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Although these proteins are biochemically distinct and play different roles in actin dynamics, they all appear to use the ADF-H domain for their interactions with actin.The ADF-H domain consists of a six-stranded mixed beta-sheet in which the four central strands (beta2-beta5) are anti-parallel and the two edge strands (beta1 and beta6) run parallel with the neighbouring strands. The sheet is surrounded by two alpha-helices on each side . == References == | https://en.wikipedia.org/wiki/ADF-H_domain |
In molecular biology, ATP-binding domain of ABC transporters is a water-soluble domain of transmembrane ABC transporters. ABC transporters belong to the ATP-Binding Cassette superfamily, which uses the hydrolysis of ATP to translocate a variety of compounds across biological membranes. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. | https://en.wikipedia.org/wiki/ATP-binding_domain_of_ABC_transporters |
In molecular biology, ATP10 protein (mitochondrial ATPase complex subunit ATP10) is an ATP synthase assembly factor. It is essential for the assembly of the mitochondrial F1-F0 complex. A yeast nuclear gene (ATP10) encodes a product that is essential for the assembly of a functional mitochondrial ATPase complex. Mutations in ATP10 induce a loss of rutamycin sensitivity in the mitochondrial ATPase, but do not affect the respiratory enzymes. | https://en.wikipedia.org/wiki/ATP10_protein |
ATP10 has a molecular weight of 30,293 Da and its primary structure is not related to any known subunit of the yeast or mammalian mitochondrial ATPase complexes. ATP10 is associated with the mitochondrial membrane. It is suggested that the ATP10 product is not a subunit of the ATPase complex but rather a protein required for the assembly of the F0 sector of the complex. == References == | https://en.wikipedia.org/wiki/ATP10_protein |
In molecular biology, BAG domains are protein domains found in proteins which are modulators of chaperone activity, they bind to HSP70/HSC70 proteins and promote substrate release. The proteins have anti-apoptotic activity and increase the anti-cell death function of BCL-2 induced by various stimuli. BAG-1 binds to the serine/threonine kinase Raf-1 or Hsc70/Hsp70 in a mutually exclusive interaction. BAG-1 promotes cell growth by binding to and stimulating Raf-1 activity. | https://en.wikipedia.org/wiki/BAG_domain |
The binding of Hsp70 to BAG-1 diminishes Raf-1 signalling and inhibits subsequent events, such as DNA synthesis, as well as arrests the cell cycle. BAG-1 has been suggested to function as a molecular switch that encourages cells to proliferate in normal conditions but become quiescent under a stressful environment .BAG-family proteins contain a single BAG domain, except for human BAG-5 which has four BAG repeats. The BAG domain is a conserved region located at the C terminus of the BAG-family proteins that binds the ATPase domain of Hsc70/Hsp70. | https://en.wikipedia.org/wiki/BAG_domain |
The BAG domain is evolutionarily conserved, and BAG domain containing proteins have been described and/or proven in a variety of organisms including Mus musculus (Mouse), Xenopus spp., Drosophila spp., Bombyx mori (Silk moth), Caenorhabditis elegans, Saccharomyces cerevisiae (Baker's yeast), Schizosaccharomyces pombe (Fission yeast), and Arabidopsis thaliana (Mouse-ear cress). The BAG domain has 110-124 amino acids and is composed of three anti-parallel alpha-helices, each approximately 30-40 amino acids in length. | https://en.wikipedia.org/wiki/BAG_domain |
The first and second helices interact with the serine/threonine kinase Raf-1 and the second and third helices are the sites of the BAG domain interaction with the ATPase domain of Hsc70/Hsp70. Binding of the BAG domain to the ATPase domain is mediated by both electrostatic and hydrophobic interactions in BAG-1 and is energy requiring. == References == | https://en.wikipedia.org/wiki/BAG_domain |
In molecular biology, BAR domains are highly conserved protein dimerisation domains that occur in many proteins involved in membrane dynamics in a cell. The BAR domain is banana-shaped and binds to membrane via its concave face. It is capable of sensing membrane curvature by binding preferentially to curved membranes. BAR domains are named after three proteins that they are found in: Bin, Amphiphysin and Rvs. | https://en.wikipedia.org/wiki/BAR_domain |
In molecular biology, Bacteriophage T4 beta-glucosyltransferase refers to a protein domain found in a virus of Escherichia coli named bacteriophage T4. Members of this family are enzymes encoded by bacteriophage T4, which modify DNA by transferring glucose from uridine diphosphoglucose to 5-hydroxymethyl cytosine bases of phage T4 DNA. | https://en.wikipedia.org/wiki/DNA_beta-glucosyltransferase |
In molecular biology, Beta-ketoacyl-ACP synthase EC 2.3.1.41, is an enzyme involved in fatty acid synthesis. It typically uses malonyl-CoA as a carbon source to elongate ACP-bound acyl species, resulting in the formation of ACP-bound β-ketoacyl species such as acetoacetyl-ACP. Beta-ketoacyl-ACP synthase is a highly conserved enzyme that is found in almost all life on earth as a domain in fatty acid synthase (FAS). FAS exists in two types, aptly named type I and II. | https://en.wikipedia.org/wiki/Beta-ketoacyl-ACP_synthase |
In animals, fungi, and lower eukaryotes, Beta-ketoacyl-ACP synthases make up one of the catalytic domains of larger multifunctional proteins (Type I), whereas in most prokaryotes as well as in plastids and mitochondria, Beta-ketoacyl-ACP synthases are separate protein chains that usually form dimers (Type II). Beta-ketoacyl-ACP synthase III, perhaps the most well known of this family of enzymes, catalyzes a Claisen condensation between acetyl CoA and malonyl ACP. The image below reveals how CoA fits in the active site as a substrate of synthase III. | https://en.wikipedia.org/wiki/Beta-ketoacyl-ACP_synthase |
Beta-ketoacyl-ACP synthases I and II only catalyze acyl-ACP reactions with malonyl ACP. Synthases I and II are capable of producing long-chain acyl-ACPs. Both are efficient up to acyl-ACPs with a 14 carbon chain, at which point synthase II is the more efficient choice for further carbon additions. Type I FAS catalyzes all the reactions necessary to create palmitic acid, which is a necessary function in animals for metabolic processes, one of which includes the formation of sphingosines.Beta-ketoacyl-ACP synthase is found as a component of a number of enzymatic systems, including fatty acid synthetase (FAS); the multi-functional 6-methysalicylic acid synthase (MSAS) from Penicillium patulum, which is involved in the biosynthesis of a polyketide antibiotic; polyketide antibiotic synthase enzyme systems; Emericella nidulans multifunctional protein Wa, which is involved in the biosynthesis of conidial green pigment; Rhizobium nodulation protein nodE, which probably acts as a beta-ketoacyl synthase in the synthesis of the nodulation Nod factor fatty acyl chain; and yeast mitochondrial protein CEM1. | https://en.wikipedia.org/wiki/Beta-ketoacyl-ACP_synthase |
In molecular biology, BpuJI is a type II restriction endonuclease which recognises the asymmetric sequence 5'-CCCGT and cuts at multiple sites in the surrounding area of the target sequence. The BpuJI protein consists of two distinct modules; an N-terminal DNA recognition domain, and a C-terminal dimerisation and catalysis domain. The N-terminal domain is composed of two winged-helix subdomains and a disrupted linker subdomain. Target sequence recognition occurs through major groove contacts of amino acids in the winged-helix subdomains. == References == | https://en.wikipedia.org/wiki/BpuJI |
In molecular biology, CD11 is a member of the C/D class of snoRNA which contain the C (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_CD11 |
In molecular biology, CD18 (Integrin beta chain-2) is an integrin beta chain protein that is encoded by the ITGB2 gene in humans. Upon binding with one of a number of alpha chains, CD18 is capable of forming multiple heterodimers, which play significant roles in cellular adhesion and cell surface signaling, as well as important roles in immune responses. CD18 also exists in soluble, ligand binding forms. Deficiencies in CD18 expression can lead to adhesion defects in circulating white blood cells in humans, reducing the immune system's ability to fight off foreign invaders. | https://en.wikipedia.org/wiki/Integrin_beta_2 |
In molecular biology, CD4 (cluster of differentiation 4) is a glycoprotein that serves as a co-receptor for the T-cell receptor (TCR). CD4 is found on the surface of immune cells such as T helper cells, monocytes, macrophages, and dendritic cells. It was discovered in the late 1970s and was originally known as leu-3 and T4 (after the OKT4 monoclonal antibody that reacted with it) before being named CD4 in 1984. In humans, the CD4 protein is encoded by the CD4 gene.CD4+ T helper cells are white blood cells that are an essential part of the human immune system. | https://en.wikipedia.org/wiki/CD4 |
They are often referred to as CD4 cells, T-helper cells or T4 cells. They are called helper cells because one of their main roles is to send signals to other types of immune cells, including CD8 killer cells, which then destroy the infectious particle. If CD4 cells become depleted, for example in untreated HIV infection, or following immune suppression prior to a transplant, the body is left vulnerable to a wide range of infections that it would otherwise have been able to fight. | https://en.wikipedia.org/wiki/CD4 |
In molecular biology, Caf1 capsule antigen proteins are a family of the F1 capsule antigens Caf1 synthesised by Yersinia bacteria. They adopt a structure consisting of a seven strands arranged in two beta-sheets, in a Greek-key topology, and mediate targeting of the bacterium to sites of infection. == References == | https://en.wikipedia.org/wiki/Caf1_capsule_antigen |
In molecular biology, Circular RNAs (circRNAs) refer to a class of circular RNA molecules found across all kingdoms of life. Studies in 2013 have suggested that circRNAs play important regulatory roles in miRNA activity. Researchers found that CDR1as circRNA acts as a miR-7 super-sponge that contains about 70 target sites from the same miR-7 at the same transcript. The other testis-specific circRNA, sex-determining region Y (Sry), also was found as a miR-138 sponge. | https://en.wikipedia.org/wiki/Circular_RNA_databases_and_resources |
About-mentioned examples suggesting that miRNA sponge effects achieved by circRNA formation may be a general phenomenon. As miR-7 modulates the expression of several oncogenes, ciRS-7/miR-7 interactions may play an important roles in cancer-related pathways. circRNA has also been shown in viral infection where it sequesters anti-viral protein to enhance viral replication.This Circular RNA (circRNA) databases and resources is a compilation of databases and web portals and servers used for circRNAs. == References == | https://en.wikipedia.org/wiki/Circular_RNA_databases_and_resources |
In molecular biology, D-stereospecific aminopeptidase (D-aminopeptidase) EC 3.4.11.19 is an enzyme which catalyses the release of an N-terminal D-amino acid from a peptide, Xaa-|-Yaa-, in which Xaa is preferably D-Ala, D-Ser or D-Thr. D-amino acid amides and methyl esters also are hydrolyzed, as is glycine amide. It is a dimeric enzyme with each monomer being composed of three domains. Domain B is organised to form a beta barrel made up of eight antiparallel beta strands. | https://en.wikipedia.org/wiki/D-stereospecific_aminopeptidase |
It is connected to domain A, the catalytic domain, by an eight-residue sequence, and also interacts with both domains A and C via non-covalent bonds. Domain B probably functions in maintaining domain C in a good position to interact with the catalytic domain. Domain C is organised to form a beta barrel made up of eight antiparallel beta strands. It is connected to domain B by a short linker sequence, and interacts extensively with the domain A, the catalytic domain. The gamma loop of domain C forms part of the wall of the catalytic pocket; domain C is in fact thought to confer substrate and inhibitor specificity to the enzyme. | https://en.wikipedia.org/wiki/D-stereospecific_aminopeptidase |
In molecular biology, DCTN6 is that subunit of the dynactin protein complex that is encoded by the p27 gene. Dynactin is the essential component for microtubule-based cytoplasmic dynein motor activity in intracellular transport of a variety of cargoes and organelles. | https://en.wikipedia.org/wiki/DCTN6 |
In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part of biological inheritance. This is essential for cell division during growth and repair of damaged tissues, while it also ensures that each of the new cells receives its own copy of the DNA. The cell possesses the distinctive property of division, which makes replication of DNA essential. | https://en.wikipedia.org/wiki/Replication_Fork |
DNA is made up of a double helix of two complementary strands. The double helix describes the appearance of a double-stranded DNA which is thus composed of two linear strands that run opposite to each other and twist together to form. During replication, these strands are separated. | https://en.wikipedia.org/wiki/Replication_Fork |
Each strand of the original DNA molecule then serves as a template for the production of its counterpart, a process referred to as semiconservative replication. As a result of semi-conservative replication, the new helix will be composed of an original DNA strand as well as a newly synthesized strand. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication.In a cell, DNA replication begins at specific locations, or origins of replication, in the genome which contains the genetic material of an organism. | https://en.wikipedia.org/wiki/Replication_Fork |
Unwinding of DNA at the origin and synthesis of new strands, accommodated by an enzyme known as helicase, results in replication forks growing bi-directionally from the origin. A number of proteins are associated with the replication fork to help in the initiation and continuation of DNA synthesis. Most prominently, DNA polymerase synthesizes the new strands by adding nucleotides that complement each (template) strand. | https://en.wikipedia.org/wiki/Replication_Fork |
DNA replication occurs during the S-stage of interphase. DNA replication (DNA amplification) can also be performed in vitro (artificially, outside a cell). | https://en.wikipedia.org/wiki/Replication_Fork |
DNA polymerases isolated from cells and artificial DNA primers can be used to start DNA synthesis at known sequences in a template DNA molecule. Polymerase chain reaction (PCR), ligase chain reaction (LCR), and transcription-mediated amplification (TMA) are examples. In March 2021, researchers reported evidence suggesting that a preliminary form of transfer RNA, a necessary component of translation, the biological synthesis of new proteins in accordance with the genetic code, could have been a replicator molecule itself in the very early development of life, or abiogenesis. | https://en.wikipedia.org/wiki/Replication_Fork |
In molecular biology, Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function. | https://en.wikipedia.org/wiki/B5_protein_domain |
In molecular biology, Duffy binding proteins are found in Plasmodium. Plasmodium vivax and Plasmodium knowlesi merozoites invade Homo sapiens erythrocytes that express Duffy blood group surface determinants. The Duffy receptor family is localised in micronemes, an organelle found in all organisms of the phylum Apicomplexa.The presence of duffy-binding-like domains defines the family of erythrocyte binding-like proteins (EBL), a family of cell invasion proteins universal among Plasmodium. These other members may use some other receptor, for example Glycophorin A. The other universal invasion protein is reticulocyte binding protein homologs. Both families are essential for cell invasion, as they function cooperatively.A duffy-binding-like domain is also found in proteins of the family Plasmodium falciparum erythrocyte membrane protein 1. | https://en.wikipedia.org/wiki/Duffy_binding_proteins |
In molecular biology, Endoribonuclease XendoU refers to a protein domain. This particular entry represents endoribonucleases involved in RNA biosynthesis which has been named XendoU in Xenopus laevis (African clawed frog). This protein domain belongs to a family of evolutionarily related proteins. XendoU is a U-specific metal dependent enzyme that produces products with a 2'-3' cyclic phosphate termini. | https://en.wikipedia.org/wiki/Endoribonuclease_XendoU |
In molecular biology, Enhancer of rudimentary homolog is a protein that in humans is encoded by the ERH gene.The Drosophila protein enhancer of rudimentary protein is a small protein of 104 amino acids. It has been found to be an enhancer of the rudimentary gene, involved in pyrimidine biosynthesis.From an evolutionary point of view, enhancer of rudimentary is highly conserved and has been found to exist in probably all multicellular eukaryotic organisms. It has been proposed that this protein plays a role in the cell cycle. | https://en.wikipedia.org/wiki/ERH_(gene) |
In molecular biology, FMR1 antisense RNA 1 (FMR1-AS1), also known as ASFMR1 or FMR4, is a long non-coding RNA. The FMR1-AS1 gene overlaps, and is antisense to, the CGG repeat region of the FMR1 gene. Its expression is upregulated in fragile X syndrome premutation carriers, and silenced in patients with fragile X syndrome. FMR1-AS1 has an anti-apoptotic function. | https://en.wikipedia.org/wiki/FMR1-AS1_gene |
In molecular biology, GATA zinc fingers are zinc-containing domains found in a number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins). Some members of this class of zinc fingers specifically bind the DNA sequence (A/T)GATA(A/G) in the regulatory regions of genes., giving rise to the name of the domain. In these domains, a single zinc ion is coordinated by 4 cysteine residues. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. | https://en.wikipedia.org/wiki/GATA_zinc_finger |
The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed. | https://en.wikipedia.org/wiki/GATA_zinc_finger |
Two GATA zinc fingers are found in GATA-family transcription factors. However, there are several proteins that only contain a single copy of the domain. | https://en.wikipedia.org/wiki/GATA_zinc_finger |
It is also worth noting that many GATA-type Znfs (such as those found in the proteins GATAD2B and MTA1) have not been experimentally demonstrated to be DNA-binding domains. Furthermore, several GATA-type Znfs have been demonstrated to act as protein-recognition domains. For example, the N-terminal Znf of GATA1 binds specifically to a zinc finger from the transcriptional coregulator FOG1 (ZFPM1). | https://en.wikipedia.org/wiki/GATA_zinc_finger |
In molecular biology, Glycoside hydrolase family 10 is a family of glycoside hydrolases. Glycoside hydrolases EC 3.2.1. are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different families. This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.Glycoside hydrolase family 10 CAZY GH_10 comprises enzymes with a number of known activities; xylanase (EC 3.2.1.8); endo-1,3-beta-xylanase (EC 3.2.1.32); cellobiohydrolase (EC 3.2.1.91). | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_10 |
These enzymes were formerly known as cellulase family F. The microbial degradation of cellulose and xylans requires several types of enzymes such as endoglucanases (EC 3.2.1.4), cellobiohydrolases (EC 3.2.1.91) (exoglucanases), or xylanases (EC 3.2.1.8). Fungi and bacteria produces a spectrum of cellulolytic enzymes (cellulases) and xylanases which, on the basis of sequence similarities, can be classified into families. One of these families is known as the cellulase family F or as the glycosyl hydrolases family 10. == References == | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_10 |
In molecular biology, Glycoside hydrolase family 11 is a family of glycoside hydrolases. Glycoside hydrolases EC 3.2.1. are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different families. | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_11 |
This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.Glycoside hydrolase family 11 CAZY GH_11 comprises enzymes with only one known activity, xylanase (EC 3.2.1.8). These enzymes were formerly known as cellulase family G. == References == | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_11 |
In molecular biology, Glycoside hydrolase family 12 is a family of glycoside hydrolases. Glycoside hydrolases EC 3.2.1. are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different families. | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_12 |
This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.Glycoside hydrolase family 12 CAZY GH_12 comprises enzymes with the following activities: endoglucanase (EC 3.2.1.4), xyloglucan hydrolase (EC 3.2.1.151), β-1,3-1,4-glucanase (EC 3.2.1.73) and xyloglucan endotransglycosylase (EC 3.2.1.207). These enzymes were formerly known as cellulase family H. == References == | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_12 |
In molecular biology, Glycoside hydrolase family 14 is a family of glycoside hydrolases. Glycoside hydrolases EC 3.2.1. are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different families. This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.Glycoside hydrolase family 14 CAZY GH_14 comprises enzymes with only one known activity; beta-amylase (EC 3.2.1.2). | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_14 |
A Glu residue has been proposed as a catalytic residue, but it is not known if it is the nucleophile or the proton donor. Beta-amylase is an enzyme that hydrolyzes 1,4-alpha-glucosidic linkages in starch-type polysaccharide substrates so as to remove successive maltose units from the non-reducing ends of the chains. Beta-amylase is present in certain bacteria as well as in plants. | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_14 |
Three highly conserved sequence regions are found in all known beta-amylases. The first of these regions is located in the N-terminal section of the enzymes and contains an aspartate which is known to be involved in the catalytic mechanism. The second, located in a more central location, is centred on a glutamate which is also involved in the catalytic mechanism. | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_14 |
The 3D structure of a complex of soybean beta-amylase with an inhibitor (alpha-cyclodextrin) has been determined to 3.0A resolution by X-ray diffraction. The enzyme folds into large and small domains: the large domain has a (beta alpha)8 super-secondary structural core, while the smaller is formed from two long loops extending from the beta-3 and beta-4 strands of the (beta alpha)8 fold. The interface of the two domains, together with shorter loops from the (beta alpha)8 core, form a deep cleft, in which the inhibitor binds. Two maltose molecules also bind in the cleft, one sharing a binding site with alpha-cyclodextrin, and the other sitting more deeply in the cleft. == References == | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_14 |
In molecular biology, Glycoside hydrolase family 16 is a family of glycoside hydrolases. Glycoside hydrolases EC 3.2.1. are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different families. | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_16 |
This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes. y9 Glycoside hydrolase family 16 CAZY GH_16 comprises enzymes with a number of known activities; lichenase (EC 3.2.1.73); xyloglucan xyloglucosyltransferase (EC 2.4.1.207); agarase (EC 3.2.1.81); kappa-carrageenase (EC 3.2.1.83); endo-beta-1,3-glucanase (EC 3.2.1.39); endo-beta-1,3-1,4-glucanase (EC 3.2.1.6); endo-beta-galactosidase (EC 3.2.1.103). == References == | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_16 |
In molecular biology, Glycoside hydrolase family 17 is a family of glycoside hydrolases. It folds into a TIM barrel. Glycoside hydrolases EC 3.2.1. are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different families. | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_17 |
This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes. y9 Glycoside hydrolase family 17 CAZY GH_17 comprises enzymes with several known activities; endo-1,3-beta-glucosidase (EC 3.2.1.39); lichenase (EC 3.2.1.73); exo-1,3-glucanase (EC 3.2.1.58). Currently these enzymes have only been found in plants and in fungi. == References == | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_17 |
In molecular biology, Glycoside hydrolase family 18 is a family of glycoside hydrolases. Glycoside hydrolases EC 3.2.1. are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different families. This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.Some members of this family, CAZY GH_18, belong to the chitinase class II group which includes chitinase, chitodextrinase and the killer toxin of Kluyveromyces lactis. | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_18 |
The chitinases hydrolyse chitin oligosaccharides. Another chitinase II member is the novel gene Chitinase domain-containing protein 1. The family also includes various glycoproteins from mammals; cartilage glycoprotein and the oviduct-specific glycoproteins are two examples. == References == | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_18 |
In molecular biology, Glycoside hydrolase family 19 is a family of glycoside hydrolases. Glycoside hydrolases EC 3.2.1. are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different families. This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes. | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_19 |
y9 Glycoside hydrolase family 19 CAZY GH_19 comprises enzymes with only one known activity; chitinase (EC 3.2.1.14). Chitinases are enzymes that catalyze the hydrolysis of the beta-1,4-N-acetyl-D-glucosamine linkages in chitin polymers. Chitinases belong to glycoside hydrolase families 18 or 19. | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_19 |
Chitinases of family 19 (also known as classes IA or I and IB or II) are enzymes from plants that function in the defence against fungal and insect pathogens by destroying their chitin-containing cell wall. Class IA/I and IB/II enzymes differ in the presence (IA/I) or absence (IB/II) of a N-terminal chitin-binding domain. The catalytic domain of these enzymes consist of about 220 to 230 amino acid residues. | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_19 |
In molecular biology, Glycoside hydrolase family 2 is a family of glycoside hydrolases EC 3.2.1., which are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different families. This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.Glycoside hydrolase family 2 comprises enzymes with several known activities: beta-galactosidase (EC 3.2.1.23); beta-mannosidase (EC 3.2.1.25); beta-glucuronidase (EC 3.2.1.31). | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_2 |
These enzymes contain a conserved glutamic acid residue which has been shown, in Escherichia coli lacZ (P00722), to be the general acid/base catalyst in the active site of the enzyme. The catalytic domain of Beta-galactosidases have a TIM barrel core surrounded several other largely beta domains. The sugar binding domain of these proteins has a jelly-roll fold. These enzymes also include an immunoglobulin-like beta-sandwich domain. | https://en.wikipedia.org/wiki/Glycoside_hydrolase_family_2 |
In molecular biology, Human Accelerated Region 1 (Highly Accelerated Region 1, HAR1) is a segment of the human genome found on the long arm of chromosome 20. It is a human accelerated region. It is located within a pair of overlapping long non-coding RNA genes, HAR1A (HAR1F) and HAR1B (HAR1R). | https://en.wikipedia.org/wiki/Human_accelerated_region_1 |
In molecular biology, LSm proteins are a family of RNA-binding proteins found in virtually every cellular organism. LSm is a contraction of 'like Sm', because the first identified members of the LSm protein family were the Sm proteins. LSm proteins are defined by a characteristic three-dimensional structure and their assembly into rings of six or seven individual LSm protein molecules, and play a large number of various roles in mRNA processing and regulation. The Sm proteins were first discovered as antigens targeted by so-called anti-Sm antibodies in a patient with a form of systemic lupus erythematosus (SLE), a debilitating autoimmune disease. | https://en.wikipedia.org/wiki/Smith_antigen |
They were named Sm proteins in honor of Stephanie Smith, a patient who suffered from SLE. Other proteins with very similar structures were subsequently discovered and named LSm proteins. | https://en.wikipedia.org/wiki/Smith_antigen |
New members of the LSm protein family continue to be identified and reported. Proteins with similar structures are grouped into a hierarchy of protein families, superfamilies, and folds. The LSm protein structure is an example of a small beta sheet folded into a short barrel. | https://en.wikipedia.org/wiki/Smith_antigen |
Individual LSm proteins assemble into a six or seven member doughnut ring (more properly termed a torus), which usually binds to a small RNA molecule to form a ribonucleoprotein complex. The LSm torus assists the RNA molecule to assume and maintain its proper three-dimensional structure. Depending on which LSm proteins and RNA molecule are involved, this ribonucleoprotein complex facilitates a wide variety of RNA processing including degradation, editing, splicing, and regulation. Alternate terms for LSm family are LSm fold and Sm-like fold, and alternate capitalization styles such as lsm, LSM, and Lsm are common and equally acceptable. | https://en.wikipedia.org/wiki/Smith_antigen |
In molecular biology, LcrV is a protein found in Yersinia pestis and several other bacterial species. It forms part of the Yersinia pestis virulence protein factors that also includes all Yops, or Yersinia outer protein, but the name has been kept out of convention. LcrV's main function is not actually known, but it is essential for the production of other Yops. | https://en.wikipedia.org/wiki/LcrV |
The type III secretion system of Gram-negative bacteria is used to transport virulence factors from the pathogen directly into the host cell and is only triggered when the bacterium comes into close contact with the host. Effector proteins secreted by the type III system do not possess a secretion signal, and are considered unique because of this. Yersinia spp. | https://en.wikipedia.org/wiki/LcrV |
secrete effector proteins called YopB and YopD that facilitate the spread of other translocated proteins through the type III needle and the host cell cytoplasm. In turn, the transcription of these moieties is thought to be regulated by another gene, lcrV, found on the Yops virulon that encodes the entire type III system. The product of this gene, LcrV protein, also regulates the secretion of YopD through the type III translocon, and itself acts as a protective "V" antigen for Yersinia pestis, the causative agent of plague.A homologue of the Y. pestis LcrV protein, PcrV, has been found in Pseudomonas aeruginosa, an opportunistic pathogen. | https://en.wikipedia.org/wiki/LcrV |
In vivo studies using mice found that immunisation with the protein protected burned animals from infection by P. aeruginosa, and enhanced survival. In addition, it is speculated that PcrV determines the size of the needle pore for type III secreted effectors.LcrV is a multifunctional protein that has been shown to act at the level of secretion control by binding the Ysc inner-gate protein LcrG and to modulate the host immune response by altering cytokine production. LcrV is also necessary for full induction of low-calcium response (LCR) stimulon virulence gene transcription.The polypeptide is encoded on a plasmid and is only present when the surroundings are around 37o Celsius | https://en.wikipedia.org/wiki/LcrV |
In molecular biology, MobiDB is a curated biological database designed to offer a centralized resource for annotations of intrinsic protein disorder. Protein disorder is a structural feature characterizing a large number of proteins with prominent members known as intrinsically unstructured (or disordered) proteins. The database features three levels of annotation: manually curated, indirect and predicted. By combining different data sources of protein disorder into a consensus annotation, MobiDB aims at giving the best possible picture of the "disorder landscape" of a given protein of interest. | https://en.wikipedia.org/wiki/MobiDB |
In molecular biology, MvirDB is a publicly available database that stores information on toxins, virulence factors and antibiotic resistance genes. Sources that this database uses for DNA and protein information include: Tox-Prot, SCORPION, the PRINTS Virulence Factors, VFDB, TVFac, Islander, ARGO and VIDA. The database provides a BLAST tool that allows the user to query their sequence against all DNA and protein sequences in MvirDB. | https://en.wikipedia.org/wiki/MvirDB |
Information on virulence factors can be obtained from the usage of the provided browser tool. Once the browser tool is used, the results are returned as a readable table that is organized by ascending E-Values, each of which are hyperlinked to their related page. MvirDB is implemented in an Oracle 10g relational database. | https://en.wikipedia.org/wiki/MvirDB |
In molecular biology, OST4 (Dolichyl-diphosphooligosaccharide—protein glycosyltransferase subunit 4) is a subunit of the oligosaccharyltransferase complex. OST4 is a very short, approximately 30 amino acids, protein found from fungi to vertebrates. It appears to be an integral membrane protein that mediates the en bloc transfer of a pre-assembled high-mannose oligosaccharide onto asparagine residues of nascent polypeptides as they enter the lumen of the rough endoplasmic reticulum. | https://en.wikipedia.org/wiki/Oligosaccaryltransferase |
In molecular biology, Ornithine decarboxylase antizyme (ODC-AZ) is an ornithine decarboxylase inhibitor. It binds to, and destabilises, ornithine decarboxylase (ODC), a key enzyme in polyamine synthesis. ODC is then rapidly degraded. | https://en.wikipedia.org/wiki/Ornithine_decarboxylase_antizyme |
It was first characterized in 1981. The expression of ODC-AZ requires programmed, ribosomal frameshifting which is modulated according to the cellular concentration of polyamines. High levels of polyamines induce a +1 ribosomal frameshift in the translation of mRNA for the antizyme leading to the expression of a full-length protein. At least two forms of ODC-AZ exist in mammals and the protein has been found in Drosophila (protein Gutfeeling) as well as in Saccharomyces yeast (encoded by the OAZ1 gene).Human genes encoding Ornithine decarboxylase antizymes are OAZ1, OAZ2, and OAZ3. | https://en.wikipedia.org/wiki/Ornithine_decarboxylase_antizyme |
In molecular biology, Phosphotyrosine-binding domains are protein domains which bind to phosphotyrosine. The phosphotyrosine-binding domain (PTB, also phosphotyrosine-interaction or PI domain) in the protein tensin tends to be found at the C-terminus. Tensin is a multi-domain protein that binds to actin filaments and functions as a focal-adhesion molecule (focal adhesions are regions of plasma membrane through which cells attach to the extracellular matrix). Human tensin has actin-binding sites, an SH2 (Pfam PF00017) domain and a region similar to the tumour suppressor PTEN. | https://en.wikipedia.org/wiki/PTB_domain |
The PTB domain interacts with the cytoplasmic tails of beta integrin by binding to an NPXY motif.The phosphotyrosine-binding domain of insulin receptor substrate-1 is not related to the phosphotyrosine-binding domain of tensin. Insulin receptor substrate-1 proteins contain both a pleckstrin homology domain and a phosphotyrosine binding (PTB) domain. The PTB domains facilitate interaction with the activated tyrosine-phosphorylated insulin receptor. | https://en.wikipedia.org/wiki/PTB_domain |
The PTB domain is situated towards the N terminus. Two arginines in this domain are responsible for hydrogen bonding phosphotyrosine residues on an Ac-LYASSNPApY-NH2 peptide in the juxtamembrane region of the insulin receptor. Further interactions via "bridged" water molecules are coordinated by residues an Asn and a Ser residue. The PTB domain has a compact, 7-stranded beta-sandwich structure, capped by a C-terminal helix. The substrate peptide fits into an L-shaped surface cleft formed from the C-terminal helix and strands 5 and 6. | https://en.wikipedia.org/wiki/PTB_domain |
In molecular biology, Proteinase K (EC 3.4.21.64, protease K, endopeptidase K, Tritirachium alkaline proteinase, Tritirachium album serine proteinase, Tritirachium album proteinase K) is a broad-spectrum serine protease. The enzyme was discovered in 1974 in extracts of the fungus Parengyodontium album (formerly Engyodontium album or Tritirachium album). Proteinase K is able to digest hair (keratin), hence, the name "Proteinase K". | https://en.wikipedia.org/wiki/Proteinase_K |
The predominant site of cleavage is the peptide bond adjacent to the carboxyl group of aliphatic and aromatic amino acids with blocked alpha amino groups. It is commonly used for its broad specificity. This enzyme belongs to Peptidase family S8 (subtilisin). The molecular weight of Proteinase K is 28,900 daltons (28.9 kDa). | https://en.wikipedia.org/wiki/Proteinase_K |
In molecular biology, Pulmonary surfactant protein D (SP-D) is a protein domain predominantly found in lung surfactant. This protein plays a special role; its primary task is to act as a defence protein against any pathogens that may invade the lung. It also plays a role in lubricating the lung and preventing it from collapse. It has an interesting structure as it forms a triple-helical parallel coiled coil, helps the protein to fold into a trimer. | https://en.wikipedia.org/wiki/Pulmonary_surfactant_protein_D |
In molecular biology, Pyrococcus C/D box small nucleolar RNA are non-coding RNA (ncRNA) molecules identified in the archaeal genus Pyrococcus which function in the modification of ribosomal RNA (rRNA) and transfer RNA (tRNA). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell, which is a major site of ribosomal RNA and snRNA biogenesis, but there is no corresponding visible structure in archaeal cells. This group of ncRNAs are known as small nucleolar RNAs (snoRNA) and also often referred to as a guide RNAs because they direct associated protein enzymes to add a modification to specific nucleotides in target RNAs. | https://en.wikipedia.org/wiki/Pyrococcus_C/D_box_small_nucleolar_RNA |
C/D box RNAs guide the addition of a methyl group (-CH3) to the 2'-O position in the RNA backbone. Computational screens of archaeal genomes have identified C/D box snoRNAs in a number of genomes. In particular 46 small RNAs were identified to be conserved in the genomes of three hyperthermophile Pyrococcus species. | https://en.wikipedia.org/wiki/Pyrococcus_C/D_box_small_nucleolar_RNA |
In molecular biology, R64/Z200 is a member of the C/D class of small nucleolar RNA which guide the site-specific 2'-O-methylation of substrate RNA. This family can be found in Arabidopsis thaliana (R64) and Oryza sativa (Z200). | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_R64/Z200_family |
In molecular biology, REBASE is a database of information about restriction enzymes and DNA methyltransferases. REBASE contains an extensive set of references, sites of recognition and cleavage, sequences and structures. It also contains information on the commercial availability of each enzyme. REBASE is one of the longest running biological databases having its roots in a collection of restriction enzymes maintained by Richard J. Roberts since before 1980. Since that time there have been regular descriptions of the resource in the journal Nucleic Acids Research. | https://en.wikipedia.org/wiki/REBASE_(database) |
In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that catalyzes the chemical reactions that synthesize RNA from a DNA template. Using the enzyme helicase, RNAP locally opens the double-stranded DNA so that one strand of the exposed nucleotides can be used as a template for the synthesis of RNA, a process called transcription. A transcription factor and its associated transcription mediator complex must be attached to a DNA binding site called a promoter region before RNAP can initiate the DNA unwinding at that position. RNAP not only initiates RNA transcription, it also guides the nucleotides into position, facilitates attachment and elongation, has intrinsic proofreading and replacement capabilities, and termination recognition capability. | https://en.wikipedia.org/wiki/RNA_polymerases |
In eukaryotes, RNAP can build chains as long as 2.4 million nucleotides. RNAP produces RNA that, functionally, is either for protein coding, i.e. messenger RNA (mRNA); or non-coding (so-called "RNA genes"). | https://en.wikipedia.org/wiki/RNA_polymerases |
At least four functional types of RNA genes exist: Transfer RNA (tRNA) Transfers specific amino acids to growing polypeptide chains at the ribosomal site of protein synthesis during translation; Ribosomal RNA (rRNA) Incorporates into ribosomes; Micro RNA (miRNA) Regulates gene activity; and, RNA silencing Catalytic RNA (ribozyme) Functions as an enzymatically active RNA molecule.RNA polymerase is essential to life, and is found in all living organisms and many viruses. Depending on the organism, a RNA polymerase can be a protein complex (multi-subunit RNAP) or only consist of one subunit (single-subunit RNAP, ssRNAP), each representing an independent lineage. The former is found in bacteria, archaea, and eukaryotes alike, sharing a similar core structure and mechanism. | https://en.wikipedia.org/wiki/RNA_polymerases |
The latter is found in phages as well as eukaryotic chloroplasts and mitochondria, and is related to modern DNA polymerases. Eukaryotic and archaeal RNAPs have more subunits than bacterial ones do, and are controlled differently. Bacteria and archaea only have one RNA polymerase. Eukaryotes have multiple types of nuclear RNAP, each responsible for synthesis of a distinct subset of RNA: | https://en.wikipedia.org/wiki/RNA_polymerases |
In molecular biology, S4 domain refers to a small RNA-binding protein domain found in a ribosomal protein named uS4 (called S9 in eukaryotes). The S4 domain is approximately 60-65 amino acid residues long, occurs in a single copy at various positions in different proteins and was originally found in pseudouridine syntheses, a bacterial ribosome-associated protein.The S4 protein helps to initiate assembly of the 16S rRNA. In this way proteins serve to organise and stabilise the rRNA tertiary structure. | https://en.wikipedia.org/wiki/S4_protein_domain |
In molecular biology, SNORA1 (also known as ACA1) is a member of the H/ACA class of small nucleolar RNA that guide the sites of modification of uridines to pseudouridines. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_SNORA1 |
In molecular biology, SNORA13 (also known as ACA13) is a member of the H/ACA class of small nucleolar RNA that guide the sites of modification of uridines to pseudouridines. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_SNORA13 |
In molecular biology, SNORA14 (also known as ACA14) is a member of the H/ACA class of small nucleolar RNA that guide the sites of modification of uridines to pseudouridines. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_SNORA14 |
In molecular biology, SNORA15 (also known as ACA15) is a member of the H/ACA class of small nucleolar RNA that guide the sites of modification of uridines to pseudouridines.This family also includes the mouse MBI-79 sequence. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_SNORA15 |
In molecular biology, SNORA17 (also known as ACA17) is a member of the H/ACA class of small nucleolar RNA that guide the sites of modification of uridines to pseudouridines. Specifically, it is predicted to guide pseudouridylation of the 28S rRNA at positions U4659 and U4598. It shares the same host gene together with ACA43. There are many closely related sequences that do not appear to have conserved H and ACA boxes, and may be pseudogenes. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_SNORA17 |
In molecular biology, SNORA18 (also known as ACA18) is a member of the H/ACA class of small nucleolar RNA that guide the sites of modification of uridines to pseudouridines. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_SNORA18 |
In molecular biology, SNORA19 (also known as ACA19) is a member of the H/ACA class of small nucleolar RNA that guide the sites of modification of uridines to pseudouridines.The family also includes the mouse sequence MBI-51. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_SNORA19 |
In molecular biology, SNORA2 (also known as ACA2) is a non-coding RNA (ncRNA) which modifies other small nuclear RNAs (snRNAs). It is a member of the H/ACA class of small nucleolar RNA that guide the sites of modification of uridines to pseudouridines.ACA2 was originally cloned from HeLa cells by association with GAR1 protein. It has the predicted hairpin-hinge-hairpin-tail structure and has the conserved H/ACA-box motifs. Originally two sequence variants of ACA2 were identified (called ACA2a and ACA2b). | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_SNORA2 |
Both variants share approximately 66% sequence identity to another snoRNA characterised in the same study called ACA34 (also known as SNORA34). In the human genome all three snoRNAs (ACA2a, ACA2b and ACA34) are found to be located in the introns of the same gene. This gene encodes a predicted protein referred to as FLJ20436.Both variants of ACA2 have the same two predicted target sites (U4263 and U4282) in 28S ribosomal RNA (rRNA). ACA34 is also predicted to target one of these sites (U4282) in addition to U4269 of 28S rRNA. The sequence similarity, genomic location and the predicted target sites of these three snoRNAs suggest they have been generated by subsequent gene duplications during evolution. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_SNORA2 |
In molecular biology, SNORA20 (also known as ACA20) is a member of the H/ACA class of small nucleolar RNA that guide the sites of modification of uridines to pseudouridines. | https://en.wikipedia.org/wiki/Small_nucleolar_RNA_SNORA20 |
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