. In humans, it is encoded by the MLYCD gene and its main function is to catalyze the conversion of malonyl-CoA into acetyl-CoA and carbon dioxide. It is involved in fatty acid biosynthesis, to some degree, it reverses the action of Acetyl-CoA carboxylase. MCD presents two isoforms which can be transcribed form one gene, an isoform, distributed in mitochondria. MCD is a tetramer, an oligomer formed by a dimer of heterodimers related by an axis of binary symmetry with a rotation angle of about 180 degrees. The strong structural asymmetry between the monomers of the heterodimer suggests a half of the reactivity, in which only half of the active sites are functional simultaneously. The C-terminus one is where malonyl-CoA catalysis takes place and which is present in GCN5- Histone acetyiltranferase family and it also includes a cluster of seven helixes. According to this, the half of the mechanism might present a consumption of catalytic energy. As a result, the conformational changes synchronised in the pair of subunits facilitates the catalysis despite the reduction of the number of active sites. Each monomer of that structure exhibits a large hydrophobic interface with the possibility to form an inter subunit disulfide bridge, heterodimers are also interconnected by a small C-terminus domain interface, where a pair of cysteines is properly disposed. The disulfide bonds gives to MCD the capability to form a tetrameric enzyme linked by inter subunits covalent bonds in the presence of such as hydrogen peroxide. The polypeptide chain in the protein is comprised between amino acid 40 and 493. In order to turn into an active enzyme, MCD undergoes 8 post-translational modifications in different amino acids, the last one, which consists of an acetylation in the amino acid lysine in position 472, activates malonyl-CoA decarboxylase activity. Similarly, a deacetylation in this specific amino acid by SIRT4 represses the enzyme activity, the malonyl-CoA decarboxylase gene is located in chromosome 16. This gene has 2 transcripts or splice variants, one of which encodes MCD and it has also 59 orthologues,1 paralogue and it is associated with 5 phenotypes. MLYCD is strongly expressed in heart, liver and some other tissues like kidney and this gene is also weakly expressed in many other tissues such as brain, placenta, testis, etc. The enzyme malonyl-CoA decarboxylase functions as an indirect via of conversion from malonic semi aldehyde to acetyl-CoA in peroxisomes and this is due to the fact that the beta oxidation of long chain fatty acids with an odd number of carbons produces propionyl-CoA
18.
Ornithine decarboxylase
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The enzyme ornithine decarboxylase catalyzes the decarboxylation of ornithine to form putrescine. This reaction is the step in polyamine synthesis. In humans, this protein has 461 amino acids and forms a homodimer, lysine 69 on ornithine decarboxylase binds the cofactor pyridoxal phosphate to form a Schiff base. Ornithine displaces the lysine to form a Schiff base attached to ODC and this intermediate rearranges to form a Schiff base attached to putrescine, which is attacked by lysine to release putrescine product and reform PLP-bound ODC. This is the first step and the step in humans for the production of polyamines. The active form of ornithine decarboyxlase is a homodimer, each monomer contains a barrel domain, consisting of an alpha-beta barrel, and a sheet domain, composed of two beta-sheets. The domains are connected by loops, the monomers connect to each other via interactions between the barrel of one monomer and the sheet of the other. Binding between monomers is relatively weak, and ODC interconverts rapidly between monomeric and dimeric forms in the cell, the pyridoxal phosphate cofactor binds lysine 69 at the C-terminus end of the barrel domain. The active site is at the interface of the two domains, in a cavity formed by loops from both monomers, the ornithine decarboxylation reaction catalyzed by ornithine decarboxylase is the first and committed step in the synthesis of polyamines, particularly putrescine, spermidine and spermine. Polyamines are important for stabilizing DNA structure, the DNA double strand-break repair pathway, therefore, ornithine decarboxylase is an essential enzyme for cell growth, producing the polyamines necessary to stabilize newly synthesized DNA. Lack of ODC causes cell apoptosis in embryonic mice, induced by DNA damage, ODC is the most well-characterized cellular protein subject to ubiquitin-independent proteasomal degradation. The ODC degradation process is regulated in a feedback loop by its reaction products. Until a report by Sheaff et al, ODC is a transcriptional target of the oncogene Myc and is upregulated in a wide variety of cancers. The polyamine products of the pathway initialized by ODC are associated with increased cell growth, ultraviolet light, asbestos and androgens released by the prostate gland are all known to induce increased ODC activity associated with cancer. Inhibitors of ODC such as eflornithine have been shown to effectively reduce cancers in animal models, the mechanism by which ODC promotes carcinogenesis is complex and not entirely known. Along with their effect on DNA stability, polyamines also upregulate gap junction genes. Gap junction genes are involved in communication between cells and tight junction genes act as tumor suppressors. ODC gene expression is induced by a number of biological stimuli including seizure activity in the brain
19.
Phosphoenolpyruvate carboxykinase
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Phosphoenolpyruvate carboxykinase is an enzyme in the lyase family used in the metabolic pathway of gluconeogenesis. It converts oxaloacetate into phosphoenolpyruvate and carbon dioxide and it is found in two forms, cytosolic and mitochondrial. In humans there are two isoforms of PEPCK, a form and a mitochondrial isoform which have 63. 4% sequence identity. The cytosolic form is important in gluconeogenesis, however, there is a known transport mechanism to move PEP from the mitochondria to the cytosol, using specific membrane transport proteins. X-ray structures of PEPCK provide insight into the structure and the mechanism of PEPCK enzymatic activity, the mitochondrial isoform of chicken liver PEPCK complexed with Mn2+, Mn2+-phosphoenolpyruvate, and Mn2+-GDP provides information about its structure and how this enzyme catalyzes reactions. Delbaere et al. resolved PEPCK in E. coli and found the site sitting between a C-terminal domain and an N-terminal domain. The active site was observed to be closed upon rotation of these domains, phosphoryl groups are transferred during PEPCK action, which is likely facilitated by the eclipsed conformation of the phosphoryl groups when ATP is bound to PEPCK. Since the eclipsed formation is one that is high in energy, phosphoryl group transfer has an energy of activation. This transfer likely happens via a similar to SN2 displacement. PEPCK gene transcription occurs in species, and the amino acid sequence of PEPCK is distinct for each species. For example, its structure and its specificity differ in humans, Escherichia coli, pEPCase converts oxaloacetate into phosphoenolpyruvate and carbon dioxide. As PEPCK acts at the junction between glycolysis and the Krebs cycle, it causes decarboxylation of a C4 molecule, creating a C3 molecule, as the first committed step in gluconeogenesis, PEPCK decarboxylates and phosphorylates oxaloacetate for its conversion to PEP, when GTP is present. As a phosphate is transferred, the results in a GDP molecule. Although this reaction is possible, the kinetics are so unfavorable that the mutants grow at a slow pace or do not grow at all. PEPCK-C catalyzes an irreversible step of gluconeogenesis, the process whereby glucose is synthesized, the enzyme has therefore been thought to be essential in glucose homeostasis, as evidenced by laboratory mice that contracted diabetes mellitus type 2 as a result of the overexpression of PEPCK-C. The role that PEPCK-C plays in gluconeogenesis may be mediated by the citric acid cycle, PEPCK-C levels alone were not highly correlated with gluconeogenesis in the mouse liver, as previous studies have suggested. While the mouse liver almost exclusively expresses PEPCK-C, humans present a mitochondrial isozyme. PEPCK-M has gluconeogenic potential per se, therefore, the role of PEPCK-C and PEPCK-M in gluconeogenesis may be more complex and involve more factors than was previously believed
20.
Phosphoenolpyruvate carboxylase
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The enzyme structure and its two step catalytic, irreversible mechanism have been well studied. PEP carboxylase is highly regulated, both by phosphorylation and allostery, the PEP carboxylase enzyme is present in plants and some types of bacteria, but not in fungi or animals. The genes vary between organisms, but are strictly conserved around the active and allosteric sites discussed in the mechanism, tertiary structure of the enzyme is also conserved. The crystal structure of PEP carboxylase in multiple organisms, including Zea mays, the overall enzyme exists as a dimer-of-dimers, two identical subunits closely interact to form a dimer through salt bridges between arginine and glutamic acid residues. This dimer assembles with another of its kind to form the four subunit complex, the monomer subunits are mainly composed of alpha helices, and have a mass of 106kDa each. The sequence length is about 966 amino acids, see figure 1 for a PyMOL generated structure of the enzyme’s single subunit from the organism Flaveria trinervia. The enzyme active site is not completely characterized and it includes a conserved aspartic acid and a glutamic acid residue that non-covalently bind a divalent metal cofactor ion through the carboxylic acid functional groups. This metal ion can be magnesium, manganese or cobalt depending on the organism, a histidine residue at the active site is believed to facilitate proton transfer during the catalytic mechanism. The mechanism of PEP carboxylase has been well studied, the enzymatic mechanism of forming oxaloacetate is very exothermic and thereby irreversible, the biological Gibbs free energy change is -30kJmol−1. The substrates and cofactor bind in the order, metal cofactor, PEP. The mechanism proceeds in two steps, as described below and shown in figure 2,1. The bicarbonate acts as a nucleophile to attack the group in PEP. This results in the splitting of PEP into a carboxyphosphate and the form of pyruvate. Proton transfer takes place at the carboxyphosphate and this is most likely modulated by a histidine residue that first deprotonates the carboxy side, and then, as an acid, protonates the phosphate part. The carboxyphosphate then exothermically decomposes into carbon dioxide and inorganic phosphate, finally, after the decomposition, the carbon dioxide is attacked by the enolate to form oxaloacetate. The metal cofactor is necessary to coordinate the enolate and carbon dioxide intermediates, the active site is hydrophobic to exclude water, since the carboxyphosphate intermediate is susceptible to hydrolysis. The three most important roles that PEP carboxylase plays in plants and bacteria metabolism are in the C4 cycle, the CAM cycle, and the citric acid cycle biosynthesis flux. However, at temperatures and lower CO2 concentrations, RuBisCO adds oxygen instead of carbon dioxide
21.
Pyruvate decarboxylase
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It is also called 2-oxo-acid carboxylase, alpha-ketoacid carboxylase, and pyruvic decarboxylase. In anaerobic conditions, this enzyme is part of the process that occurs in yeast, especially of the Saccharomyces genus. It is also present in species of fish where it permits the fish to perform ethanol fermentation when oxygen is scarce. Pyruvate decarboxylase starts this process by converting pyruvate into acetaldehyde and carbon dioxide, pyruvate decarboxylase depends on cofactors thiamine pyrophosphate and magnesium. This enzyme should not be mistaken for the enzyme pyruvate dehydrogenase, an oxidoreductase. Pyruvate decarboxylase occurs as a dimer of dimers with two active sites shared between the monomers of each dimer, the enzyme contains a beta-alpha-beta structure, yielding parallel beta-sheets. It contains 563 residue subunits in each dimer, the enzyme has strong intermonomer attractions and this enzyme is a homotetramer, and therefore has four active sites. The active sites are inside a cavity in the core of the enzyme where hydrogen bonding can occur, each active site has 20 amino acids, including the acidic Glu-477 and Glu-51. These Glutamates also contribute to forming the TPP ylid, acting as proton donators to the TPP aminopyrimidine ring, the microenvironment around this Glu 477 is very nonpolar, contributing to a higher than normal pKa. The lipophilic residues Ile-476, Ile-480 and Pro-26 contribute to the nonpolarity of the area around Glu-477, the only other negatively charged residue apart from TPP coenzyme is the Asp-28, which also aids in increasing the pKa of Glu-477. Thus, the environment of the enzyme must allow for the protonation of the group of Glu-477 to be around pH6. The aminopyrimidine ring on TPP acts as a base, once in its imine form and this must occur because the enzyme has no basic side chains present to deprotonate the TPP C2. A mutation at the site involving these Glu can result in the inefficiency or inactivity of the enzyme. This inactivity has been proven in experiments in which either the N1 and/or 4-amino groups are missing. In NMR analysis, it has determined that when TPP is bound to the enzyme along with the substate-analog pyruvamide. Also, the rate of mutation of Glu 51 to Gln reduces this rate significantly, also included are Asp-444 and Asp-28 which stabilize the active site. These act as stabilizers for the Mg2+ ion that is present in active site. To ensure that only pyruvate binds, two Cys-221 and His-92 trigger a change which inhibits or activates the enzyme depending on the substrate that interacts with it
22.
RuBisCO
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In chemical terms, it catalyzes the carboxylation of ribulose-1, 5-bisphosphate. It is probably the most abundant enzyme on Earth, RuBisCO is important biologically because it catalyzes the primary chemical reaction by which inorganic carbon enters the organic biosphere. Phosphoenolpyruvate carboxylase, unlike RuBisCO, only temporarily fixes carbon, reflecting its importance, RuBisCO is the most abundant protein in leaves, accounting for 50% of soluble leaf protein in C3 plants and 30% of soluble leaf protein in C4 plants. Given its important role in the biosphere, the engineering of RuBisCO in crops is of continuing interest. In plants, algae, cyanobacteria, and phototrophic and chemoautotrophic proteobacteria, the large-chain gene is encoded by the chloroplast DNA in plants. The enzymatically active substrate binding sites are located in the chains that form dimers as shown in Figure 1 in which amino acids from each large chain contribute to the binding sites. A total of eight large-chains and eight small chains assemble into a complex of about 540,000 Da. In some proteobacteria and dinoflagellates, enzymes consisting of large subunits have been found. Magnesium ions are needed for enzymatic activity, correct positioning of Mg2+ in the active site of the enzyme involves addition of an activating carbon dioxide molecule to a lysine in the active site. Formation of the carbamate is favored by an alkaline pH, the pH and the concentration of magnesium ions in the fluid compartment increases in the light. The role of changing pH and magnesium ion levels in the regulation of RuBisCO enzyme activity is discussed below, as shown in Figure 2, RuBisCO is one of many enzymes in the Calvin cycle. During carbon fixation, the molecules for RuBisCO are ribulose-1, 5-bisphosphate. RuBisCO also catalyses a reaction between ribulose-1, 5-bisphosphate and molecular oxygen instead of carbon dioxide, the extremely unstable molecule created by the initial carboxylation was unknown until 1988, when it was isolated. The 3-phosphoglycerate can be used to larger molecules such as glucose. Also, Rubisco side activities can lead to useless or inhibitory by-products, one product is xylulose-1, 5-bisphosphate. When molecular oxygen is the substrate, the products of the reaction are phosphoglycolate and 3-phosphoglycerate. Phosphoglycolate is recycled through a sequence of reactions called photorespiration, which involves enzymes and cytochromes located in the mitochondria, in this process, two molecules of phosphoglycolate are converted to one molecule of carbon dioxide and one molecule of 3-phosphoglycerate, which can reenter the Calvin cycle. Some of the phosphoglycolate entering this pathway can be retained by plants to other molecules such as glycine
23.
Uridine monophosphate synthetase
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Uridine monophosphate synthetase is the enzyme that catalyses the formation of uridine monophosphate, an energy-carrying molecule in many important biosynthetic pathways. In humans, the gene codes for this enzyme is located on the long arm of chromosome 3. This bifunctional enzyme has two domains, an orotate phosphoribosyltransferase subunit and an orotidine-5’-phosphate decarboxylase subunit. These two sites catalyze the last two steps of the de novo uridine monophosphate biosynthetic pathway, after addition of ribose-P to orotate by OPRTase to form orotidine-5’-monophosphate, OMP is decarboxylated to form uridine monophosphate by ODCase. In microorganisms, these two domains are separate proteins, but, in eukaryotes, the two catalytic sites are expressed on a single protein, uridine monophosphate synthetase. UMPS exists in forms, depending on external conditions. In vitro, monomeric UMPS, with a sedimentation coefficient S20, w of 3.6 will become a dimer, S20, in the presence of OMP, the product of the OPRTase, the dimer changes to a faster-sedimenting form S20, w 5.6. It is believed that the two catalytic sites fused into a single protein to stabilize its monomeric form. Other microorganisms with separated enzymes must retain higher concentrations to keep their enzymes in their more active dimeric form, fusion events between OPRTase and ODCase, which have led to the formation of the bifunctional enzyme UMPS, have occurred distinctly in different branches of the tree of life. Moreover, other groups, such as Fungi, conserve both enzymes as separate proteins. However important the order is, the evolutionary origin of each catalytic domain in UMPS is also a matter of study. Both OPRTase and ODCase have passed through lateral gene transfer, resulting in eukaryotes having enzymes from bacterial, for instance, Metazoa, Amoebozoa, Plantae, and Heterolobosea have eukaryotic ODCase and OPRTase, whereas Alveolata and stramenopiles have bacterial ones. Other rearrangements are also possible, since Fungi have bacterial OPRTase and eukaryotic ODCase, merging both the fusion order and evolutionary origin, organisms end up having fused UMPS where one of its catalytic domains comes from bacteria and the other from eukaryotes. The driving force for these fusion events seems to be the thermal stability. Homo sapiens OPRTase and ODCase activities lower to an extent when heated than the fused protein does. To determine the force of protein association, several experiments have been performed separating both domains and changing the linker peptide that keeps them together. In Plasmodium falciparum, the OPRTase-OMPDCase complex increases the kinetic and thermal stability compared to monofunctional enzymes. In H. sapiens, eventhough separate and fused domains have a similar activity, also, the linker peptide can be removed without inactivating catalysis
24.
Orotidine 5'-phosphate decarboxylase
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Orotidine 5’-phosphate decarboxylase or orotidylate decarboxylase is an enzyme involved in pyrimidine biosynthesis. It catalyzes the decarboxylation of orotidine monophosphate to form uridine monophosphate, the function of this enzyme is essential to the de novo biosynthesis of the pyrimidine nucleotides uridine triphosphate, cytidine triphosphate, and thymidine triphosphate. OMP decarboxylase is known for being an efficient catalyst capable of accelerating the uncatalyzed reaction rate by a factor of 1017. To put this in perspective, a reaction that would take 78 million years in the absence of enzyme takes 18 milliseconds when it is enzyme catalyzed and this extreme enzymatic efficiency is especially interesting because OMP decarboxylases uses no cofactor and contains no metal sites or prosthetic groups. The catalysis relies on a handful of charged amino acid residues positioned within the site of the enzyme. The exact mechanism by which OMP decarboxylase catalyzes its reaction has been a subject of scientific investigation. There have been multiple hypotheses about what form the state takes before protonation of the C6 carbon occurs to yield the final product. Current consensus suggests that the proceeds through a stabilized carbanion at the C6 after loss of carbon dioxide. This mechanism was suggested from studies investigating kinetic isotope effects in conjunction with competitive inhibition, in this mechanism the short-lived carbanion species is stabilized by a nearby lysine residue, before it is quenched by a proton. In yeast and bacteria, OMP decarboxylase is a single-function enzyme, however, in mammals, OMP decarboxylase is part of a single protein with two catalytic activities. In organisms utilizing OMP decarboxylase, this reaction is catalyzed by orotate phosphoribosyltransferase, mutations in the gene encoding OMP decarboxylase in yeast leads to auxotrophy in uracil. in addition, a function OMP decarboxylase renders yeast strains sensitive to the molecule 5-fluoroorotic acid
25.
Uroporphyrinogen III decarboxylase
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Uroporphyrinogen III decarboxylase is an enzyme that in humans is encoded by the UROD gene. The enzyme functions as a dimer in solution, and both the enzymes from human and tobacco have been crystallized and solved at good resolutions, uroD is regarded as an unusual decarboxylase, since it performs decarboxylations without the intervention of any cofactors, unlike the vast majority of decarboxylases. Its mechanism has recently proposed to proceed through substrate protonation by an arginine residue
26.
Aldehyde
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The group—without R—is the aldehyde group, also known as the formyl group. Aldehydes are common in organic chemistry, Aldehydes feature an sp2-hybridized, planar carbon center that is connected by a double bond to oxygen and a single bond to hydrogen. The C–H bond is not ordinarily acidic, because of resonance stabilization of the conjugate base, an α-hydrogen in an aldehyde is far more acidic, with a pKa near 15, compared to the acidity of a typical alkane. This acidification is attributed to the quality of the formyl center and the fact that the conjugate base. Related to, the group is somewhat polar. Aldehydes can exist in either the keto or the enol tautomer, keto-enol tautomerism is catalyzed by either acid or base. Usually the enol is the minority tautomer, but it is more reactive, the common names for aldehydes do not strictly follow official guidelines, such as those recommended by IUPAC, but these rules are useful. IUPAC prescribes the following nomenclature for aldehydes, Acyclic aliphatic aldehydes are named as derivatives of the longest carbon chain containing the aldehyde group, thus, HCHO is named as a derivative of methane, and CH3CH2CH2CHO is named as a derivative of butane. The name is formed by changing the suffix -e of the parent alkane to -al, so that HCHO is named methanal, in other cases, such as when a -CHO group is attached to a ring, the suffix -carbaldehyde may be used. Thus, C6H11CHO is known as cyclohexanecarbaldehyde, if the presence of another functional group demands the use of a suffix, the aldehyde group is named with the prefix formyl-. This prefix is preferred to methanoyl-, the word aldehyde was coined by Justus von Liebig as a contraction of the Latin alcohol dehydrogenatus. In the past, aldehydes were sometimes named after the corresponding alcohols, for example, the term formyl group is derived from the Latin word formica ant. This word can be recognized in the simplest aldehyde, formaldehyde, Aldehydes have properties that are diverse and that depend on the remainder of the molecule. Smaller aldehydes are more soluble in water, formaldehyde and acetaldehyde completely so, the volatile aldehydes have pungent odors. Aldehydes degrade in air via the process of autoxidation, the two aldehydes of greatest importance in industry, formaldehyde and acetaldehyde, have complicated behavior because of their tendency to oligomerize or polymerize. They also tend to hydrate, forming the geminal diol, the oligomers/polymers and the hydrates exist in equilibrium with the parent aldehyde. Aldehydes are readily identified by spectroscopic methods, using IR spectroscopy, they display a strong νCO band near 1700 cm−1. In their 1H NMR spectra, the formyl hydrogen center absorbs near δH =9 and this signal shows the characteristic coupling to any protons on the alpha carbon
27.
Fructose-bisphosphate aldolase
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Aldolase can also produce DHAP from other -ketose 1-phosphates such as fructose 1-phosphate and sedoheptulose 1, 7-bisphosphate. Gluconeogenesis and the Calvin cycle, which are anabolic pathways, use the reverse reaction, glycolysis, a catabolic pathway, uses the forward reaction. Aldolase is divided into two classes by mechanism, the word aldolase also refers, more generally, to an enzyme that performs an aldol reaction or its reverse, such as the one that forms sialic acid. Class I proteins form a protonated Schiff base intermediate linking a highly conserved active site lysine with the DHAP carbonyl carbon, additionally, tyrosine residues are crucial to this mechanism in acting as stabilizing hydrogen acceptors. Class II proteins use a different mechanism which polarizes the carbonyl group with a divalent cation like Zn2+, two histidine residues in the first half of the sequence of these homologs have been shown to be involved in binding zinc. The protein subunits of both classes each have an α/β domain folded into a TIM barrel containing the active site, several subunits are assembled into the complete protein. The two classes share little sequence identity, with few exceptions only class I proteins have been found in animals, plants, and green algae. With few exceptions only class II proteins have been found in fungi, both classes have been found widely in other eukaryotes and in bacteria. The two classes are present together in the same organism. Plants and algae have plastidal aldolase, sometimes a relic of endosymbiosis, a bifunctional fructose-bisphosphate aldolase/phosphatase, with class I mechanism, has been found widely in archaea and in some bacteria. The active site of this archaeal aldolase is also in a TIM barrel, gluconeogenesis and glycolysis share a series of six reversible reactions. In gluconeogenesis glyeraldehyde-3-phosphate is reduced to fructose 1, 6-bisphosphate with aldolase, in glycolysis fructose 1, 6-bisphosphate is made into glyceraldehyde-3-phosphate and dihydroxyacetone phosphate through the use of aldolase. The aldolase used in gluconeogenesis and glycolysis is a cytoplasmic protein, three forms of class I protein are found in vertebrates. Aldolase A is preferentially expressed in muscle and brain, aldolase B in liver, kidney, and in enterocytes, aldolases A and C are mainly involved in glycolysis, while aldolase B is involved in both glycolysis and gluconeogenesis. Some defects in aldolase B cause hereditary fructose intolerance, the metabolism of free fructose in liver exploits the ability of aldolase B to use fructose 1-phosphate as a substrate. Archaeal fructose-bisphosphate aldolase/phosphatase is presumably involved in gluconeogenesis because its product is fructose 6-phosphate, the Calvin cycle is a carbon fixation pathway. It and gluconeogenesis share a series of four reversible reactions, in both pathways 3-phosphoglycerate is reduced to fructose 1, 6-bisphosphate with aldolase catalyzing the last reaction. A fifth reaction, catalyzed in both pathways by fructose 1, 6-bisphosphatase, hydrolyzes the fructose 1-6-bisphosphate to fructose 6-phosphate and inorganic phosphate, the large decrease in free energy makes this reaction irreversible
28.
Aldolase A
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Aldolase A, also known as fructose-bisphosphate aldolase, is an enzyme that in humans is encoded by the ALDOA gene on chromosome 16. The protein encoded by this gene is an enzyme that catalyzes the reversible conversion of fructose-1, 6-bisphosphate to glyceraldehyde 3-phosphate. Three aldolase isozymes, encoded by three different genes, are expressed during development. Aldolase A is found in the embryo and is produced in even greater amounts in adult muscle. Aldolase A expression is repressed in adult liver, kidney and intestine and similar to aldolase C levels in brain, aldolase A deficiency has been associated with myopathy and hemolytic anemia. Alternative splicing and alternative promoter usage results in transcript variants. Related pseudogenes have been identified on chromosomes 3 and 10, ALDOA is a homotetramer and one of the three aldolase isozymes, encoded by three different genes. The ALDOA gene contains 8 exons and the 5 UTR IB, key amino acids responsible for its catalytic function have been identified. Residue Glu187 participates in multiple functions, including FBP aldolase catalysis, acid–base catalysis during substrate binding, dehydration, though ALDOA localizes to the nucleus, it lacks any known nuclear localization signals. In mammalian aldolase, the key amino acid residues involved in the reaction are lysine and tyrosine. The tyrosine acts as an efficient hydrogen acceptor while the lysine covalently binds, many bacteria use two magnesium ions in place of the lysine. Compound C05378 at KEGG Pathway Database, enzyme 4.1.2.13 at KEGG Pathway Database. Compound C00111 at KEGG Pathway Database, compound C00118 at KEGG Pathway Database. The numbering of the carbon atoms indicates the fate of the according to their position in fructose 6-phosphate. ALDOA is a key enzyme in the step of glycolysis. It catalyzes the conversion of fructose-1, 6-bisphosphate to glyceraldehydes-3-phosphate. As a result, it is a player in ATP biosynthesis. ALDOA likely regulates actin cytoskeleton remodeling through interacting with cytohesin-2 and Arf6, ALDOA is ubiquitously expressed in most tissues, though it is predominantly expressed in developing embryo and adult muscle
29.
Aldolase B
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In mammals, aldolase B is preferentially expressed in the liver, while aldolase A is expressed in muscle and erythrocytes and aldolase C is expressed in the brain. Slight differences in isozyme structure result in different activities for the two molecules, FBP and fructose 1-phosphate. Aldolase B exhibits no preference and thus catalyzes both reactions, while aldolases A and C prefer FBP, in humans, aldolase B is encoded by the ALDOB gene located on chromosome 9. The gene is 14,500 base pairs long and contains 9 exons, defects in this gene have been identified as the cause of hereditary fructose intolerance. The generic fructose bisphosphate aldolase enzyme cleaves a 6-carbon fructose sugar into two 3-carbon products in an aldol reaction. After Schiff base formation, the hydroxyl group on the fructose backbone is then deprotonated by an aspartate residue. Schiff base hydrolysis yields two 3-carbon products, depending on the reactant, F1P or FBP, the products are DHAP and glyceraldehyde or glyceraldehyde 3-phosphate, respectively. The ΔG°’ of this reaction is +23.9 kJ/mol, though the reaction may seem too uphill to occur, it is of note that under physiological conditions, the ΔG of the reaction falls to close to or below zero. For example, the ΔG of this reaction under physiological conditions in erythrocytes is -0.23 kJ/mol, click on genes, proteins and metabolites below to link to respective articles. Aldolase B is an enzyme, composed of four subunits with molecular weights of 36 kDa with local 222 symmetry. Each subunit has a weight of 36 kDa and contains an eight-stranded α/β barrel. Such regions have been denoted isozyme-specific regions and these regions are thought to give isozymes their specificities and structural differences. ISRs 1-3 are all found in exon 3 of the ALDOB gene, ISR4 is the most variable of the four and is found at the c-terminal end of the protein. ISRs 1-3 are found predominantly in patches on the surface of the enzyme and these patches do not overlap with the active site, indicating that ISRs may change specific isozyme substrate specificity from a distance or cause the C-terminus interactions with the active site. A recent theory suggests that ISRs may allow for different conformational dynamics in the enzyme that account for its specificity. Aldolase B plays a key role in metabolism as it catalyzes one of the major steps of the glycolytic-gluconeogenic pathway. Though it does catalyze the breakdown of glucose, it plays an important role in fructose metabolism, which occurs mostly in the liver, renal cortex. When fructose is absorbed, it is phosphorylated by fructokinase to form fructose 1-phosphate, aldolase B then catalyzes F1P breakdown into glyceraldehyde and DHAP
30.
Aldolase C
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Aldolase C, fructose-bisphosphate, is an enzyme that, in humans, is encoded by the ALDOC gene on chromosome 17. This gene encodes a member of the class I fructose-bisphosphate aldolase gene family, ALDOC is one of the three aldolase isozymes, encoded by three different genes. The amino acid sequence of ALDOC is highly similar to those of the other isozymes, sharing a 68% identity with ALDOB and 78% identity with ALDOA. In particular, the residues Asp33, Arg42, Lys107, Lys146, Glu187, Ser271, Arg303 and this active site is located in the center of the homotetrameric αβ-barrel structure of these aldolases. However, several structural details set ALDOC apart, for instance, the Arg303 residue in ALDOC adopts an intermediate conformation between the liganded and unliganded structures observed in the other isozymes. Also, the C-terminal region between Glu332 and Lys71 forms a bridge with the barrel region that is absent in the A and B isoforms. Moreover, the surface of ALDOC is more negatively charged. Four ALDOC-specific residues may be key for ALDOC-specific functions, ALDOC is a key enzyme in the fourth step of glycolysis, as well as in the reverse pathway gluconeogenesis. It catalyzes the conversion of fructose-1, 6-bisphosphate to glyceraldehydes-3-phosphate, or glyceraldehyde. As a result, it is a player in ATP biosynthesis. As an aldolase, ALDOC putatively also contributes to other moonlighting functions, for instance, it binds less tightly to the cytoskeleton than the other isozymes do, likely due to its more acidic pI. In addition, ALDOC participates in the pathway for lung epithelial cell function during hypoxia. ALDOC is ubiquitously expressed in most tissues, though it is expressed in brain, smooth muscle. However, since the ALDOA isoform is co-expressed with ALDOC in the nervous system. Moreover, its presence within other types, such as platelets and mast cells. Within cells, it localizes to the cytoplasm and this aldolase has been associated with cancer. ALDOC is found to be upregulated in the brains of schizophrenia patients and it is likely that ALDOC is involved in SCZ through its role in glycolysis, which is a central biochemical pathway in SCZ. Furthermore, ALDOC is reported to undergo oxidation in brains affected by mild cognitive impairment, click on genes, proteins and metabolites below to link to respective articles
. PMID 16894175.
