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D-alanine—D-alanine Ligase
In enzymology, a D-alanine—D-alanine ligase () is an enzyme that catalysis, catalyzes the chemical reaction :ATP + 2 D-alanine \rightleftharpoons ADP + phosphate + D-alanyl-D-alanine Thus, the two substrate (biochemistry), substrates of this enzyme are adenosine triphosphate, ATP and D-alanine, whereas its 3 product (chemistry), products are adenosine diphosphate, ADP, phosphate, and D-alanyl-D-alanine. This enzyme belongs to the family of ligases, specifically those forming carbon-nitrogen bonds as acid-D-amino-acid ligases (peptide synthases). The List of enzymes, systematic name of this enzyme class is D-alanine:D-alanine ligase (ADP-forming). Other names in common use include alanine:alanine ligase (ADP-forming), and alanylalanine synthetase. This enzyme participates in d-alanine metabolism and peptidoglycan biosynthesis. Phosphinate and D-cycloserine are known to enzyme inhibitor, inhibit this enzyme. The N-terminal region of the D-alanine—D-alanine ligase is thought ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
N-terminus
The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the amine group is bonded to the carboxylic group of another amino acid, making it a chain. That leaves a free carboxylic group at one end of the peptide, called the C-terminus, and a free amine group on the other end called the N-terminus. By convention, peptide sequences are written N-terminus to C-terminus, left to right (in LTR writing systems). This correlates the translation direction to the text direction, because when a protein is translated from messenger RNA, it is created from the N-terminus to the C-terminus, as amino acids are added to the carboxyl end of the protein. Chemistry Each amino acid has an amine group and a carboxylic group. Amino acids link to one another by peptide bonds which form through a dehydration reaction that ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Enzymes
This article lists enzymes by their classification in the International Union of Biochemistry and Molecular Biology's Enzyme Commission (EC) numbering system. * List of EC numbers (EC 5) * List of EC numbers (EC 6) :Oxidoreductases (EC 1) (Oxidoreductase) *Dehydrogenase * Luciferase *DMSO reductase :EC 1.1 (act on the CH-OH group of donors) * :EC 1.1.1 (with NAD+ or NADP+ as acceptor) ** Alcohol dehydrogenase (NAD) ** Alcohol dehydrogenase (NADP) **Homoserine dehydrogenase ** Aminopropanol oxidoreductase **Diacetyl reductase **Glycerol dehydrogenase **Propanediol-phosphate dehydrogenase ** glycerol-3-phosphate dehydrogenase (NAD+) ** D-xylulose reductase **L-xylulose reductase **Lactate dehydrogenase **Malate dehydrogenase **Isocitrate dehydrogenase ** HMG-CoA reductase * :EC 1.1.2 (with a cytochrome as acceptor) * :EC 1.1.3 (with oxygen as acceptor) **Glucose oxidase **L-gulonolactone oxidase **Thiamine oxidase **Xanthine oxidase * :EC 1.1.4 (with a disul ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Data Bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, RCSB, and BMRB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB. The PDB is a key in areas of structural biology, such as structural genomics. 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. History Two force ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tertiary Structure
Protein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains may interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure.Branden C. and Tooze J. "Introduction to Protein Structure" Garland Publishing, New York. 1990 and 1991. A number of tertiary structures may fold into a quaternary structure.Kyte, J. "Structure in Protein Chemistry." Garland Publishing, New York. 1995. History The science of the tertiary structure of proteins has progressed from one of hypothesis to one of detailed definition. Although Emil Fischer had suggested proteins were made of polypept ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Catalytic
Catalysis () is the process of increasing the rate of a chemical reaction by adding a substance known as a catalyst (). Catalysts are not consumed in the reaction and remain unchanged after it. If the reaction is rapid and the catalyst recycles quickly, very small amounts of catalyst often suffice; mixing, surface area, and temperature are important factors in reaction rate. Catalysts generally react with one or more reactants to form intermediates that subsequently give the final reaction product, in the process of regenerating the catalyst. Catalysis may be classified as either homogeneous, whose components are dispersed in the same phase (usually gaseous or liquid) as the reactant, or heterogeneous, whose components are not in the same phase. Enzymes and other biocatalysts are often considered as a third category. Catalysis is ubiquitous in chemical industry of all kinds. Estimates are that 90% of all commercially produced chemical products involve catalysts at some stag ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Binding (molecular)
Molecular binding is an attractive interaction between two molecules that results in a stable association in which the molecules are in close proximity to each other. It is formed when atoms or molecules bind together by sharing of electrons. It often, but not always, involves some chemical bonding. In some cases, the associations can be quite strong—for example, the protein streptavidin and the vitamin biotin have a dissociation constant (reflecting the ratio between bound and free biotin) on the order of 10−14—and so the reactions are effectively irreversible. The result of molecular binding is sometimes the formation of a molecular complex in which the attractive forces holding the components together are generally non-covalent, and thus are normally energetically weaker than covalent bonds. Molecular binding occurs in biological complexes (e.g., between pairs or sets of proteins, or between a protein and a small molecule ligand it binds) and also in abiologic chemic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Enzyme Substrate
In chemistry, the term substrate is highly context-dependent. Broadly speaking, it can refer either to a chemical species being observed in a chemical reaction, or to a surface on which other chemical reactions or microscopy are performed. In the former sense, a reagent is added to the ''substrate'' to generate a product through a chemical reaction. The term is used in a similar sense in synthetic and organic chemistry, where the substrate is the chemical of interest that is being modified. In biochemistry, an enzyme substrate is the material upon which an enzyme acts. When referring to Le Chatelier's principle, the substrate is the reagent whose concentration is changed. ;Spontaneous reaction : :*Where S is substrate and P is product. ;Catalysed reaction : :*Where S is substrate, P is product and C is catalyst. In the latter sense, it may refer to a surface on which other chemical reactions are performed or play a supporting role in a variety of spectroscopic and microsco ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Enzyme Inhibitor
An enzyme inhibitor is a molecule that binds to an enzyme and blocks its activity. Enzymes are proteins that speed up chemical reactions necessary for life, in which substrate molecules are converted into products. An enzyme facilitates a specific chemical reaction by binding the substrate to its active site, a specialized area on the enzyme that accelerates the most difficult step of the reaction. An enzyme inhibitor stops ("inhibits") this process, either by binding to the enzyme's active site (thus preventing the substrate itself from binding) or by binding to another site on the enzyme such that the enzyme's catalysis of the reaction is blocked. Enzyme inhibitors may bind reversibly or irreversibly. Irreversible inhibitors form a chemical bond with the enzyme such that the enzyme is inhibited until the chemical bond is broken. By contrast, reversible inhibitors bind non-covalently and may spontaneously leave the enzyme, allowing the enzyme to resume its function. Reve ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
D-cycloserine
Cycloserine, sold under the brand name Seromycin, is a GABA transaminase inhibitor and an antibiotic, used to treat tuberculosis. Specifically it is used, along with other antituberculosis medications, for active drug resistant tuberculosis. It is given by mouth. Common side effects include allergic reactions, seizures, sleepiness, unsteadiness, and numbness. It is not recommended in people who have kidney failure, epilepsy, depression, or are alcoholics. It is unclear if use during pregnancy is safe for the baby. Cycloserine is similar in structure to the amino acid D-alanine and works by interfering with the formation of the bacteria's cell wall. Cycloserine was discovered in 1954 from a type of ''Streptomyces''. It is on the World Health Organization's List of Essential Medicines. Medical uses Tuberculosis For the treatment of tuberculosis, cycloserine is classified as a second-line drug, i.e. its use is only considered if one or more first-line drugs cannot be used. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phosphinate
Phosphinates or hypophosphites are a class of phosphorus compounds conceptually based on the structure of hypophosphorous acid. IUPAC prefers the term phosphinate in all cases, however in practice hypophosphite is usually used to describe inorganic species (e.g. sodium hypophosphite), while phosphinate typically refers to organophosphorus species. Hypophosphites The hypophosphite ion is . The salts are prepared by heating white phosphorus in warm aqueous alkali e.g. Ca(OH)2: :P4 + 2 Ca(OH)2 + 4 H2O → 2 Ca(H2PO2)2 + 2 H2 Hypophosphites are reducing agents: : + 3 OH− → + 2 H2O + 2 e− Hypophosphites are used in electroless nickel plating as the reducing agent to deposit for example Ni metal from Ni salts. The hypophosphite ion is thermodynamically unstable, and disproportionates on heating to phosphine and phosphate salts: : 2 → PH3 + See also *Organophosphinic acid *Phosphine - PR3 * Phosphine oxide - OPR3 *Phosphite - P(OR)3 *Phosphonate - OP(OR)2 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Peptidoglycan Biosynthesis
Peptidoglycan or murein is a unique large macromolecule, a polysaccharide, consisting of sugars and amino acids that forms a mesh-like peptidoglycan layer outside the plasma membrane, the rigid cell wall (murein sacculus) characteristic of most bacteria (domain ''Bacteria''). The sugar component consists of alternating residues of β-(1,4) linked ''N''-acetylglucosamine (NAG) and ''N''-acetylmuramic acid (NAM). Attached to the ''N''-acetylmuramic acid is a oligopeptide chain made of three to five amino acids. The peptide chain can be cross-linked to the peptide chain of another strand forming the 3D mesh-like layer. Peptidoglycan serves a structural role in the bacterial cell wall, giving structural strength, as well as counteracting the osmotic pressure of the cytoplasm. This repetitive linking results in a dense peptidoglycan layer which is critical for maintaining cell form and withstanding high osmotic pressures, and it is regularly replaced by peptidoglycan production. Peptid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
D-alanine Metabolism
Alanine (symbol Ala or A), or α-alanine, is an α-amino acid that is used in the biosynthesis of proteins. It contains an amine group and a carboxylic acid group, both attached to the central carbon atom which also carries a methyl group side chain. Consequently, its IUPAC systematic name is 2-aminopropanoic acid, and it is classified as a nonpolar, aliphatic α-amino acid. Under biological conditions, it exists in its zwitterionic form with its amine group protonated (as −NH3+) and its carboxyl group deprotonated (as −CO2−). It is non-essential to humans as it can be synthesised metabolically and does not need to be present in the diet. It is encoded by all codons starting with GC (GCU, GCC, GCA, and GCG). The L-isomer of alanine ( left-handed) is the one that is incorporated into proteins. L-alanine is second only to leucine in rate of occurrence, accounting for 7.8% of the primary structure in a sample of 1,150 proteins. The right-handed form, D-alanine, occurs ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
