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Ribulose-phosphate 3-epimerase
Phosphopentose epimerase (also known as ribulose-phosphate 3-epimerase and ribulose 5-phosphate 3-epimerase, ) encoded in humans by the ''RPE'' gene is a metalloprotein that catalyzes the interconversion between D-ribulose 5-phosphate and D-xylulose 5-phosphate. :D-ribulose 5-phosphate \rightleftharpoons D-xylulose 5-phosphate This reversible conversion is required for carbon fixation in plants – through the Calvin cycle – and for the nonoxidative phase of the pentose phosphate pathway. This enzyme has also been implicated in additional pentose and glucuronate interconversions. In ''Cupriavidus metallidurans'' two copies of the gene coding for PPE are known, one is chromosomally encoded , the other one is on a plasmid . PPE has been found in a wide range of bacteria, archaebacteria, fungi and plants. All the proteins have from 209 to 241 amino acid residues. The enzyme has a TIM barrel structure. Nomenclature The List of enzymes, systematic name of this enzyme class i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Metalloprotein
Metalloprotein is a generic term for a protein that contains a metal ion cofactor. A large proportion of all proteins are part of this category. For instance, at least 1000 human proteins (out of ~20,000) contain zinc-binding protein domains although there may be up to 3000 human zinc metalloproteins. Abundance It is estimated that approximately half of all proteins contain a metal. In another estimate, about one quarter to one third of all proteins are proposed to require metals to carry out their functions. Thus, metalloproteins have many different functions in cells, such as storage and transport of proteins, enzymes and signal transduction proteins, or infectious diseases. The abundance of metal binding proteins may be inherent to the amino acids that proteins use, as even artificial proteins without evolutionary history will readily bind metals. Most metals in the human body are bound to proteins. For instance, the relatively high concentration of iron in the human body ... [...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, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained and deposited by biologists and biochemists worldwide through the use of experimental methodologies such as X-ray crystallography, Nuclear magnetic resonance spectroscopy of proteins, NMR spectroscopy, and, increasingly, cryo-electron microscopy. All submitted data are reviewed by expert Biocuration, biocurators and, once approved, are made freely available on the Internet under the CC0 Public Domain Dedication. Global access to the data is provided by the websites of the wwPDB member organizations (PDBe, PDBj, RCSB PDB, and BMRB). 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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Atoms
Atoms are the basic particles of the chemical elements. An atom consists of a nucleus of protons and generally neutrons, surrounded by an electromagnetically bound swarm of electrons. The chemical elements are distinguished from each other by the number of protons that are in their atoms. For example, any atom that contains 11 protons is sodium, and any atom that contains 29 protons is copper. Atoms with the same number of protons but a different number of neutrons are called isotopes of the same element. Atoms are extremely small, typically around 100 picometers across. A human hair is about a million carbon atoms wide. Atoms are smaller than the shortest wavelength of visible light, which means humans cannot see atoms with conventional microscopes. They are so small that accurately predicting their behavior using classical physics is not possible due to quantum effects. More than 99.94% of an atom's mass is in the nucleus. Protons have a positive electric charge a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Catalysis
Catalysis () is the increase in rate of a chemical reaction due to an added substance known as a catalyst (). Catalysts are not consumed by 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. The rate increase occurs because the catalyst allows the reaction to occur by an alternative mechanism which may be much faster than the noncatalyzed mechanism. However the noncatalyzed mechanism does remain possible, so that the total rate (catalyzed plus noncatalyzed) can only increase in the presence of the catalyst and never decrease. Catalysis may be classified as either homogeneous, whose components are dispersed in the same phase (usual ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cation
An ion () is an atom or molecule with a net electrical charge. The charge of an electron is considered to be negative by convention and this charge is equal and opposite to the charge of a proton, which is considered to be positive by convention. The net charge of an ion is not zero because its total number of electrons is unequal to its total number of protons. A cation is a positively charged ion with fewer electrons than protons (e.g. K+ ( potassium ion)) while an anion is a negatively charged ion with more electrons than protons (e.g. Cl− ( chloride ion) and OH− ( hydroxide ion)). Opposite electric charges are pulled towards one another by electrostatic force, so cations and anions attract each other and readily form ionic compounds. Ions consisting of only a single atom are termed ''monatomic ions'', ''atomic ions'' or ''simple ions'', while ions consisting of two or more atoms are termed polyatomic ions or ''molecular ions''. If only a + or − is present, it indic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Divalent
In chemistry, the valence (US spelling) or valency (British spelling) of an atom is a measure of its combining capacity with other atoms when it forms chemical compounds or molecules. Valence is generally understood to be the number of chemical bonds that each atom of a given chemical element typically forms. Double bonds are considered to be two bonds, triple bonds to be three, quadruple bonds to be four, quintuple bonds to be five and sextuple bonds to be six. In most compounds, the valence of hydrogen is 1, of oxygen is 2, of nitrogen is 3, and of carbon is 4. Valence is not to be confused with the related concepts of the coordination number, the oxidation state, or the number of valence electrons for a given atom. Description The valence is the combining capacity of an atom of a given element, determined by the number of hydrogen atoms that it combines with. In methane, carbon has a valence of 4; in ammonia, nitrogen has a valence of 3; in water, oxygen has a valence ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cofactor (biochemistry)
A cofactor is a non-protein chemical compound or metallic ion that is required for an enzyme's role as a catalyst (a catalyst is a substance that increases the rate of a chemical reaction). Cofactors can be considered "helper molecules" that assist in biochemical transformations. The rates at which these happen are characterized in an area of study called enzyme kinetics. Cofactors typically differ from ligands in that they often derive their function by remaining bound. Cofactors can be classified into two types: inorganic ions and complex organic molecules called coenzymes. Coenzymes are mostly derived from vitamins and other organic essential nutrients in small amounts. (Some scientists limit the use of the term "cofactor" for inorganic substances; both types are included here.) Coenzymes are further divided into two types. The first is called a " prosthetic group", which consists of a coenzyme that is tightly (or even covalently and, therefore, permanently) bound to a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Active Site
In biology and biochemistry, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid residues that form temporary bonds with the substrate, the ''binding site'', and residues that catalyse a reaction of that substrate, the ''catalytic site''. Although the active site occupies only ~10–20% of the volume of an enzyme, it is the most important part as it directly catalyzes the chemical reaction. It usually consists of three to four amino acids, while other amino acids within the protein are required to maintain the tertiary structure of the enzymes. Each active site is evolved to be optimised to bind a particular substrate and catalyse a particular reaction, resulting in high specificity. This specificity is determined by the arrangement of amino acids within the active site and the structure of the substrates. Sometimes enzymes also need to bind with some cofactors to fulfil their functio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Helix
A helix (; ) is a shape like a cylindrical coil spring or the thread of a machine screw. It is a type of smooth space curve with tangent lines at a constant angle to a fixed axis. Helices are important in biology, as the DNA molecule is formed as two intertwined helices, and many proteins have helical substructures, known as alpha helices. The word ''helix'' comes from the Greek word , "twisted, curved". A "filled-in" helix – for example, a "spiral" (helical) ramp – is a surface called a '' helicoid''. Properties and types The pitch of a helix is the height of one complete helix turn, measured parallel to the axis of the helix. A double helix consists of two (typically congruent) helices with the same axis, differing by a translation along the axis. A circular helix (i.e. one with constant radius) has constant band curvature and constant torsion. The slope of a circular helix is commonly defined as the ratio of the circumference of the circular cylinder that it ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Substrate (biology)
In biology, a substrate is the surface on which an organism (such as a plant, fungus, or animal) lives. A substrate can include biotic or abiotic materials and animals. For example, encrusting algae that lives on a rock (its substrate) can be itself a substrate for an animal that lives on top of the algae. Inert substrates are used as growing support materials in the hydroponic cultivation of plants. In biology substrates are often activated by the nanoscopic process of substrate presentation. In agriculture and horticulture * Cellulose substrate * Expanded clay aggregate (LECA) * Rock wool * Potting soil * Soil In animal biotechnology Requirements for animal cell and tissue culture Requirements for animal cell and tissue culture are the same as described for plant cell, tissue and organ culture (In Vitro Culture Techniques: The Biotechnological Principles). Desirable requirements are (i) air conditioning of a room, (ii) hot room with temperature recorder, (iii) microsc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Helices
A helix (; ) is a shape like a cylindrical coil spring or the thread of a machine screw. It is a type of smoothness (mathematics), smooth space curve with tangent lines at a constant angle to a fixed axis. Helices are important in biology, as the DNA molecule is formed as double helix, two intertwined helices, and many proteins have helical substructures, known as alpha helix, alpha helices. The word ''helix'' comes from the Greek language, Greek word , "twisted, curved". A "filled-in" helix – for example, a "spiral" (helical) ramp – is a surface called a ''helicoid''. Properties and types The pitch of a helix is the height of one complete helix turn (angle), turn, measured parallel to the axis of the helix. A double helix consists of two (typically congruence (geometry), congruent) helices with the same axis, differing by a translation along the axis. A circular helix (i.e. one with constant radius) has constant band curvature and constant Torsion of curves, torsion. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Beta Sheet
The beta sheet (β-sheet, also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A β-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation. The supramolecular association of β-sheets has been implicated in the formation of the fibrils and protein aggregates observed in amyloidosis, Alzheimer's disease and other proteinopathies. History The first β-sheet structure was proposed by William Astbury in the 1930s. He proposed the idea of hydrogen bonding between the peptide bonds of parallel or antiparallel extended β-strands. However, Astbury did not have the necessary data on the bond geometry of the amino acids in order to build accurate models, especially since he did not then know that the peptide bond was planar. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
