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.
Hydrolysis
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Hydrolysis usually means the cleavage of chemical bonds by the addition of water. When a carbohydrate is broken into its component sugar molecules by hydrolysis, generally, hydrolysis or saccharification is a step in the degradation of a substance. Hydrolysis can be the reverse of a reaction in which two molecules join together into a larger one and eject a water molecule. Thus hydrolysis adds water to break down, whereas condensation builds up by removing water, usually hydrolysis is a chemical process in which a molecule of water is added to a substance. Sometimes this addition causes both substance and water molecule to split into two parts, in such reactions, one fragment of the target molecule gains a hydrogen ion. A common kind of hydrolysis occurs when a salt of an acid or weak base is dissolved in water. Water spontaneously ionizes into hydroxide anions and hydronium cations, the salt also dissociates into its constituent anions and cations. For example, sodium acetate dissociates in water into sodium and acetate ions, sodium ions react very little with the hydroxide ions whereas the acetate ions combine with hydronium ions to produce acetic acid. In this case the net result is an excess of hydroxide ions. For example, dissolving sulfuric acid in water is accompanied by hydrolysis to give hydronium and bisulfate, for a more technical discussion of what occurs during such a hydrolysis, see Brønsted–Lowry acid–base theory. Acid–base-catalysed hydrolyses are very common, one example is the hydrolysis of amides or esters and their hydrolysis occurs when the nucleophile attacks the carbon of the carbonyl group of the ester or amide. In an aqueous base, hydroxyl ions are better nucleophiles than polar molecules such as water, in acids, the carbonyl group becomes protonated, and this leads to a much easier nucleophilic attack. The products for both hydrolyses are compounds with carboxylic acid groups, perhaps the oldest commercially practiced example of ester hydrolysis is saponification. It is the hydrolysis of a triglyceride with a base such as sodium hydroxide. During the process, glycerol is formed, and the fatty acids react with the base and these salts are called soaps, commonly used in households. In addition, in living systems, most biochemical reactions take place during the catalysis of enzymes, the catalytic action of enzymes allows the hydrolysis of proteins, fats, oils, and carbohydrates. As an example, one may consider proteases and they catalyse the hydrolysis of interior peptide bonds in peptide chains, as opposed to exopeptidases. However, proteases do not catalyse the hydrolysis of all kinds of proteins and their action is stereo-selective, Only proteins with a certain tertiary structure are targeted as some kind of orienting force is needed to place the amide group in the proper position for catalysis
10.
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
11.
Glycoside hydrolase
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Glycoside hydrolases assist in the hydrolysis of glycosidic bonds in complex sugars. Together with glycosyltransferases, glycosidases form the catalytic machinery for the synthesis. Glycoside hydrolases are found in all domains of life. In prokaryotes, they are both as intracellular and extracellular enzymes that are largely involved in nutrient acquisition. One of the important occurrences of glycoside hydrolases in bacteria is the enzyme beta-galactosidase, deficiency in specific lysosomal glycoside hydrolases can lead to a range of lysosomal storage disorders that result in developmental problems or death. Glycoside hydrolases are found in the tract and in saliva where they degrade complex carbohydrates such as lactose, starch. In the gut they are found as glycosylphosphatidyl anchored enzymes on endothelial cells, the enzyme O-GlcNAcase is involved in removal of N-acetylglucosamine groups from serine and threonine residues in the cytoplasm and nucleus of the cell. The glycoside hydrolases are involved in the biosynthesis and degradation of glycogen in the body, glycoside hydrolases are classified into EC3.2.1 as enzymes catalyzing the hydrolysis of O- or S-glycosides. Glycoside hydrolases can also be classified according to the outcome of the hydrolysis reaction. Glycoside hydrolases can also be classified as exo or endo acting, dependent upon whether they act at the end or in the middle, respectively, glycoside hydrolases may also be classified by sequence or structure based methods. Sequence-based classifications are among the most powerful method for suggesting function for newly sequenced enzymes for which function has not been biochemically demonstrated. A classification system for glycosyl hydrolases, based on similarity, has led to the definition of more than 100 different families. This classification is available on the CAZy web site, the database provides a series of regularly updated sequence based classification that allow reliable prediction of mechanism, active site residues and possible substrates. The online database is supported by CAZypedia, an encyclopedia of carbohydrate active enzymes. Based on three-dimensional structural similarities, the families have been classified into clans of related structure. Recent progress in glycosidase sequence analysis and 3D structure comparison has allowed the proposal of a hierarchical classification of the glycoside hydrolases. Again, two residues are involved, which are usually enzyme-borne carboxylates, one acts as a nucleophile and the other as an acid/base. In the first step the nucleophile attacks the centre, resulting in the formation of a glycosyl enzyme intermediate
12.
Sucrase-isomaltase
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Sucrase-isomaltase (EC3.2.1.10, is a glucosidase enzyme located in on the brush border of the small intestine. Sucrase-isomaltase is a type II transmembrane glycoprotein located in the border of the small intestine. It has preferential expression in the membranes of enterocytes. The enzyme’s purpose is to digest dietary carbohydrates such as starch, glucose, by further processing the broken-down products, energy in the form of ATP can be generated. The systematic name of systematic name of sucrase-isomaltase is oligosaccharide 6-alpha-glucohydrolase and this enzyme catalyses the following chemical reaction Hydrolysis of -alpha-D-glucosidic linkages in some oligosaccharides produced from starch and glycogen by enzyme EC3.2.1.1. Hydrolysis uses water to cleave chemical bonds, sucrase-isomaltase’s mechanism results in a net retention of configuration at the anomeric center. Sucrase-isomaltase consists of two subunits, sucrase and isomaltase. The subunits originate from a precursor, pro-SI. By heterodimerizing the two subunits, the complex is formed. The enzyme is anchored in the brush border membrane by a hydrophobic segment located near the N-terminal of the isomaltase subunit. Before the enzyme is anchored to the membrane, pro-SI is mannose-rich and glycosylated, it moves from the ER to the Golgi, the O-linked glycosylation is necessary to target the protein to the apical membrane. In addition, there is a segment that is both O-linked glycosylated and Ser/Thr-rich, sucrase-isomaltase is composed of duplicated catalytic domains, N- and C-terminal. Scientists have discovered the structure for N-terminal human sucrase-isomaltase in apo form to 3.2 Å. The crystal structure shows that exists as a monomer. The researchers claim that the observance of SI dimers is dependent on experimental conditions, ntSI’s four monomers, A, B, C, and D are included in the crystal asymmetric unit and have identical active sites. The active site is composed of a binding pocket including -1. The non-reducing end of substrates binds to the pocket, while the non-reducing sugar ring has interactions with the buried -1 subsite, the reducing ring has interactions with the surface exposed +1 subsite. Furthermore, hydrophobic interactions with Leu233, Trp327, Trp435, Phe479, Val605, kotalonal, the inhibitor, It interacts with the catalytic nucleophile Asp472 and acid base catalyst Asp571
13.
Maltase
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Maltase is an enzyme located in on the brush border of the small intestine that breaks down the disaccharide maltose. Maltase catalyzes the hydrolysis of maltose to the sugar glucose. This enzyme is found in plants, bacteria, and yeast, acid maltase deficiency is categorized into three separate types based on the age of onset of symptoms in the affected individual. In humans, maltase will break down the form of the maltose. Vampire bats are the only known to not exhibit intestinal maltase activity. Maltase-glucoamylase Sucrase-isomaltase Maltases at the US National Library of Medicine Medical Subject Headings Structure and evolution of the mammalian maltase-glucoamylase and sucrase-isomaltase
14.
Trehalase
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Trehalase is a glycoside hydrolase enzyme located in on the brush border of the small intestine that catalyzes the conversion of trehalose to glucose. It is found in most animals, the non-reducing disaccharide trehalose is one of the most important storage carbohydrates, which is present in almost all forms of life except mammals. The disaccharide is hydrolyzed into two molecules of glucose by the enzyme trehalase, there are two types of trehalases found in Saccharomyces cerevisiae, viz. neutral trehalase and acid trehalase classified according to their pH optima. NT has an optimum pH of 7.0, while that of AT is 4.5, recently it has been reported that more than 90% of total AT activity in S. cerevisiae is extracellular and cleaves extracellular trehalose into glucose in the periplasmic space. One molecule of trehalose is hydrolyzed to two molecules of glucose by the enzyme trehalase, enzymatic hydrolysis of trehalose was first observed in Aspergillus niger by Bourquelot in 1893. Fischer reported this reaction in S. cerevisiae in 1895, since then the trehalose hydrolyzing enzyme, trehalase has been reported from many other organisms including plants and animals. Though trehalose is not known to be present in mammals, trehalase enzyme is found to be present in the brush border membrane. In the intestine the function of enzyme is to hydrolyze ingested trehalose. Individuals with a defect in their intestinal trehalase have diarrhea when they eat foods with high trehalose content, trehalose hydrolysis by trehalase enzyme is an important physiological process for various organisms, such as fungal spore germination, insect flight, and the resumption of growth in resting cells. Trehalose has been reported to be present as a carbohydrate in Pseudomonas, Bacillus, Rhizobium and in several actinomycetes. Most of the trehalase enzymes isolated from bacteria have as optimum pH of 6. 5-7.5, the trehalase enzyme of Mycobacterium smegmatis is a membrane bound protein. Periplasmic trehalase of Escherichia coli K12 is induced by growth at high osmolarity, the hydrolysis of trehalose into glucose takes place in the periplasm, and the glucose is then transported into the bacterial cell. Another cytoplasmic trehalase has also reported from E. coli. The gene, which encodes this cytoplasmic trehalase, exhibits high homology to the periplasmic trehalase, but, the enzyme trehalase is ubiquitous in plants. This is puzzling that trehalase is present in plants, though its substrate is absent. No clear role has been demonstrated for trehalase activity in plants and it has been suggested that trehalases could play a role in defense mechanisms or the enzyme could play a role in the degradation of trehalose derived from plant-associated microorganisms. In S. cerevisiae at least two distinct trehalases have been reported, one was reported to be regulated by cAMP-dependent phosphorylation. This enzyme activity was found in the cytosol, a second trehalase activity was found in the vacuoles of the same oraganism12
15.
Lactase
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Lactase is an enzyme produced by many organisms. It is located in the border of the small intestine of humans. Lactase is essential to the digestion of whole milk, it breaks down lactose. Lacking lactase, a person consuming dairy products may experience the symptoms of lactose intolerance, Lactase can be purchased as a food supplement, and is added to milk to produce lactose-free milk products. Lactase, a part of the family of enzymes, is a glycoside hydrolase involved in the hydrolysis of the disaccharide lactose into constituent galactose and glucose monomers. Lactase is present predominantly along the brush border membrane of the differentiated enterocytes lining the villi of the small intestine, in humans, lactase is encoded by the LCT gene. Lactase supplements are used to treat lactose intolerance. Lactase produced commercially can be extracted both from yeasts such as Kluyveromyces fragilis and Kluyveromyces lactis and from molds, such as Aspergillus niger, Lactase is also used to screen for blue white colonies in the multiple cloning sites of various plasmid vectors in Escherichia coli or other bacteria. Mechanism The optimum temperature for human lactase is about 37 °C for its activity and has an optimum pH of 6, in metabolism, the β-glycosidic bond in D-lactose is hydrolyzed to form D-galactose and D-glucose, which can be absorbed through the intestinal walls and into the bloodstream. The overall reaction that lactase catalyzes is C12H22O11 + H2O → C6H12O6 + C6H12O6 + heat, the catalytic mechanism of D-lactose hydrolysis retains the substrate anomeric configuration in the products. While the details of the mechanism are uncertain, the retention is achieved through a double displacement reaction. Studies of E. coli lactase have proposed that hydrolysis is initiated when a nucleophile on the enzyme attacks from the axial side of the galactosyl carbon in the β-glycosidic bond. The removal of the D-glucose leaving group may be facilitated by Mg-dependent acid catalysis, the enzyme is liberated from the α-galactosyl moiety upon equatorial nucleophilic attack by water, which produces D-galactose. Substrate modification studies have demonstrated that the 3′-OH and 2′-OH moieties on the ring are essential for enzymatic recognition. The 3′-hydroxy group is involved in binding to the substrate while the 2′- group is not necessary for recognition. This is demonstrated by the fact that a 2-deoxy analog is a competitive inhibitor. Elimination of specific hydroxyl groups on the glucopyranose moiety does not completely eliminate catalysis, Lactase also catalyzes the conversion of phlorizin to phloretin and glucose. Preprolactase, the primary product, has a single polypeptide primary structure consisting of 1927 amino acids
16.
Cellulase
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Cellulase is any of several enzymes produced chiefly by fungi, bacteria, and protozoans that catalyze cellulolysis, the decomposition of cellulose and of some related polysaccharides. The name is used for any naturally occurring mixture or complex of various such enzymes. Cellulases break down the molecule into monosaccharides such as beta-glucose. Cellulose breakdown is of economic importance, because it makes a major constituent of plants available for consumption. The specific reaction involved is the hydrolysis of the 1, 4-beta-D-glycosidic linkages in cellulose, hemicellulose, lichenin, because cellulose molecules bind strongly to each other, cellulolysis is relatively difficult compared to the breakdown of other polysaccharides such as starch. Most mammals have very limited ability to digest dietary fibres such as cellulose by themselves. In many herbivorous animals such as ruminants like cattle and sheep, cellulases are produced by a few types of animals, such as some termites. Several different kinds of cellulases are known, which differ structurally and mechanistically.5 cellulase, enzymes that cleave lignin are occasionally called cellulases, but this is usually considered erroneous. Five general types of cellulases based on the type of reaction catalyzed, exocellulases or cellobiohydrolases cleave two to four units from the ends of the exposed chains produced by endocellulase, resulting in tetrasaccharides or disaccharides, such as cellobiose. Exocellulases are further classified into type I, that work processively from the end of the cellulose chain, and type II. Cellobiases or beta-glucosidases hydrolyse the product into individual monosaccharides. Oxidative cellulases depolymerize cellulose by radical reactions, as for instance cellobiose dehydrogenase, cellulose phosphorylases depolymerize cellulose using phosphates instead of water. Avicelase has almost exclusively exo-cellulase activity, since avicel is a highly micro-crystalline substrate, within the above types there are also progressive and nonprogressive types. Progressive cellulase will continue to interact with a single polysaccharide strand, cellulase action is considered to be synergistic as all three classes of cellulase can yield much more sugar than the addition of all three separately. Most fungal cellulases have a structure, with one catalytic domain and one cellulose binding domain. This structure is adapted for working on a substrate. However, there are also cellulases that lack cellulose binding domains and these enzymes might have a swelling function. In many bacteria, cellulases in-vivo are complex enzyme structures organized in supramolecular complexes, numerous signature sequences known as dockerins and cohesins have been identified in the genomes of bacteria that produce cellulosomes
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Alpha-glucosidase
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Alpha-glucosidase is a glucosidase located in the brush border of the small intestine that acts upon α bonds. This is in contrast to beta-glucosidase, Alpha-glucosidase breaks down starch and disaccharides to glucose. Maltase, an enzyme that cleaves maltose, is nearly functionally equivalent. Other glucosidases include, Cellulase Beta-glucosidase Debranching enzyme Alpha-glucosidase hydrolyzes terminal non-reducing -linked alpha-glucose residues to release a single alpha-glucose molecule, Alpha-glucosidase is a carbohydrate-hydrolase that releases alpha-glucose as opposed to beta-glucose. Beta-glucose residues can be released by glucoamylase, a similar enzyme. The substrate selectivity of alpha-glucosidase is due to subsite affinities of the active site. Two proposed mechanisms include a displacement and an oxocarbenium ion intermediate. Rhodnius prolixus, an insect, forms hemozoin during digestion of host hemoglobin. Hemozoin synthesis is dependent on the binding site of alpha-glucosidase. Trout liver alpha-glucosidases were extracted and characterized and it was shown that for one of the trout liver alpha-glucosidases maximum activity of the enzyme was increased by 80% during exercise in comparison to a resting trout. This change was shown to correlate to an activity increase for liver glycogen phosphorylase and it is proposed that alpha-glucosidase in the glucosidic path plays an important part in complementing the phosphorolytic pathway in the liver’s metabolic response to energy demands of exercise. Yeast and rat small intestinal alpha-glucosidases have been shown to be inhibited by several groups of flavonoids, alpha-glucosidases can potentially be split, according to primary structure, into two families. The gene coding for human lysosomal alpha-glucosidase is about 20 kb long, human lysosomal alpha-glucosidase has been studied for the significance of the Asp-518 and other residues in proximity of the enzyme’s active site. It was found that substituting Asp-513 with Glu-513 interferes with posttranslational modification, additionally, the Trp-516 and Asp-518 residues have been deemed critical for the enzyme’s catalytic functionality. Kinetic changes in alpha-glucosidase have been shown to be induced by such as guanidinium chloride. These denaturants cause loss of activity and conformational change, a loss of enzyme activity occurs at much lower concentrations of denaturant than required for conformational changes. This leads to a conclusion that the active site conformation is less stable than the whole enzyme conformation in response to the two denaturants. Pompe disease, a disorder in which alpha-glucosidase is deficient, in 2006, the drug alglucosidase alfa became the first released treatment for Pompe disease and acts as an analog to alpha-glucosidase
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Acid alpha-glucosidase
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Lysosomal alpha-glucosidase, also called α-1, 4-glucosidase and acid maltase, is an enzyme that in humans is encoded by the GAA gene. Errors in this gene cause glycogen storage disease type II and this gene encodes acid alpha-glucosidase, which is essential for the degradation of glycogen to glucose in lysosomes. Different forms of acid alpha-glucosidase are obtained by proteolytic processing, defects in this gene are the cause of glycogen storage disease II, also known as Pompe disease, which is an autosomal recessive disorder with a broad clinical spectrum. Three transcript variants encoding the protein have been found for this gene. GeneReview/NIH/UW entry on Glycogen Storage Disease Type II Human GAA genome location and GAA gene details page in the UCSC Genome Browser
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Beta-glucosidase
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Beta-glucosidase catalyzes the hydrolysis of the glycosidic bonds to terminal non-reducing residues in beta-D-glucosides and oligosaccharides, with release of glucose. Cellulose is a composed of beta-1, 4-linked glucosyl residues. Cellulases, cellobiosidases, and beta-glucosidases are required by organisms that can consume it and these enzymes are powerful tools for degradation of plant cell walls by pathogens and other organisms consuming plant biomass
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Glycogen debranching enzyme
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A debranching enzyme is a molecule that helps facilitate the breakdown of glycogen, which serves as a store of glucose in the body, through glucosyltransferase and glucosidase activity. Together with phosphorylases, debranching enzymes mobilize glucose reserves from glycogen deposits in the muscles and this constitutes a major source of energy reserves in most organisms. Glycogen breakdown is highly regulated in the body, especially in the liver, by various hormones including insulin and glucagon, when glycogen breakdown is compromised by mutations in the glycogen debranching enzyme, metabolic diseases such as Glycogen storage disease type III can result. Glucosyltransferase and glucosidase are performed by an enzyme in mammals, yeast, and some bacteria. Proteins that catalyze both functions are referred to as glycogen debranching enzymes, when glucosyltransferase and glucosidase are catalyzed by distinct enzymes, glycogen debranching enzyme usually refers to the glucosidase enzyme. In some literature, an enzyme capable only of glucosidase is referred to as a debranching enzyme, together with phosphorylase, glycogen debranching enzymes function in glycogen breakdown and glucose mobilization. When phosphorylase has digested a glycogen branch down to four glucose residues, Glycogen debranching enzymes assist phosphorylase, the primary enzyme involved in glycogen breakdown, mobilize glycogen stores. Phosphorylase can only cleave α-1, 4- glycosidic bond between adjacent glucose molecules in glycogen but branches exist as α-1,6 linkages. The mechanism by which the glucosidase cleaves the α -1, 6-linkage is not fully known because the amino acids in the site have not yet been identified. It is thought to proceed through a two step acid base assistance type mechanism, with an oxocarbenium ion intermediate, and retention of configuration in glucose. This is a method through which to cleave bonds, with an acid below the site of hydrolysis to lend a proton. These acids and bases are amino acid chains in the active site of the enzyme. A scheme for the mechanism is shown in the figure below, thus the debranching enzymes, transferase and α-1, 6- glucosidase converts the branched glycogen structure into a linear one, paving the way for further cleavage by phosphorylase. In E. coli and other bacteria, glucosyltransferase and glucosidase functions are performed by two distinct enzymes, in E. coli, Glucose transfer is performed by 4-alpha-glucanotransferase, a 78.5 kDa protein coded for by the gene malQ. A second protein, referred to as debranching enzyme, performs α-1 and this enzyme has a molecular mass of 73.6 kDa, and is coded for by the gene glgX. Activity of the two enzymes is not always necessarily coupled, in E. coli glgX selectively catalyzes the cleavage of 4-subunit branches, without the action of glucanotransferase. The product of cleavage, maltotetraose, is further degraded by maltodextrin phosphorylase. E. coli GlgX is structurally similar to the protein isoamylase, the monomeric protein contains a central domain in which eight parallel beta-strands are surrounded by eight parallel alpha strands
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Amylase
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An amylase is an enzyme that catalyses the hydrolysis of starch into sugars. Amylase is present in the saliva of humans and some other mammals, foods that contain large amounts of starch but little sugar, such as rice and potatoes, may acquire a slightly sweet taste as they are chewed because amylase degrades some of their starch into sugar. The pancreas and salivary gland make amylase to hydrolyse dietary starch into disaccharides and trisaccharides which are converted by enzymes to glucose to supply the body with energy. Plants and some also produce amylase. As diastase, amylase was the first enzyme to be discovered and isolated, specific amylase proteins are designated by different Greek letters. All amylases are glycoside hydrolases and act on α-1, 4-glycosidic bonds, because it can act anywhere on the substrate, α-amylase tends to be faster-acting than β-amylase. In animals, it is a digestive enzyme, and its optimum pH is 6. 7–7.0. In human physiology, both the salivary and pancreatic amylases are α-amylases, the α-amylases form is also found in plants, fungi and bacteria Another form of amylase, β-amylase is also synthesized by bacteria, fungi, and plants. Working from the end, β-amylase catalyzes the hydrolysis of the second α-1,4 glycosidic bond. During the ripening of fruit, β-amylase breaks starch into maltose, both α-amylase and β-amylase are present in seeds, β-amylase is present in an inactive form prior to germination, whereas α-amylase and proteases appear once germination has begun. Many microbes also produce amylase to degrade extracellular starches, animal tissues do not contain β-amylase, although it may be present in microorganisms contained within the digestive tract. The optimum pH for β-amylase is 4. 0–5.0 γ-Amylase will cleave α glycosidic linkages, as well as the last αglycosidic linkages at the end of amylose and amylopectin. The γ-amylase has most acidic optimum pH of all amylases because it is most active around pH3, alpha and beta amylases are important in brewing beer and liquor made from sugars derived from starch. In fermentation, yeast ingest sugars and excrete alcohol, in beer and some liquors, the sugars present at the beginning of fermentation have been produced by mashing grains or other starch sources. Different temperatures optimize the activity of alpha or beta amylase, resulting in different mixtures of fermentable and unfermentable sugars, in selecting mash temperature and grain-to-water ratio, a brewer can change the alcohol content, mouthfeel, aroma, and flavor of the finished beer. In some historic methods of producing alcoholic beverages, the conversion of starch to sugar starts with the brewer chewing grain to mix it with saliva and this practice is no longer widely in use. Amylases are used in breadmaking and to break down sugars, such as starch. Yeast then feeds on these simple sugars and converts it into the products of alcohol
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Alpha-amylase
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α-Amylase is a protein enzyme EC3.2.1.1 that hydrolyses alpha bonds of large, alpha-linked polysaccharides, such as starch and glycogen, yielding glucose and maltose. It is the form of amylase found in humans and other mammals. It is also present in seeds containing starch as a food reserve, although found in many tissues, amylase is most prominent in pancreatic juice and saliva, each of which has its own isoform of human α-amylase. They behave differently on isoelectric focusing, and can also be separated in testing by using specific monoclonal antibodies, in humans, all amylase isoforms link to chromosome 1p21. Amylase is found in saliva and breaks starch into maltose and dextrin and this form of amylase is also called ptyalin /ˈtaɪəlɪn/ It will break large, insoluble starch molecules into soluble starches producing successively smaller starches and ultimately maltose. Ptyalin acts on linear α glycosidic linkages, but compound hydrolysis requires an enzyme that acts on branched products, salivary amylase is inactivated in the stomach by gastric acid. In gastric juice adjusted to pH3.3, ptyalin was totally inactivated in 20 minutes at 37 °C, in contrast, 50% of amylase activity remained after 150 minutes of exposure to gastric juice at pH4.3. Both starch, the substrate for ptyalin, and the product are able to protect it against inactivation by gastric acid. The number of gene copies correlates with the levels of salivary amylase, gene copy number is associated with apparent evolutionary exposure to high-starch diets. For example, a Japanese individual had 14 copies of the amylase gene, the Japanese diet has traditionally contained large amounts of rice starch. In contrast, a Biaka individual carried six copies, the Biaka are rainforest hunter-gatherers who have traditionally consumed a low-starch diet. Perry and colleagues speculated the increased number of the salivary amylase gene may have enhanced survival coincident to a shift to a starchy diet during human evolution. Pancreatic α-amylase randomly cleaves the α glycosidic linkages of amylose to yield dextrin, maltose and it adopts a double displacement mechanism with retention of anomeric configuration. The test for amylase is easier to perform than that for lipase, making it the primary test used to detect, medical laboratories will usually measure either pancreatic amylase or total amylase. If only pancreatic amylase is measured, an increase will not be noted with mumps or other salivary gland trauma, however, because of the small amount present, timing is critical when sampling blood for this measurement. Blood should be taken soon after a bout of pancreatitis pain, salivary α-amylase has been used as a biomarker for stress that does not require a blood draw. Five to 10 times the ULN may indicate ileus or duodenal disease or renal failure, α-Amylase is used in ethanol production to break starches in grains into fermentable sugars. The first step in the production of corn syrup is the treatment of cornstarch with α-amylase
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Chitinase
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Chitinases are hydrolytic enzymes that break down glycosidic bonds in chitin. Chitinivorous organisms include bacteria, which may be pathogenic or detritivorous. They attack living arthropods, zooplankton or fungi or they may degrade the remains of these organisms, fungi, such as Coccidioides immitis, also possess degradative chitinases related to their role as detritivores and also to their potential as arthropod pathogens. Chitinases are also present in plants, some of these are pathogenesis related proteins that are induced as part of acquired resistance. Expression is mediated by the NPR1 gene and the salicylic acid pathway, other plant chitinases may be required for creating fungal symbioses. Like cellulose, chitin is an abundant biopolymer that is resistant to degradation. It is typically not digested by animals, though certain fish are able to digest chitin and it is currently assumed that chitin digestion by animals requires bacterial symbionts and lengthy fermentations, similar to cellulase digestion by ruminants. Nevertheless, chitinases have been isolated from the stomachs of certain mammals, Chitinase activity can also be detected in human blood and possibly cartilage. As in plant chitinases this may be related to pathogen resistance, chitinases produced in the human body may be related in response to allergies, and asthma has been linked to enhanced chitinase expression levels. Human chitinases may explain the link between some of the most common allergies and worm infections, as part of one version of the hygiene hypothesis. Finally, the link between chitinases and salicylic acid in plants is well established—but there is a link between salicylic acid and allergies in humans. Chitinases occur naturally in many common foods, bananas, chestnuts, kiwis, avocados, papaya, and tomatoes, for example, all contain significant levels of chitinase, as defense against fungal and invertebrate attack. Stress, or environmental signals like ethylene gas, may stimulate increased production of chitinase, chitinases have a wealth of applications, some of which has already been realized by the industry. Chitin Ligninase Chitinase at the US National Library of Medicine Medical Subject Headings The X-ray structure of a chitinase from the pathogenic fungus Coccidioides immitis
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Lysozyme
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Lysozyme, also known as muramidase or N-acetylmuramide glycanhydrolase is an antimicrobial enzyme produced by animals that forms part of the innate immune system. This hydrolysis in turn compromises the integrity of cell walls causing lysis of the bacteria. Lysozyme is abundant in a number of secretions, such as tears, saliva, human milk and it is also present in cytoplasmic granules of the macrophages and the polymorphonuclear neutrophils. Large amounts of lysozyme can be found in egg white, c-type lysozymes are closely related to alpha-lactalbumin in sequence and structure, making them part of the same family. In humans, the enzyme is encoded by the LYZ gene. Lysozyme is thermally stable, with a melting point reaching up to 72 ℃ at pH5.0, however, in human milk it loses activity very fast at that temperature. In a large range of pH lysozyme can survive, the enzyme functions by attacking, hydrolyzing, and breaking glycosidic bonds in peptidoglycans. The enzyme can also break glycosidic bonds in chitin, although not as effective as true chitinases, the ability to break down both oligosaccharides suggests a similar mechanism between the breakdown of the two molecules. Lysozymes active site binds the peptidoglycan molecule in the prominent cleft between its two domains and it attacks peptidoglyans, its natural substrate, between N-acetylmuramic acid and the fourth carbon atom of N-acetylglucosamine. Shorter saccharides like tetrasaccharide have also shown to be viable substrates, chitin has also been show to be a viable lysozyme substrate. Artificial substrates have also developed and used in lysozyme. The Phillips Mechanism proposed that the enzymes catalytic power came from both steric strain on the substrate and electrostatic stabilization of the oxo-carbenium intermediate. From x-ray crystallography data, Phillips proposed the lysozymes active site binds to a hexasaccharide, the lysozyme distorts the fourth sugar in hexasaccharide into a half-chair conformation. In this stressed state, the bond is more easily broken. An ionic intermediate containing an oxo-carbenium is created as a result of the glycosidic bond breaking, thus distortion causing the substrate molecule to adopt a strained conformation similar to that of the transition state will lower the energy barrier of the reaction. This oxo-carbonium intermediate was proposed to be electrostatically stabilized by Arieh Warshel in 1978. Residues in the site, such as aspartate and glutamate are able to stabilize this intermediate. The electrostatic stabilization argument was based on comparison to bulk water, in Warshels model, the enzyme acts as a super-sovlent, which fixes the orientation of ion pairs and provides super-solvation, and especially lower the energy when to ions are close to each other
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Neuraminidase
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Neuraminidase enzymes are glycoside hydrolase enzymes that cleave the glycosidic linkages of neuraminic acids. Neuraminidase enzymes are a family, found in a range of organisms. The best-known neuraminidase is the viral neuraminidase, a target for the prevention of the spread of influenza infection. The viral neuraminidases are frequently used as antigenic determinants found on the surface of the influenza virus, some variants of the influenza neuraminidase confer more virulence to the virus than others. Other homologues are found in cells, which have a range of functions. At least four mammalian sialidase homologues have been described in the human genome, sialidase activities include assistance in the mobility of virus particles through the respiratory tract mucus and in the elution of virion progeny from the infected cell. Swiss-Prot lists 137 types of neuraminidase from various species as of October 18,2006, nine subtypes of influenza neuraminidase are known, many occur only in various species of duck and chicken. Subtypes N1 and N2 have been linked to epidemics in man. It has a head consisting of four co-planar and roughly spherical subunits, and it comprises a single polypeptide chain that is oriented in the opposite direction to the hemagglutinin antigen. The composition of the polypeptide is a chain of six conserved polar amino acids, followed by hydrophilic. β-Sheets predominate as the level of protein conformation. The enzymatic mechanism of influenza virus sialidase has been studied by Taylor et al. shown in Figure 1, the enzyme catalysis process has four steps. The first step involves the distortion of the α-sialoside from a 2C5 chair conformation to a pseudoboat conformation when the sialoside binds to the sialidase, the second step leads to an oxocarbocation intermediate, the sialosyl cation. The third step is the formation of Neu5Ac initially as the α-anomer, there are two major proteins on the surface of influenza virus particles. One is the lectin haemagglutinin protein with three relatively shallow sialic acid-binding sites and the other is enzyme sialidase with the site in a pocket. After the X-ray crystal structures of several influenza virus sialidases were available, the unsaturated sialic acid derivative 2-deoxy-2, 3-didehydro-D-N-acetylneuraminic acid, a sialosyl cation transition-state analogue, is believed the most potent inhibitor core template. Structurally modified Neu5Ac2en derivatives may give more effective inhibitors, many Neu5Ac2en-based compounds have been synthesized and tested for their influenza virus sialidase inhibitory potential. A series of amide-linked C9 modified Neu5Ac2en have been reported by Megesh, glycoside hydrolase Neuraminidase inhibitors Neuraminidase at the US National Library of Medicine Medical Subject Headings Orthomyxoviruses, Robert B
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NEU1
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Sialidase 1, also known as NEU1 is a mammalian lysosomal neuraminidase enzyme which in humans is encoded by the NEU1 gene. The protein encoded by this gene encodes the enzyme, which cleaves terminal sialic acid residues from substrates such as glycoproteins. In the lysosome, this enzyme is part of a complex together with beta-galactosidase. Mutations in this gene can lead to sialidosis, deficiencies in the human enzyme NEU1 leads to sialidosis, a rare lysosomal storage disease. Sialidase has also shown to enhance recovery from spinal cord contusion injury when injected in rats. NEU1 has been shown to interact with Cathepsin A
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NEU3
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Sialidase-3 is an enzyme that in humans is encoded by the NEU3 gene. This gene product belongs to a family of enzymes which remove sialic acid residues from glycoproteins. It is localized in the membrane, and its activity is specific for gangliosides. It may play a role in modulating the ganglioside content of the lipid bilayer, NEU3 has been shown to interact with Grb2
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Viral neuraminidase
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Viral neuraminidase is a type of neuraminidase found on the surface of influenza viruses that enables the virus to be released from the host cell. Neuraminidases are enzymes that cleave sialic acid groups from glycoproteins and are required for influenza virus replication, when influenza virus replicates, it attaches to the interior cell surface using hemagglutinin, a molecule found on the surface of the virus that binds to sialic acid groups. Sialic acids are found on various glycoproteins at the host cell surface, in order for the virus to be released from the cell, neuraminidase must enzymatically cleave the sialic acid groups from host glycoproteins. Since the cleavage of the groups is an integral part of influenza replication. A single hemagglutinin-neuraminidase protein can combine neuraminidase and hemagglutinin functions, such as in mumps virus, the enzyme helps viruses to be released from a host cell. Influenza virus membranes contain two glycoproteins, hemagglutinin and neuraminidase, while the hemagglutinin on the surface of the virion is needed for infection, its presence inhibits release of the particle after budding. Viral neuraminidase cleaves terminal neuraminic acid residues from glycan structures on the surface of the infected cell and this promotes the release of progeny viruses and the spread of the virus from the host cell to uninfected surrounding cells. Neuraminidase also cleaves sialic acid residues from viral proteins, preventing aggregation of viruses, Neuraminidase has been targeted in structure-based enzyme inhibitor design programmes that have resulted in the production of two drugs, zanamivir and oseltamivir. Administration of neuraminidase inhibitors is a treatment that limits the severity, on February 27,2005, a 14-year-old Vietnamese girl was documented to be carrying an H5N1 influenza virus strain that was resistant to the drug oseltamivir. The drug is used to treat patients that have contracted influenza, however, the Vietnamese girl who had received a prophylactic dose was found to be non-responsive to the medication. In growing fears of an avian flu pandemic, scientists began to look for a cause of resistance to the Tamiflu medication. The cause was determined to be a substitution at position 274 in its neuraminidase protein. A new class of inhibitors that covalently attach to the enzyme have shown activity against drug-resistant virus in vitro. In ideal circumstances, influenza virus neuraminidase should act on the type of receptor the virus hemagglutinin binds to. It is not quite clear how the virus manages to function there is no close match between the specificities of NA and HA. Neuraminidase enzymes can have endo- or exo-glycosidase activity, and are classified as EC3.2.1.29, H5N1 genetic structure Antigenic shift Influenza research Hemagglutinin Influenza Research Database Database of influenza sequences. Proteopedia Influenza Neuraminidase, Tamiflu and Relenza Avian Influenza Neuraminidase, Tamiflu and Relenza
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Alpha-galactosidase
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Alpha-galactosidase is a glycoside hydrolase enzyme that hydrolyses the terminal alpha-galactosyl moieties from glycolipids and glycoproteins. It is encoded by the GLA gene, two recombinant forms of alpha-galactosidase are called agalsidase alfa and agalsidase beta. This enzyme is a glycoprotein that hydrolyses the terminal alpha-galactosyl moieties from glycolipids. It predominantly hydrolyzes ceramide trihexoside, and it can catalyze the hydrolysis of melibiose into galactose and glucose, two enzyme replacement therapies are available to functionally compensate for alpha-galactosidase deficiency. Agalsidase alpha and beta are both recombinant forms of the human α-galactosidase A enzyme and both have the amino acid sequence as the native enzyme. Agalsidase alpha and beta differ in the structures of their side chains. The pharmaceutical company Shire manufactures agalsidase alfa under the trade name Replagal as a treatment for Fabrys disease, FDA approval was applied for the United States. However, in 2012, Shire withdrew their application for approval in the United States citing that the agency will require additional clinical trials before approval, the pharmaceutical company Genzyme produces synthetic agalsidase beta under the trade name Fabrazyme for treatment of Fabrys disease. In 2009, contamination at Genzymes Allston, Massachusetts plant caused a shortage of Fabrazyme. Some patients have petitioned to break the companys patent on the drug under the provisions of the Bayh–Dole Act. Alpha-galactosidase is an ingredient in Beano, CVS BeanAid. These products are marketed to reduce stomach gas production after eating foods known to cause gas, there are dozens of generic brands containing the enzyme in the United States. It is optimally active at 55 degrees C, after which its half-life is 120 minutes and this article incorporates text from the United States National Library of Medicine, which is in the public domain
