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DD-Transpeptidase Mechanism Fixed
DD-transpeptidase (, ''DD-peptidase'', ''DD-transpeptidase'', ''DD-carboxypeptidase'', ''D-alanyl-D-alanine carboxypeptidase'', ''D-alanyl-D-alanine-cleaving-peptidase'', ''D-alanine carboxypeptidase'', ''D-alanyl carboxypeptidase'', and ''serine-type D-Ala-D-Ala carboxypeptidase''.) is a bacterial enzyme that catalyzes the transfer of the R-L-aca-D-alanyl moiety of R-L-aca-D-alanyl-D-alanine carbonyl donors to the γ-OH of their active-site serine and from this to a final acceptor. It is involved in bacterial cell wall biosynthesis, namely, the transpeptidation that crosslinks the peptide side chains of peptidoglycan strands. The antibiotic penicillin irreversibly binds to and inhibits the activity of the transpeptidase enzyme by forming a highly stable penicilloyl-enzyme intermediate. Because of the interaction between penicillin and transpeptidase, this enzyme is also known as penicillin-binding protein (PBP). Mechanism DD-transpeptidase is mechanistically similar to the prote ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Carboxypeptidase
A carboxypeptidase ( EC number 3.4.16 - 3.4.18) is a protease enzyme that hydrolyzes (cleaves) a peptide bond at the carboxy-terminal (C-terminal) end of a protein or peptide. This is in contrast to an aminopeptidases, which cleave peptide bonds at the N-terminus of proteins. Humans, animals, bacteria and plants contain several types of carboxypeptidases that have diverse functions ranging from catabolism to protein maturation. At least two mechanisms have been discussed. Functions Initial studies on carboxypeptidases focused on pancreatic carboxypeptidases A1, A2, and B in the digestion of food. Most carboxypeptidases are not, however, involved in catabolism. Instead they help to mature proteins, for example Post-translational modification. They also regulate biological processes, such as the biosynthesis of neuroendocrine peptides such as insulin requires a carboxypeptidase. Carboxypeptidases also function in blood clotting, growth factor production, wound healing, reproduction, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Streptomyces
''Streptomyces'' is the largest genus of Actinomycetota and the type genus of the family Streptomycetaceae. Over 500 species of ''Streptomyces'' bacteria have been described. As with the other Actinomycetota, streptomycetes are gram-positive, and have genomes with high GC content. Found predominantly in soil and decaying vegetation, most streptomycetes produce spores, and are noted for their distinct "earthy" odor that results from production of a volatile metabolite, geosmin. Streptomycetes are characterised by a complex secondary metabolism. They produce over two-thirds of the clinically useful antibiotics of natural origin (e.g., neomycin, streptomycin, cypemycin, grisemycin, bottromycins and chloramphenicol). The antibiotic streptomycin takes its name directly from ''Streptomyces''. Streptomycetes are infrequent pathogens, though infections in humans, such as mycetoma, can be caused by '' S. somaliensis'' and '' S. sudanensis'', and in plants can be caused by '' S. cavi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MEROPS
MEROPS is an online database for peptidases (also known as proteases, proteinases and proteolytic enzymes) and their inhibitors. The classification scheme for peptidases was published by Rawlings & Barrett in 1993, and that for protein inhibitors by Rawlings ''et al.'' in 2004.Rawlings, N.D., Tolle, D.P. & Barrett, A.J. (2004) "Evolutionary families of peptidase inhibitors." ''Biochem J'' 378, 705-716. The most recent version, MEROPS 12.3, was released in September 2020. Overview The classification is based on similarities at the tertiary and primary structural levels. Comparisons are restricted to that part of the sequence directly involved in the reaction, which in the case of a peptidase must include the active site, and for a protein inhibitor the reactive site. The classification is hierarchical: sequences are assembled into families, and families are assembled into clans. Each peptidase, family, and clan has a unique identifier. Classification Family The families of pe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Glycosyltransferase
Glycosyltransferases (GTFs, Gtfs) are enzymes ( EC 2.4) that establish natural glycosidic linkages. They catalyze the transfer of saccharide moieties from an activated nucleotide sugar (also known as the "glycosyl donor") to a nucleophilic glycosyl acceptor molecule, the nucleophile of which can be oxygen- carbon-, nitrogen-, or sulfur-based. The result of glycosyl transfer can be a carbohydrate, glycoside, oligosaccharide, or a polysaccharide. Some glycosyltransferases catalyse transfer to inorganic phosphate or water. Glycosyl transfer can also occur to protein residues, usually to tyrosine, serine, or threonine to give O-linked glycoproteins, or to asparagine to give N-linked glycoproteins. Mannosyl groups may be transferred to tryptophan to generate C-mannosyl tryptophan, which is relatively abundant in eukaryotes. Transferases may also use lipids as an acceptor, forming glycolipids, and even use lipid-linked sugar phosphate donors, such as dolichol phosphates in eukaryotic o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Vancomycin
Vancomycin is a glycopeptide antibiotic medication used to treat a number of bacterial infections. It is recommended intravenously as a treatment for complicated skin infections, bloodstream infections, endocarditis, bone and joint infections, and meningitis caused by methicillin-resistant ''Staphylococcus aureus''. Blood levels may be measured to determine the correct dose. Vancomycin is also taken by mouth as a treatment for severe ''Clostridium difficile'' colitis. When taken by mouth it is poorly absorbed. Common side effects include pain in the area of injection and allergic reactions. Occasionally, hearing loss, low blood pressure, or bone marrow suppression occur. Safety in pregnancy is not clear, but no evidence of harm has been found, and it is likely safe for use when breastfeeding. It is a type of glycopeptide antibiotic and works by blocking the construction of a cell wall. Vancomycin was approved for medical use in the United States in 1958. It is on the World ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Penicillin Binding Proteins
Penicillin-binding proteins (PBPs) are a group of proteins that are characterized by their affinity for and binding of penicillin. They are a normal constituent of many bacteria; the name just reflects the way by which the protein was discovered. All β-lactam antibiotics (except for tabtoxinine-β-lactam, which inhibits glutamine synthetase) bind to PBPs, which are essential for bacterial cell wall synthesis. PBPs are members of a subgroup of enzymes called transpeptidases. Specifically, PBPs are DD-transpeptidases. Diversity There are a large number of PBPs, usually several in each organism, and they are found as both membrane-bound and cytoplasmic proteins. For example, Spratt (1977) reports that six different PBPs are routinely detected in all strains of ''E. coli'' ranging in molecular weight from 40,000 to 91,000. The different PBPs occur in different numbers per cell and have varied affinities for penicillin. The PBPs are usually broadly classified into high-molecular ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
β-lactam Antibiotic
β-lactam antibiotics (beta-lactam antibiotics) are antibiotics that contain a beta-lactam ring in their chemical structure. This includes penicillin derivatives (penams), cephalosporins and cephamycins (cephems), monobactams, carbapenems and carbacephems. Most β-lactam antibiotics work by inhibiting cell wall biosynthesis in the bacterial organism and are the most widely used group of antibiotics. Until 2003, when measured by sales, more than half of all commercially available antibiotics in use were β-lactam compounds. The first β-lactam antibiotic discovered, penicillin, was isolated from a rare variant of ''Penicillium notatum'' (since renamed ''Penicillium chrysogenum)''. Bacteria often develop resistance to β-lactam antibiotics by synthesizing a β-lactamase, an enzyme that attacks the β-lactam ring. To overcome this resistance, β-lactam antibiotics can be given with β-lactamase inhibitors such as clavulanic acid. Medical use β-lactam antibiotics are indicated for ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Periplasm
The periplasm is a concentrated gel-like matrix in the space between the inner cytoplasmic membrane and the bacterial outer membrane called the ''periplasmic space'' in gram-negative bacteria. Using cryo-electron microscopy it has been found that a much smaller periplasmic space is also present in gram-positive bacteria., Matias, V. R., and T. J. Beveridge. 2005. Cryo-electron microscopy reveals native polymeric cell wall structure in Bacillus subtilis 168 and the existence of a periplasmic space. Mol. Microbiol. 56:240-251. ., Zuber B, Haenni M, Ribeiro T, Minnig K, Lopes F, Moreillon P, Dubochet J. 2006. Granular layer in the periplasmic space of Gram-positive bacteria and fine structures of Enterococcus gallinarum and Streptococcus gordonii septa revealed by cryo-electron microscopy of vitreous sections. J Bacteriol. 188:6652-6660. The periplasm may constitute up to 40% of the total cell volume of gram-negative bacteria, but is a much smaller percentage in gram-positive bacteri ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Penicillin Vs PG Terminus Structure
Penicillins (P, PCN or PEN) are a group of β-lactam antibiotics originally obtained from ''Penicillium'' moulds, principally '' P. chrysogenum'' and '' P. rubens''. Most penicillins in clinical use are synthesised by P. chrysogenum using deep tank fermentation and then purified. A number of natural penicillins have been discovered, but only two purified compounds are in clinical use: penicillin G (intramuscular or intravenous use) and penicillin V (given by mouth). Penicillins were among the first medications to be effective against many bacterial infections caused by staphylococci and streptococci. They are still widely used today for different bacterial infections, though many types of bacteria have developed resistance following extensive use. 10% of the population claims penicillin allergies but because the frequency of positive skin test results decreases by 10% with each year of avoidance, 90% of these patients can tolerate penicillin. Additionally, those with pe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Oxyanion Hole
An oxyanion hole is a pocket in the active site of an enzyme that stabilizes transition state negative charge on a deprotonated oxygen or alkoxide. The pocket typically consists of backbone amides or positively charged residues. Stabilising the transition state lowers the activation energy necessary for the reaction, and so promotes catalysis. For example, proteases such as chymotrypsin contain an oxyanion hole to stabilise the tetrahedral intermediate anion formed during proteolysis and protects substrate's negatively charged oxygen from water molecules. Additionally, it may allow for insertion or positioning of a substrate, which would suffer from steric hindrance Steric effects arise from the spatial arrangement of atoms. When atoms come close together there is a rise in the energy of the molecule. Steric effects are nonbonding interactions that influence the shape ( conformation) and reactivity of ions ... if it could not occupy the hole (such as 2,3-Bisphosphoglycerate, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Fold Class
In molecular biology, protein fold classes are broad categories of protein tertiary structure topology. They describe groups of proteins that share similar amino acid and secondary structure proportions. Each class contains multiple, independent protein superfamilies (i.e. are not necessarily evolutionarily related to one another). Generally recognised classes Four large classes of protein that are generally agreed upon by the two main structure classification databases (SCOP and CATH). all-α All-α proteins are a class of structural domains in which the secondary structure is composed entirely of α-helices, with the possible exception of a few isolated β-sheets on the periphery. Common examples include the bromodomain, the globin fold and the homeodomain fold. all-β All-β proteins are a class of structural domains in which the secondary structure is composed entirely of β-sheets, with the possible exception of a few isolated α-helices on the periphery. Common e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Moiety (chemistry)
In organic chemistry, a moiety ( ) is a part of a molecule that is given a name because it is identified as a part of other molecules as well. Typically, the term is used to describe the larger and characteristic parts of organic molecules, and it should not be used to describe or name smaller functional groups of atoms that chemically react in similar ways in most molecules that contain them. Occasionally, a moiety may contain smaller moieties and functional groups. A moiety that acts as a branch extending from the backbone of a hydrocarbon molecule is called a substituent or side chain, which typically can be removed from the molecule and substituted with others. Active moiety In pharmacology, an active moiety is the part of a molecule or ion – excluding appended inactive portions – that is responsible for the physiological or pharmacological action of a drug substance. Inactive appended portions of the drug substance may include either the alcohol or acid moiety of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
