|
Asparagine Peptide Lyase
Asparagine peptide lyase are one of the seven groups in which proteases, also termed proteolytic enzymes, peptidases, or proteinases, are classified according to their catalytic residue. The catalytic mechanism of the asparagine peptide lyases involves an asparagine residue acting as nucleophile to perform a nucleophilic elimination reaction, rather than hydrolysis, to catalyse the breaking of a peptide bond. The existence of this seventh catalytic type of proteases, in which the peptide bond cleavage occurs by self-processing instead of hydrolysis, was demonstrated with the discovery of the crystal structure of the self-cleaving precursor of the Tsh autotransporter from ''E. coli''. Synthesis These enzymes are synthesized as precursors or propeptides, which cleave themselves by an autoproteolytic reaction. The self-cleaving nature of asparagine peptide lyases contradicts the general definition of an enzyme given that the enzymatic activity destroys the enzyme. However, the self ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protease
A protease (also called a peptidase, proteinase, or proteolytic enzyme) is an enzyme that catalysis, catalyzes proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurring the formation of new protein products. They do this by cleaving the peptide bonds within proteins by hydrolysis, a reaction where water breaks Covalent bond, bonds. Proteases are involved in numerous biological pathways, including Digestion#Protein digestion, digestion of ingested proteins, protein catabolism (breakdown of old proteins), and cell signaling. In the absence of functional accelerants, proteolysis would be very slow, taking hundreds of years. Proteases can be found in all forms of life and viruses. They have independently convergent evolution, evolved multiple times, and different classes of protease can perform the same reaction by completely different catalytic mechanisms. Classification Based on catalytic residue Proteases can be classified into seven broad ... [...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] |
Extein
Protein splicing is an intramolecular reaction of a particular protein in which an internal protein segment (called an intein) is removed from a precursor protein with a ligation of C-terminus, C-terminal and N-terminus, N-terminal external proteins (called exteins) on both sides. The splicing junction of the precursor protein is mainly a cysteine or a serine, which are amino acids containing a Nucleophile, nucleophilic side chain. The protein splicing reactions which are known now do not require exogenous cofactors or energy sources such as adenosine triphosphate (ATP) or guanosine triphosphate (GTP). Normally, splicing is associated only with Splicing (genetics), pre-mRNA splicing. This precursor protein contains three segments—an N-extein followed by the intein followed by a C-extein. After splicing has taken place, the resulting protein contains the N-extein linked to the C-extein; this splicing product is also termed an extein. History The first intein was discovered in 1988 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Intein
Protein splicing is an intramolecular reaction of a particular protein in which an internal protein segment (called an intein) is removed from a precursor protein with a ligation of C-terminal and N-terminal external proteins (called exteins) on both sides. The splicing junction of the precursor protein is mainly a cysteine or a serine, which are amino acids containing a nucleophilic side chain. The protein splicing reactions which are known now do not require exogenous cofactors or energy sources such as adenosine triphosphate (ATP) or guanosine triphosphate (GTP). Normally, splicing is associated only with pre-mRNA splicing. This precursor protein contains three segments—an N-extein followed by the intein followed by a C-extein. After splicing has taken place, the resulting protein contains the N-extein linked to the C-extein; this splicing product is also termed an extein. History The first intein was discovered in 1988 through sequence comparison between the ''Neurospora cr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Injectisome
The type III secretion system (T3SS or TTSS) is one of the bacterial secretion systems used by bacteria to secrete their effector proteins into the host's cells to promote virulence and colonisation. While the type III secretion system has been widely regarded as equivalent to the injectisome, many argue that the injectisome is only part of the type III secretion system, which also include structures like the flagellar export apparatus. The T3SS is a needle-like protein complex found in several species of pathogenic gram-negative bacteria. Overview The term '''Type III secretion system was coined in 1993. This secretion system is distinguished from at least five other secretion systems found in gram-negative bacteria. Many animal and plant associated bacteria possess similar T3SSs. These T3SSs are similar as a result of convergent evolution and phylogenetic analysis supports a model in which gram-negative bacteria can transfer the T3SS gene cassette horizontally to other spe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Endopeptidases
Endopeptidase or endoproteinase are proteolytic peptidases that break peptide bonds of nonterminal amino acids (i.e. within the molecule), in contrast to exopeptidases, which break peptide bonds from end-pieces of terminal amino acids. For this reason, endopeptidases cannot break down peptides into monomers, while exopeptidases can break down proteins into monomers. A particular case of endopeptidase is the oligopeptidase, whose substrates are oligopeptides instead of proteins. They are usually very specific for certain amino acids. Examples of endopeptidases include: * Trypsin - cuts after Arg or Lys, unless followed by Pro. Very strict. Works best at pH 8. * Chymotrypsin - cuts after Phe, Trp, or Tyr, unless followed by Pro. Cuts more slowly after His, Met or Leu. Works best at pH 8. * Elastase - cuts after Ala, Gly, Ser, or Val, unless followed by Pro. * Thermolysin - cuts ''before'' Ile, Met, Phe, Trp, Tyr, or Val, unless ''preceded'' by Pro. Sometimes cuts after Ala, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Beta Barrel
In protein structures, a beta barrel (β barrel) is a beta sheet (β sheet) composed of tandem repeats that twists and coils to form a closed toroidal structure in which the first strand is bonded to the last strand (hydrogen bond). Beta-strands in many beta-barrels are arranged in an antiparallel fashion. Beta barrel structures are named for resemblance to the barrels used to contain liquids. Most of them are water-soluble outer membrane proteins and frequently bind hydrophobic ligands in the barrel center, as in lipocalins. Others span cell membranes and are commonly found in porins. Porin-like barrel structures are encoded by as many as 2–3% of the genes in Gram-negative bacteria. It has been shown that more than 600 proteins with various function such as oxidase, dismutase, and amylase contain the beta barrel structure. In many cases, the strands contain alternating polar and non-polar (hydrophilic and hydrophobic) amino acids, so that the hydrophobic residues are orient ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Autotransporter Domain
In molecular biology, an autotransporter domain is a structural domain found in some bacterial outer membrane proteins. The domain is always located at the C-terminal end of the protein and forms a beta-barrel structure. The barrel is oriented in the membrane such that the N-terminal portion of the protein, termed the passenger domain, is presented on the cell surface. These proteins are typically virulence factors, associated with infection or virulence in pathogenic bacteria. The name autotransporter derives from an initial understanding that the protein was self-sufficient in transporting the passenger domain through the outermembrane. This view has since been challenged by Benz and Schmidt. Secretion of polypeptide chains through the outer membrane of Gram-negative bacteria can occur via a number of different pathways. The type V(a), or autotransporter, secretion pathway constitutes the largest number of secreted virulence factors of any one of the seven known types of secreti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gram-negative Bacteria
Gram-negative bacteria are bacteria that, unlike gram-positive bacteria, do not retain the Crystal violet, crystal violet stain used in the Gram staining method of bacterial differentiation. Their defining characteristic is that their cell envelope consists of a thin peptidoglycan gram-negative cell wall, cell wall sandwiched between an inner (Cytoplasm, cytoplasmic) Cell membrane, membrane and an Bacterial outer membrane, outer membrane. These bacteria are found in all environments that support life on Earth. Within this category, notable species include the model organism ''Escherichia coli'', along with various pathogenic bacteria, such as ''Pseudomonas aeruginosa'', ''Chlamydia trachomatis'', and ''Yersinia pestis''. They pose significant challenges in the medical field due to their outer membrane, which acts as a protective barrier against numerous Antibiotic, antibiotics (including penicillin), Detergent, detergents that would normally damage the inner cell membrane, and the ... [...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] |
Poliovirus
Poliovirus, the causative agent of polio (also known as poliomyelitis), is a serotype of the species '' Enterovirus C'', in the family of '' Picornaviridae''. There are three poliovirus serotypes, numbered 1, 2, and 3. Poliovirus is composed of an RNA genome and a protein capsid. The genome is a single-stranded positive-sense RNA (+ssRNA) genome that is about 7500 nucleotides long. The viral particle is about 30 nm in diameter with icosahedral symmetry. Because of its short genome and its simple composition—only a strand of RNA and a nonenveloped icosahedral protein coat encapsulating it—poliovirus is widely regarded as the simplest significant virus. Poliovirus is one of the most well-characterized viruses, and has become a useful model system for understanding the biology of RNA viruses. Replication cycle Poliovirus infects human cells by binding to an immunoglobulin-like receptor, CD155 (also known as the poliovirus receptor or PVR) on the cell surface. Inte ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
