Multiple Epidermal Growth Factor-like Domains 8

"Megf8" also known as Multiple Epidermal Growth Factor-like Domains 8, is a protein coding gene that encodes a single pass membrane protein, known to participate in developmental regulation and cellular communication. It is located on chromosome 19 at the 49th open reading frame in humans (19q13.2). There are two isoform constructs known for MEGF8, which differ by a 67 amino acid indel. The isoform 2 splice version (analyzed throughout this page) is 2785 amino acids long, and predicted to be 296.6 kdal in mass. Isoform 1 is composed of 2845 amino acids and predicted to weigh 303.1 kdal. Using BLAST searches, orthologs were found primarily in mammals, but MEGF8 is also conserved in invertebrates and fishes, and rarely in birds, reptiles, and amphibians. A notably important paralog to multiple epidermal growth factor-like domains 8 is ATRNL1 (Attractin-like 1), which is also a single pass transmembrane protein, with several of the same key features and motifs as MEGF8, as indicated by Simple Modular Architecture Research Tool (SMART) which is hosted by the European Molecular Biology Laboratory located in Heidelberg, Germany. MEGF8 has been predicted to be a key player in several developmental processes, such as left-right patterning and limb formation. Currently, researchers have found MEGF8 SNP mutations to be the cause of Carpenter syndrome subtype 2.
Gene.
Evolution & Orthologs.
A fairly highly conserved protein, MEGF8 has conserved orthologs from P. paniscus to N. vectensis. Orthologs are found in mammals, amphibians, fish, insects, crustaceans, and invertebrates. Organization of the data showed that as time since divergence between humans and orthologs increased, the sequence identity decreased.
Paralogs.
MEGF8 has one known paralog: ATRNL1. The ATRNL1 protein is approximately half the length of MEGF8, and contains several of the same conserved domains, including the CUB domain and transmembrane sequence. It is key to note that ATRNL1 is found in many birds and amphibians, where MEGF8 is not found in any birds, and only one amphibian.
Promoters.
Genomatix's ElDorado (http://www.genomatix.de/), a gene promoter database, predicted ten different possible promoters for "megf8." The promoter having promoter ID number GXP_1262882 and transcript ID GXT_22531930, was predicted with the highest confidence. This promoter is located on the plus strand of chromosome 19, ranging from nucleotide 42829077 to 42830497, making it a 1421 nucleotide long sequence. The promoter sequence overlaps with the transcriptional start codon in the gene.
Transcription Factors.
More than one hundred transcription factor binding sites were predicted to be found in the "megf8" promoter region through Genomatix. The top twenty most confidently predicted factors include the following:
Protein Architecture.
Primary Structure.
MEGF8 is composed of either 2845 amino acids (Isoform 1) or 2778 amino acids (Isoform 2). Isoform 2 undergoes a 67 amino acid removal from 700-766, which accounts for its shortened length; otherwise, the two isoforms are identical. Using SAPS, a Statistical Analysis of Protein Sequence software, amino acid bias was able to be determined. Isoform one is rich in cysteine and glycine, and deficient in isoleucine and lysine. Isoform 2 of MEGF8 was found to have very high levels of cysteine, moderately high levels of glycine, and low levels of isoleucine and lysine.
The high levels of cysteine residues contributes to the numerous disulfide bonds found in the mature protein's folded structure. Overall, MEGF8 has a pH between 6.4 and 7.0, depending on the organism's sequence. Human MEGF8's pH is 6.4. This nearly neutral pH enables the protein to fold properly and inhibits denaturation. The twenty most conserved amino acids, found through a multiple sequence alignment of 20 orthologs, were found to be located in the CUB and transmembrane domains.
Secondary Structure.
Prediction software PELE from UCSC Biology Workbench indicated that MEGF8 is primarily composed of beta-folded sheets, with occasional short alpha helix segments. PELE uses eight different prediction programs to compare and confirm predictions, enhancing the confidence level. The beta-folded sheets occur at many of the key domains, including the EGF-domains, kelch domains, and EGF-laminin domains. This information from PELE also corresponded with the secondary structure and 3D structure predictions made by PHYRE2
Predicted Key Domains & Features.
MEGF8 is predicted to contain several different types of features, domains, and motifs that play a key role in the protein's function, structure, and location. These are listed in Table 1. Functions, found through SMART analysis, as well as NCBI Conserved Domains Search include:
Tertiary Structure.
One of the key attributes of MEGF8's tertiary structure is its 7-bladed beta propeller which is formed by the kelch motif found in its D1k3ia3 structural domain, which was identified by SCOP. SCOP also indicated that the beta-propeller in MEGF8 is a member of the galactose oxidase super family. Each of the seven blades are made up of a four stranded beta-folded motifs. It is also important to note that although many phosphorylation sites are predicted at high confidence, several other topographic predictions (i.e. disulfide bonds, glycosylation, other extracellular features), do not support these predictions.
Expression.
MEGF8 is found to be expressed at high levels in cardiac myocytes and fetal brain tissue, according to GeoProfiles, from NCBI. This GeoProfile also indicated that MEGF8 was found to be at moderate to moderately low expression levels in all other tissues examined. NCBI GeoProfile data also provided the tissue expression graph for MEGF8 in humans, which is displayed to the right, further illustrating specific sites and levels of expression
Function and Mechanisms in Cellular Processes.
Molecular Function.
According to BioGPS<ref name="10.1186/gb-2009-10-11-r130"></ref> gene ontology information, MEGF8 is an active participant in receptor activity, calcium ion binding, protein binding.
Role in Biological Processes.
Analysis of gene ontology information by BioGPS was able to produce a list of biological processes in each of which MEGF8 plays a significant role:
Putative Interactions.
In the table below, all predicted interactions, except SMARCD3, are supported by two-hybrid screen experimental data. This information is supported by both NextProt database and IntAct database. The two interactions with the highest confidence value are also supported by materials found by text-mining in STRING. Together, it is with reasonably high confidence that the proteins in red are interacting with MEGF8, and with moderate confidence that the proteins in green interact with MEGF8. The confidence level for the proteins in blue is much lower, which may mean that the two-hybrid assay provided a false positive, or that they actually are interacting.
Alternative Splicing, Mutations, & Phenotypic Impacts.
Splice Variants.
The four primary splice variants and their distinctions are described below (labels correspond to those in image below):
A: has spliced out Exon 13. Looking at the attached working conceptual translation, it can be seen that exon 3 does not code for any feature, domain, motif or other functional section of aa, and is likely therefore not key to the function of MEGF8 protein. This is the variant that corresponds to the splice model of the analyzed megf8.
B: Spliced out exons 1-6; these exons hold several key domains and motifs including the CUB domain, two PSI domains, a D1k3ia3 structural domain, and a kelch repeat. This may result in a misfolded protein without the structural segments, and inhibit participation in development events (loss of PSI and CUB). Still has signal and TMEM so may still be able to partially function
 C: part of the D1k3ia3 structural domain remains in exon 29, but the kelch repeat has been excised, which could lead to structural issues. Also this variant contains almost 3 PSI domains, and an area of low complexity in exons 32-35, which may allow this variant to function in the cell, but no signal or TMEM to place in membrane so not a normal function
D: This variant is exons 36-40, excised 41, and a shortened 42 exon. It possesses EGF calcium domains and EGF/EGF-like domains. Loss of 41 will drastically alter the function as it possesses the TMEM segment. It depends on where 41 is lost and 42 is cleaved.
Common Mutations.
SNPs.
There are several SNPs, found through NCBI GeneView, that cause missense or silent mutations in MEGF8. However, three SNP mutations were identified as causes of Carpenter Syndrome 2 by Twigg et al.<ref name="10.1016/j.ajhg.2012.08.027"></ref> The three SNP mutations are: Gly199 to Arg; Arg1499 to His; Ser2367 to Gly. The article by Twigg includes a supplementary data set that shows a multiple sequence alignment of the regions surrounding the SNPs and the domain in which the SNP lies. The Gly199 to Arg mutation is located inside an EGF-domain; the Arg1499 to His mutation is located within a kelch domain in the 7-bladed beta-sheet propeller; the Ser2367 to Gly is located within an EGF-Laminin domain. These domain are important to maintaining a properly folded protein and its function.
Carpenter Syndrome 2.
Visit Carpenter syndrome for more extensive details related to the disease. Genetic mutations in MEGF8 have been found to be a principal cause of this rare genetic syndrome.
Adverse Phenotypic Consequences.
Mutations in MEGF8 have been found to be linked to defective lateralization during development, as reported by Twigg et al. Common features of individuals with Carpenter Syndrome Subtype II include the following:
Current Research.
There is no research being done currently to develop treatment or cures for Carpenter Syndrome 2. Researchers are still striving to understand the cause of the point mutations in MEGF8 that result in this extremely rare genetic disease.


Maltotriose

Maltotriose is a trisaccharide (three-part sugar) consisting of three glucose molecules linked with α-1,4 glycosidic bonds.
It is most commonly produced by the digestive enzyme alpha-amylase (a common enzyme in human saliva) on amylose in starch. The creation of both maltotriose and maltose during this process is due to the random manner in which alpha amylase hydrolyses α-1,4 glycosidic bonds.
It is the shortest chain oligosaccharide that can be classified as maltodextrin


Amine oxidase (copper-containing)

Amine oxidase (copper-containing) (AOC) ( and ; formerly ) is a family of amine oxidase enzymes which includes both primary-amine oxidase and diamine oxidase; these enzymes catalyze the oxidation of a wide range of biogenic amines including many neurotransmitters, histamine and xenobiotic amines. They act as a disulphide-linked homodimer. They catalyse the oxidation of primary amines to aldehydes, with the subsequent release of ammonia and hydrogen peroxide, which requires one copper ion per subunit and topaquinone as cofactor:
The 3 substrates of this enzyme are primary amines (RCH2NH2), H2O, and O2, whereas its 3 products are RCHO, NH3, and H2O2.
Copper-containing amine oxidases are found in bacteria, fungi, plants and animals. In prokaryotes, the enzyme enables various amine substrates to be used as sources of carbon and nitrogen.
This enzyme belongs to oxidoreductases, specifically those acting on the CH-NH2 group of donors with oxygen as acceptor. The systematic name of this enzyme class is amine:oxygen oxidoreductase (deaminating) (copper-containing). This enzyme participates in 8 metabolic pathways: urea cycle and metabolism of amino groups, glycine, serine and threonine metabolism, histidine metabolism, tyrosine metabolism, phenylalanine metabolism, tryptophan metabolism, beta-alanine metabolism, and alkaloid biosynthesis ii. It has 2 cofactors: copper, and PQQ.
Structure.
The copper amine oxidase 3-dimensional structure was determined through X-ray crystallography.
The copper amine oxidases occur as mushroom-shaped homodimers of 70-95 kDa, each monomer containing a copper ion and a covalently bound redox cofactor, topaquinone (TPQ). TPQ is formed by post-translational modification of a conserved tyrosine residue. The copper ion is coordinated with three histidine residues and two water molecules in a distorted square pyramidal geometry, and has a dual function in catalysis and TPQ biogenesis. The catalytic domain is the largest of the 3-4 domains found in copper amine oxidases, and consists of a beta sandwich of 18 strands in two sheets. The active site is buried and requires a conformational change to allow the substrate access.
The N2 and N3 N-terminal domains share a common structural fold, its core consisting of alpha-beta(4), where the helix is packed against the coiled anti-parallel beta-sheets. An additional domain is found at the N-terminal of some copper amine oxidases, as well as in related proteins such as cell wall hydrolase and N-acetylmuramoyl-L-alanine amidase. This domain consists of a five-stranded antiparallel beta-sheet twisted around an alpha helix.
Function.
In eukaryotes they have a broader range of functions, including cell differentiation and growth, wound healing, detoxification and cell signalling; one AOC enzyme (AOC3) functions as a vascular adhesion protein (VAP-1) in some mammalian tissues.


Ure2p

Ure2p is a yeast protein that represses transcription of genes involved in nitrogen catabolism. It specifically regulates the utilization of poor nitrogen sources in the presence of preferred nutrients such as ammonia or glutamine. Ure2p is one of the few yeast proteins that are known to be prions. At low frequency the protein adopts an alternative conformation that is auto-catalytic and self-propagating. Yeast cells that carry the protein in the prion conformation are designated as [URE3]. Autocatalytic conversion of Ure2p into the inactive prion form of the protein results in a loss of repression of nitrogen catabolic genes.


3beta-hydroxy-5alpha-steroid dehydrogenase

In enzymology, a 3β-hydroxy-5α-steroid dehydrogenase () is an enzyme that catalyzes the chemical reaction
Thus, the two substrates of this enzyme are 3β-hydroxy-5α-pregnane-20-one (allopregnanolone) and NADP+, whereas its 3 products are 5α-pregnan-3,20-dione, NADPH, and H+.
This enzyme belongs to the family of oxidoreductases, specifically those acting on the CH-OH group of donor with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is 3β-hydroxy-5α-steroid:NADP+ 3-oxidoreductase.


Cerberus gene family


Dimethylcarbamoyl fluoride

Dimethylcarbamoyl fluoride is a chemical compound that can be produced by fluorinating the dimethylcarbamoyl chloride with potassium fluoride. It's a colorless liquid that is soluble and stable in water.
Dimethylcarbamoyl fluoride is highly toxic because it's a potent cholinesterase inhibitor and is lethal even at low doses.


(S)-squalene-2,3-epoxide hydro-lyase

(S)-squalene-2,3-epoxide hydro-lyase may refer to:


Nicotinamide riboside

Nicotinamide riboside (NR, SR647) is a pyridine-nucleoside similar to vitamin B3, functioning as a precursor to nicotinamide adenine dinucleotide or NAD+.
Chemistry.
While the molecular weight of nicotinamide riboside is 255.25 g/mol, that of its chloride salt is 290.70 g/mol. As such, 100 mg of nicotinamide riboside chloride provides 88 mg of nicotinamide riboside.
History.
Nicotinamide riboside (NR) was first described in 1944 as a growth factor, termed Factor V, for "Haemophilus influenza", a bacterium that lives in and depends on blood. Factor V, purified from blood, was shown to exist in three forms: NAD+, NMN and NR. NR was the compound that led to the most rapid growth of this bacterium. "H. influenza" cannot grow on nicotinic acid, nicotinamide, tryptophan or aspartic acid, which were the previously known precursors of NAD+.
In 2000, yeast Sir2 was shown to be an NAD+-dependent protein lysine deacetylase, which led several research groups to probe yeast NAD+ metabolism for genes and enzymes that might regulate lifespan.
Synthesis.
Different biosynthetic pathways are responsible for converting the different B3 vitamins into NAD+. The enzyme nicotinamide phosphoribosyltransferase (Nampt) catalyzes the rate-limiting step of the two-step pathway converting nicotinamide to NAD+. NR kinase enzymes can also function as a salvage pathway for NAD+, but this pathway is not essential.
Commercialization.
ChromaDex licensed patents in July 2012, and began to develop a process to bring NR to market. ChromaDex has been in a patent dispute with Elysium Health over the rights to nicotinamide riboside supplements.<ref name="CEN_8/19/2018"></ref>
Biosynth Carbosynth licensed a patent to produce new NR salts . The new carboxylic acid salts in crystalline form can be used in nutritional supplements and pharmaceutical compositions.


Azurin

Azurin is a small, periplasmic, bacterial blue copper protein found in "Pseudomonas", "Bordetella", or "Alcaligenes" bacteria. Azurin moderates single-electron transfer between enzymes associated with the cytochrome chain by undergoing oxidation-reduction between Cu(I) and Cu(II). Each monomer of an azurin tetramer has a molecular weight of approximately 14kDa, contains a single copper atom, is intensively blue, and has a fluorescence emission band centered at 308 nm.
Azurins and pseudoazurins participate in the denitrification processes in bacteria., including the gram-negative bacteria "Pseudomonas aeruginosa," by interacting with cytochrome c551. Azurin from "P aeruginosa" is a type I blue copper protein (cupredoxin), while cytochrome c551 (9 kDa) is a haem-containing cytochrome. Azurin possesses a relatively large hydrophobic patch close to the active site, and two residues in this hydrophobic patch, Met-44 and Met-64, are believed to be involved in its interaction with the redox partners cytochrome c551 and nitrite reductase.
Although unrelated to its electron-transfer property, azurin has been found to have anticancer properties through its interaction with tumor-suppressor protein p53.
Enzyme mechanism.
In its oxidized form, azurin (Cu2+Az) receives an electron from its redox partner and is reduced according to the following reaction:
Cu2+Az + e− -> Cu+Az
The redox potential is 310 mV.
The highly-interconnected beta-sheet structure of azurin is strongly coupled with its electron-transfer center (the copper-binding side). Considerable experimental evidence exists to suggest that hydrogen bonds play a role in the long-distance electron transfer mechanism of azurin. Taken together, these observations suggest that electrons tunnel through the enzyme along its polypeptide and hydrogen bonds, making azurin is a useful model system for studying long-range, intraprotein electron transfer (LRET).
Enzyme structure.
Azurin is a tetrameric protein. Each monomer weighs approximately 14kDa and is composed of 128 amino acids forming eight beta-strands arranged in a beta-barrel formation. The strands are connected by turns and a single alpha-helical insertion. A single-atom copper binding site is located about 7A below each monomer’s surface towards its northern end; the copper atom that inhabits it is coordinated by five ligands surrounded by an extensive hydrophobic patch.
The three equatorial copper ligands are composed of a thiolate (Cys112) and two imidazoles (His46, His 117), and the carbonyl oxygen atoms of Gly45 and Met121 serve as the two weak axial ligands. With the exception of Gly45, the copper-binding configuration above is common to the structures of all blue type 1 copper-binding proteins determined thus far. Once coordinated, the ligand-metal complex assumes a distorted, trigonal bi-pyramidal geometry that stabilizes the cuprous (Cu(I)) reduced state of the protein relative to the cupric (Cu(II)) oxidized state. Structurally imposed backbonding between the copper d orbitals and its ligand p orbitals may further stabilize the cuprous state.
Existing structural information about azurin has largely been derived from X-ray crystallography studies of single-site mutated forms of the protein. Notable structural features elucidated by crystallography include the beta-sandwich motif formed from eight interlocking beta strands, as well as an alpha-helical segment outside the barrel linking beta-sheets 4 and 5.
Although the Cu(I)/Cu(II) redox potential is typically higher for azurin than most other copper complexes, structural studies in which Met121 (one of azurin’s equatorial copper-coordinating ligands) is replaced have demonstrated that the absence of a thiolate copper ligand does not preclude high reduction potentials, as large hydrophobic residues in position 121 also raise the redox potential of the copper atom. Thus, the higher redox potentials have been attributed to the exclusion of water from the metal-binding site, a condition augmented by the presence of bulky hydrophobic residues.
Conversely, negatively charged residues lower the redox potential, since they stabilize the more positively charged cupric form of the copper ion.
Biological function.
When expressed in nitrogen-fixing organisms, azurin serves as the electron donor to nitrite reductase, an enzyme in the denitrification pathway of the nitrogen cycle.
Azurins support oxidative deamination of primary amines by passing electrons from aromatic amine dehydrogenase to cytochrome oxidase, as well as from some c-type cytochromes to nitrite reductases.
Disease relevance.
Azurin has garnered significant attention as a potential therapeutic for various diseases, including cancer. In vivo, it has been demonstrated to induce regression of human melanoma and breast cancer tissue with minimal toxic effects to the organism.
Azurin enters preferentially into cancer cells via the p28 domain of the enzyme, which roughly corresponds to the extended alpha-helical region of the enzyme. In cancer cells, azurin complexes with p53, stabilizing it and preventing association with E3 uiquitin ligases, which would otherwise bind and mark the protein for destruction. Four azurin molecules bind each p53 monomer with high affinity. The p53/azurin complex travels to the nucleus, where p53 upregulates the transcription of proapoptotic genes Bax and Noxa. P53 also activates the expression of cell-cycle inhibitors, preventing tumor cells from progressing beyond the G1 or S phase. Although this pathway plays a significant role in azurin’s anticancer activity, the details of the interaction between azurin and p53 are not well understood.
A phase I clinical trial in the United States demonstrated both partial and complete tumor regression effects in fifteen stage IV cancer patients treated with the p28 amino-acid fragment of azurin. Another phase I trial with the p28 fragment demonstrated azurin’s therapeutic effects against pediatric patients with brain tumors; subsequently, the USFDA approved the designation of p28 as an orphan drug for glioma.
Azurin’s other domains may also exhibit strong anticancer activity by binding to cell surface receptor tyrosine kinases such as EphB2 receptors, which induce angiogenesis in cancer cells. This is another mechanism by which azurin has been proposed to exhibit its therapeutic effects.


Zebularine

Zebularine is a nucleoside analog of cytidine. It is a transition state analog inhibitor of cytidine deaminase by binding to the active size as covalent hydrates. Also shown to inhibit DNA methylation and tumor growth both in vitro and in vivo.
In a small study of mice with a defective "Adenomatous polyposis coli" gene, oral administration of zebularine to males had no effect on the overall methylation of DNA or the number of polyps, but in females the average number of polyps was reduced from 58 to 1. It has therefore been suggested for drug use as a prototype of epigenetic therapy for cancer chemoprevention.


Hesperadin

Hesperadin is an aurora kinase inhibitor.
The small molecule inhibits chromosome alignment and segregation by limiting the function of mitotic kinases Aurora B and Aurora A. Hesperadin causes cells to enter anaphase much faster, sometimes before the chromosomes are properly mono-oriented.
Hesperadin, like other miotic inhibitors, limits and sometimes can stop the process of mitosis in cells. For this reason, some have considered hesperadin's potential as a cancer-preventing drug.
Hesperadin works as an inhibitor, attaching to the active sites of Aurora A and Aurora B kinases.


Globulin

The globulins are a family of globular proteins that have higher molecular weights than albumins and are insoluble in pure water but dissolve in dilute salt solutions. Some globulins are produced in the liver, while others are made by the immune system. Globulins, albumins, and fibrinogen are the major blood proteins. The normal concentration of globulins in human blood is about 2.6-3.5 g/dL.
The term "globulin" is sometimes used synonymously with "globular protein". However, albumins are also globular proteins, but are "not" globulins. All other serum globular proteins are globulins.
Types of globulins.
All globulins fall into one of the following four categories :
Globulins can be distinguished from one another using serum protein electrophoresis.
Globulins exert oncotic pressure. Their deficiency results in loss of carrier functions of globulins, oedema due to decreased oncotic pressure, and susceptibility to infections due to decreased gamma-globulins (immuno-globulins) leading to decreased production of antibodies.
Sizes ~ weights.
Globulins exist in various sizes. The lightest globulins are the alpha globulins, which typically have molecular weights of around 93 kDa, while the heaviest class of globulins are the gamma globulins, which typically weigh about 1193 kDa. Being the heaviest, the gamma globulins are among the slowest to segregate in gel electrophoresis.
The immunologically active gamma globulins are also called "immunoglobulins" or "antibodies".
Human blood plasma levels.
The normal concentration of globulins in human blood is about 2.6-4.6 g/dL.
Nonhuman globulins.
Globulin proteins exist not only in other animal species, but also in plants. Vicilin and legumin, from peas and other legumes, function as protein storage within seeds. These proteins can cause allergic reactions if they bind with human IgE antibodies.
Pseudoglobulins and euglobulins.
Pseudoglobulins are a class of globulins that are more soluble in ammonium sulfate than euglobulins. Pseudoglobulins are also soluble in pure water, while euglobulins are not.


6-aminohexanoate-dimer hydrolase

In enzymology, a 6-aminohexanoate-dimer hydrolase () is an enzyme that catalyzes the chemical reaction N-(6-aminohexanoyl)-6-aminohexanoate + H2O formula_1 2 6-aminohexanoate. Thus, the two substrates of this enzyme are N-(6-aminohexanoyl)-6-aminohexanoate and H2O, whereas its product is two Molecules of 6-aminohexanoate.
This enzyme belongs to the family of hydrolases, those acting on carbon-nitrogen bonds other than peptide bonds, specifically in linear amides. The systematic name of this enzyme class is N-(6-aminohexanoyl)-6-aminohexanoate amidohydrolase. This enzyme is also called 6-aminohexanoic acid oligomer hydrolase.
Structural studies.
As of late 2007, 3 structures have been solved for this class of enzymes, with PDB accession codes , , and .


Carboxypeptidase G

Carboxypeptidase G may refer to:


Hop (protein)

Hop, occasionally written HOP, is an abbreviation for Hsp70-Hsp90 Organizing Protein. It functions as a co-chaperone which reversibly links together the protein chaperones Hsp70 and Hsp90.
Hop belongs to the large group of co-chaperones, which regulate and assist the major chaperones (mainly heat shock proteins). It is one of the best studied co-chaperones of the Hsp70/Hsp90-complex. It was first discovered in yeast and homologues were identified in human, mouse, rat, insects, plants, parasites, and virus. The family of these proteins is referred to as STI1 (stress inducible protein) and can be divided into yeast, plant, and animal STI1 (Hop).
Gene.
The gene for human Hop is located on chromosome 11q13.1 and consists of 14 exons.
Structure.
STI proteins are characterized by some structural features: All homologues have nine tetratricopeptide repeat (TPR) motifs, that are clustered into domains of three TPRs. The TPR motif is a very common structural feature used by many proteins and provides the ability of directing protein-protein interactions. Crystallographic structural information is available for the N-terminal TPR1 and the central TPR2A domains in complex with Hsp90 resp. Hsp70 ligand peptides.
The Hsp70-Hsp90 Organizing Protein (Hop, STIP1 in humans) is the co-chaperone responsible for the transfer of client proteins between Hsp70 and Hsp90. Hop is evolutionarily conserved in Eukaryotes and is found in both the nucleus and cytoplasm. "Drosophila" Hop is a monomeric protein that consists of three tetratricopeptide repeat domain regions (TPR1, TPR2A, TPR2B), one aspartic acid-proline repeat domain (DP). The TPR domains interact with the c-terminals of Hsp90 and Hsp70, with TPR1 and TPR2B binding to Hsp70 and TPR2A binding preferentially to Hsp90. The intermediate structures of heat shock machinery are difficult to characterize completely because of the transient and fast paced nature of chaperone function.
Function.
The main function of Hop is to link Hsp70 and Hsp90 together. But recent investigations indicate that it also modulates the chaperone activities of the linked proteins and possibly interacts with other chaperones and proteins. Apart from its role in the Hsp70/Hsp90 "chaperone machine" it seems to participate in other protein complexes too (for example in the signal transduction complex EcR/USP and in the Hepatitis B virus reverse transcriptase complex, which enables the viral replication). It acts as a receptor for prion proteins too. Hop is located in diverse cellular regions and also moves between the cytoplasm and the nucleus.
In "Drosophila" RNA interference pathways, Hop has been shown to be an integral part of the pre-RISC complex for siRNAs. In the "Drosophila" Piwi-interacting RNA pathway, the RNA interference pathway responsible for the repression of transposable elements (transposons), Hop has been shown to interact with Piwi, and in the absence of Hop, transposons are derepressed, leading to severe genomic instability and infertility.
Interactions.
Human Hop (STIP1) has been shown to interact with PRNP and Heat shock protein 90kDa alpha (cytosolic), member A1.


SLC2A9

Solute carrier family 2, facilitated glucose transporter member 9 is a protein that in humans is encoded by the "SLC2A9" gene.
This gene encodes a member of the SLC2A facilitative glucose transporter family. Members of this family play a significant role in maintaining glucose homeostasis. The encoded protein may play a role in the development and survival of chondrocytes in cartilage matrices. Two transcript variants encoding distinct isoforms have been identified for this gene.
SLC2A9 has also recently been found to transport uric acid, and genetic variants of the transporter have been linked to increased risk of development of both hyperuricemia, gout and Alzheimer's disease.


NPMA

NPMA may refer to:


3-hydroxy-3-isohexenylglutaryl-CoA lyase

In enzymology, a 3-hydroxy-3-isohexenylglutaryl-CoA lyase () is an enzyme that catalyzes the chemical reaction
Hence, this enzyme has one substrate, 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA, and two products, 7-methyl-3-oxooct-6-enoyl-CoA and acetate.
This enzyme belongs to the family of lyases, specifically the oxo-acid-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA acetate-lyase (7-methyl-3-oxooct-6-enoyl-CoA-forming). Other names in common use include beta-hydroxy-beta-isohexenylglutaryl CoA-lyase, hydroxyisohexenylglutaryl-CoA:acetatelyase, 3-hydroxy-3-isohexenylglutaryl coenzyme A lyase, 3-hydroxy-3-isohexenylglutaryl-CoA isopentenylacetoacetyl-CoA-lyase, and 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA acetate-lyase.


Ketohexose


ErmC 23S rRNA methyltransferase

ErmC 23S rRNA methyltransferase may refer to:


Lipid storage disorder

A lipid storage disorder (or lipidosis) is any one of a group of inherited metabolic disorders in which harmful amounts of fats or lipids accumulate in some of the body’s cells and tissues. People with these disorders either do not produce enough of one of the enzymes needed to metabolize and break down lipids or they produce enzymes that do not work properly. Over time, the buildup of fats can cause permanent cellular and tissue damage, particularly in the brain, peripheral nervous system, liver, spleen and bone marrow.
Inside cells under normal conditions, lysosomes convert, or metabolize, lipids and proteins into smaller components to provide energy for the body.
Classification.
Disorders that store this intracellular material are part of the lysosomal storage diseases family of disorders.
Sphingolipidoses.
Many lipid storage disorders can be classified into the subgroup of sphingolipidoses, as they relate to sphingolipid metabolism. Members of this group include Niemann-Pick disease, Fabry disease, Krabbe disease, Gaucher disease, Tay–Sachs disease, metachromatic leukodystrophy, multiple sulfatase deficiency and Farber disease. They are generally inherited in an autosomal recessive fashion, but Fabry disease is X-linked. Taken together, sphingolipidoses have an incidence of approximately 1 in 10,000. Enzyme replacement therapy is available to treat mainly Fabry disease and Gaucher disease, and people with these types of sphingolipidoses may live well into adulthood. The other types are generally fatal by age 1 to 5 years for infantile forms, but progression may be mild for juvenile- or adult-onset forms.
Some of the sphingolipidoses may alternatively be classified into either GM1 gangliosidoses or GM2 gangliosidoses. Tay–Sachs disease belongs to the latter.
Other.
Other lipid storage disorders that are generally not classified as sphingolipidoses include fucosidosis, Schindler disease and Wolman disease.
Genetics.
Lipid storage diseases can be inherited two ways:
Autosomal recessive inheritance occurs when both parents carry and pass on a copy of the faulty gene, but neither parent show signs and symptoms of the condition and is not affected by the disorder. Each child born to these parents have a 25 percent chance of inheriting both copies of the defective gene, a 50 percent chance of being a carrier, and a 25 percent chance of not inheriting either copy of the defective gene. Children of either gender can be affected by an autosomal recessive this pattern of inheritance.
X-linked recessive (or sex linked) inheritance occurs when the mother carries the affected gene on the X chromosome that determines the child’s gender and passes it to her son. Sons of carriers have a 50 percent chance of inheriting the disorder. Daughters have a 50 percent chance of inheriting the X-linked chromosome but usually are not severely affected by the disorder. Affected men do not pass the disorder to their sons but their daughters will be carriers for the disorder.
Diagnosis.
Diagnosis of the lipid storage disorders can be achieved through the use of several tests. These tests include clinical examination, biopsy, genetic testing, molecular analysis of cells or tissues, and enzyme assays. Certain forms of this disease can also be diagnosed through urine testing, which detects the stored material. Prenatal testing is also available to determine if the fetus will have the disease or is a carrier.
Treatment.
There are no specific treatments for lipid storage disorders; however, there are some highly effective enzyme replacement therapies for people with type 1 Gaucher disease and some patients with type 3 Gaucher disease. There are other treatments such as the prescription of certain drugs like phenytoin and carbamazepine to treat pain for patients with Fabry disease. Furthermore, gene therapies and bone marrow transplantation may prove to be effective for certain lipid storage disorders. Diet restrictions do not help prevent the buildup of lipids in the tissues.


TRIM24

Tripartite motif-containing 24 (TRIM24) also known as transcriptional intermediary factor 1α (TIF1α) is a protein that, in humans, is encoded by the "TRIM24" gene.
Function.
The protein encoded by this gene mediates transcriptional control by interaction with the activation function 2 (AF2) region of several nuclear receptors, including the estrogen, retinoic acid, and vitamin D3 receptors. The protein localizes to nuclear bodies and is thought to associate with chromatin and heterochromatin-associated factors. The protein is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains – a RING, a B-box type 1 and a B-box type 2 – and a coiled-coil region. Two alternatively spliced transcript variants encoding different isoforms have been described for this gene.
Interactions.
TRIM24 has been shown to interact with Mineralocorticoid receptor, TRIM33, Estrogen receptor alpha and Retinoid X receptor alpha.


3-carboxyethylcatechol 2,3-dioxygenase

In enzymology, a 3-carboxyethylcatechol 2,3-dioxygenase () is an enzyme that catalyzes the chemical reaction
Thus, the two substrates of this enzyme are 3-(2,3-dihydroxyphenyl)propanoate and O2, whereas its product is 2-hydroxy-6-oxonona-2,4-diene-1,9-dioate.
This enzyme belongs to the family of oxidoreductases, specifically those acting on single donors with O2 as oxidant and incorporation of two atoms of oxygen into the substrate (oxygenases). The oxygen incorporated need not be derived from O2. The systematic name of this enzyme class is 3-(2,3-dihydroxyphenyl)propanoate:oxygen 1,2-oxidoreductase (decyclizing). Other names in common use include 2,3-dihydroxy-beta-phenylpropionic dioxygenase, 2,3-dihydroxy-beta-phenylpropionate oxygenase, and 3-(2,3-dihydroxyphenyl)propanoate:oxygen 1,2-oxidoreductase. This enzyme participates in phenylalanine metabolism. It employs one cofactor, iron.


GLUT5

GLUT5 is a fructose transporter expressed on the apical border of enterocytes in the small intestine. GLUT5 allows for fructose to be transported from the intestinal lumen into the enterocyte by facilitated diffusion due to fructose's high concentration in the intestinal lumen. GLUT5 is also expressed in skeletal muscle, testis, kidney, fat tissue (adipocytes), and brain.
Fructose malabsorption or Dietary Fructose Intolerance is a dietary disability of the small intestine, where the amount of fructose carrier in enterocytes is deficient.
In humans the GLUT5 protein is encoded by the "SLC2A5" gene.
Regulation.
Fructose uptake rate by GLUT5 is significantly affected by diabetes mellitus, hypertension, obesity, fructose malabsorption, and inflammation. However, age-related changes in fructose intake capability are not explained by the rate of expression of GLUT5. The absorption of fructose in the simultaneous presence of glucose is improved, while sorbitol is inhibitory. Fructose absorption by GLUT5 can be investigated using intestinal organoids.


STARD7

StAR-related lipid transfer domain protein 7 (STARD7) or gestational trophoblastic tumor gene-1 (GTT1) is a lipid transporter that specifically binds and transports phosphatidylcholine between membranes.
Function and tissue distribution.
StarD7 is found in the cytosol and associated with the mitochondrion. When overproduced in the cell, mitochondrial levels of phosphatidylcholine rise. High levels of the protein are found in tumor cells compared to normal cells, suggesting a role in cell proliferation.
Structure.
There are two forms of StarD7: StarD7-I and StarD7-II. The former is 295 amino acids long. StarD7-I possesses an additional 75 amino acids at its amino-terminus, which form a signaling sequence that targets it to the outer membrane of the mitochondrion.
StarD7 contains a StAR-related transfer domain (START), from which it derives its name. Moreover, the protein is a member of the predominantly phosphatidylcholine transporter subfamily of START proteins, the StarD2 subfamily. It shares 25% sequence identity with StarD2.


Cyclase-associated protein family

In molecular biology, the cyclase-associated protein family (CAP) is a family of highly conserved actin-binding proteins present in a wide range of organisms including yeast, flies, plants, and mammals. CAPs are multifunctional proteins that contain several structural domains. CAP is involved in species-specific signalling pathways. In "Drosophila", CAP functions in Hedgehog-mediated eye development and in establishing oocyte polarity. In "Dictyostelium discoideum" (social amoeba), CAP is involved in microfilament reorganisation near the plasma membrane in a PIP2-regulated manner and is required to perpetuate the cAMP relay signal to organise fruitbody formation. In plants, CAP is involved in plant signalling pathways required for co-ordinated organ expansion. In yeast, CAP is involved in adenylate cyclase activation, as well as in vesicle trafficking and endocytosis. In both yeast and mammals, CAPs appear to be involved in recycling G-actin monomers from ADF/cofilins for subsequent rounds of filament assembly. In mammals, there are two different CAPs (CAP1 and CAP2) that share 64% amino acid identity.
Function.
All CAPs appear to contain a C-terminal actin-binding domain that regulates actin remodelling in response to cellular signals and is required for normal cellular morphology, cell division, growth and locomotion in eukaryotes. CAP directly regulates actin filament dynamics and has been implicated in a number of complex developmental and morphological processes, including mRNA localisation and the establishment of cell polarity. Actin exists both as globular (G) (monomeric) actin subunits and assembled into filamentous (F) actin. In cells, actin cycles between these two forms. Proteins that bind F-actin often regulate F-actin assembly and its interaction with other proteins, while proteins that interact with G-actin often control the availability of unpolymerised actin.
The most conserved domain of CAPs appears to be the ADP-G-actin binding CARP domain which promotes nucleotide exchange of actin monomers from ADP-state back to polymerisable ATP-form. Recently, the crystal structure of CARP domain bound to ADP-actin was determined, which revealed that CAPs have a unique dimeric binding mode to backside of ADP-G-actin monomers. Based on the crystal structure and biochemical work, the C-terminus of CARP domain appears to be important in regulating the binding to ADP-G-actin monomers to CAP, and has a conserved role for nucleotide exchange on actin monomers. Genetic work in Saccharomyches ceravisae revealed that nucleotide exchange performed by CAP is critical for normal organisation of actin cytoskeleton.
A second unique function of CAP in regulating actin dynamics is its ability to specifically bind to pointed ends of cofilin-decorated actin filaments, and rapidly drive their depolymerisation. CAP thus is a specialised protein in recycling of actin monomers, by first rapidly dissociating ADP-actin monomers from the pointed end of actin filaments, then simultaneously driving ADP-to-ATP nucleotide exchange to make actin monomers assembly-competent.
In addition to actin-binding, CAPs can have additional roles, and may act as bifunctional proteins. In "Saccharomyces cerevisiae" (Baker's yeast), CAP is a component of the adenylyl cyclase complex (Cyr1p) that serves as an effector of Ras during normal cell signalling. "S. cerevisiae" CAP functions to expose adenylate cyclase binding sites to Ras, thereby enabling adenylate cyclase to be activated by Ras regulatory signals. In "Schizosaccharomyces pombe" (Fission yeast), CAP is also required for adenylate cyclase activity, but not through the Ras pathway. In both organisms, the N-terminal domain is responsible for adenylate cyclase activation, but the "S. cerevisiae" and "S. pombe" N-termini cannot complement one another. Yeast CAPs are unique among the CAP family of proteins, because they are the only ones to directly interact with and activate adenylate cyclase. S. cerevisiae CAP has four major domains. In addition to the N-terminal adenylate cyclase-interacting domain, and the C-terminal actin-binding domain, it possesses two other domains: a proline-rich domain that interacts with Src homology 3 (SH3) domains of specific proteins, and a domain that is responsible for CAP oligomerisation to form multimeric complexes (although oligomerisation appears to involve the N- and C-terminal domains as well). The proline-rich domain interacts with profilin, a protein that catalyses nucleotide exchange on G-actin monomers and promotes addition to barbed ends of filamentous F-actin. Since CAP can bind profilin via a proline-rich domain, and G-actin via a C-terminal domain, it has been suggested that a ternary G-actin/CAP/profilin complex could be formed.
Structure.
The N-terminal domain has an all-alpha structure consisting of six helices in a bundle with a left-handed twist and an up-and-down topology.
The C-terminal domain is responsible for G-actin-binding. This domain has a superhelical structure, where the superhelix turns are made of two beta-strands each.


2-acylglycerol O-acyltransferase

In enzymology, a 2-acylglycerol O-acyltransferase () is an enzyme that catalyzes the chemical reaction
Thus, the two substrates of this enzyme are acyl-CoA and 2-acylglycerol, whereas its two products are CoA and diacylglycerol.
This enzyme belongs to the family of transferases, specifically those acyltransferases transferring groups other than aminoacyl groups. The systematic name of this enzyme class is acyl-CoA:2-acylglycerol O-acyltransferase. Other names in common use include acylglycerol palmitoyltransferase, monoglyceride acyltransferase, acyl coenzyme A-monoglyceride acyltransferase, and monoacylglycerol acyltransferase. This enzyme participates in glycerolipid metabolism.


Cholane

Cholane is a triterpene which can exist as either of two stereoisomers, 5α-cholane and 5β-cholane. Its name is derived from the Greek word for bile (χολή, chole) in reference to its original discovery from the bile of the American bullfrog ("Rana catesbeiana"). The compound itself has no known uses; however, various functionalized analogues are produced by plants and animals, typically in the form of sterols, steroids and bile acids (e.g. cholic acid).


Chorismate lyase

In enzymology, a chorismate lyase () is an enzyme that catalyzes the chemical reaction
Hence, this enzyme has one substrate, chorismate, and two products, 4-hydroxybenzoate and pyruvate.
This enzyme belongs to the family of lyases, specifically the oxo-acid-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is chorismate pyruvate-lyase (4-hydroxybenzoate-forming). Other names in common use include CL, CPL, and UbiC.
This enzyme catalyses the first step in ubiquinone biosynthesis, the removal of pyruvate from chorismate, to yield 4-hydroxybenzoate in "Escherichia coli" and other Gram-negative bacteria. Its activity does not require metal cofactors.
Activity.
Enzymatic activity.
Inhibited by:
Pathway.
The pathway used is called the ubiquinone biosynthesis pathway, it catalyzes the first step in the biosynthesis of ubiquinone in "E. coli." Ubiquinone is a lipid-soluble electron-transporting coenzyme. They are essential electron carriers in prokaryotes and are essential in aerobic organisms to achieve ATP.
Nomenclature.
There are several different names for chorismate lyase. it is also called chorismate pyruvate lyase (4-hydroxybenzoate-forming) and it is also abbreviated several different ways: CPL, CL, and ubiC. It is sometimes referred to as ubiC, because that is the gene name. This enzyme belongs to the class Lyases; more specifically the ox-acid-lyase or the carbon-carbon-lyases.
Structure.
This enzyme is a monomer. Its secondary structure contains helixes, turns, and beta strands.


Apolipoprotein C-III

Apolipoprotein C-III also known as apo-CIII, and apolipoprotein C3, is a protein that in humans is encoded by the "APOC3" gene. Apo-CIII is secreted by the liver as well as the small intestine, and is found on triglyceride-rich lipoproteins such as chylomicrons, very low density lipoprotein (VLDL), and remnant cholesterol.
Structure.
ApoC-III is a relatively small protein containing 79 amino acids that can be glycosylated at threonine-74. The most abundant glycoforms are characterized by an O-linked disaccharide galactose linked to N-acetylgalactosamine (Gal- GalNAc), further modified with up to 2 sialic acid residues. Less abundant glycoforms are characterized by more complex and fucosylated glycan moieties.
Function.
APOC3 inhibits lipoprotein lipase and hepatic lipase; it is thought to inhibit hepatic uptake of triglyceride-rich particles. The APOA1, APOC3 and APOA4 genes are closely linked in both rat and human genomes. The A-I and A-IV genes are transcribed from the same strand, while the A-1 and C-III genes are convergently transcribed. An increase in apoC-III levels induces the development of hypertriglyceridemia.
Recent evidences suggest an intracellular role for Apo-CIII in promoting the assembly and secretion of triglyceride-rich VLDL particles from hepatic cells under lipid-rich conditions. However, two naturally occurring point mutations in human apoC3 coding sequence, namely Ala23Thr and Lys58Glu have been shown to abolish the intracellular assembly and secretion of triglyceride-rich VLDL particles from hepatic cells.
Clinical significance.
Overexpression of Apo-CIII in humans contributes to atherosclerosis. Two novel susceptibility haplotypes (specifically, P2-S2-X1 and P1-S2-X1) have been discovered in ApoAI-CIII-AIV gene cluster on chromosome 11q23; these confer approximately threefold higher risk of coronary heart disease in normal as well as non-insulin diabetes mellitus. In persons with type 2 diabetes, elevated plasma Apo-CIII is associated with higher plasma triglycerides and greater coronary artery calcification (a measure of subclinical atherosclerosis).
Apo-CIII delays the catabolism of triglyceride rich particles. HDL cholesterol particles that bear Apo-CIII are associated with increased, rather than decreased, risk for coronary heart disease.
Elevations of Apo-CIII found in genetic variation studies may predispose patients to non-alcoholic fatty liver disease.
Apolipoprotein CIII and HDL.
Apolipoprotein CIII is also found on HDL particles. Formation of APOCIII-containing HDL is not a matter of simple binding of APOCII to pre-existing HDL particles but requires the lipid transported ABCA1 in a fashion similar to APOA1-containing HDL. Accumulation of APOCIII on HDL is important for the maintenance of plasma triglyceride homeostasis since it prevents excessive amount of APOCIII on VLDL and other triglyceride rich lipoproteins, thus preventing APOCIII-mediated inhibition of LpL and the subsequent hydrolysis of plasma triglycerides. This may explain the hypertriglyceridemia associated with ABCA1-deficiency in patients with Tangier's disease.


RNA polymerase II holoenzyme

RNA polymerase II holoenzyme is a form of eukaryotic RNA polymerase II that is recruited to the promoters of protein-coding genes in living cells. It consists of RNA polymerase II, a subset of general transcription factors, and regulatory proteins known as .
RNA polymerase II.
RNA polymerase II (also called RNAP II and Pol II) is an enzyme found in eukaryotic cells. It catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA. In humans, RNAP II consists of seventeen protein molecules (gene products encoded by POLR2A-L, where the proteins synthesized from 2C-, E-, and F-form homodimers).
General transcription factors.
General transcription factors (GTFs) or basal transcription factors are protein transcription factors that have been shown to be important in the transcription of class II genes to mRNA templates. Many of them are involved in the formation of a preinitiation complex, which, together with RNA polymerase II, bind to and read the single-stranded DNA gene template. The cluster of RNA polymerase II and various transcription factors is known as a basal transcriptional complex (BTC).
Preinitiation complex.
The preinitiation complex (PIC) is a large complex of proteins that is necessary for the transcription of protein-coding genes in eukaryotes and archaea. The PIC helps position RNA polymerase II over gene transcription start sites, denatures the DNA, and positions the DNA in the RNA polymerase II active site for transcription.
The typical PIC is made up of six general transcription factors: TFIIA (GTF2A1, GTF2A2), TFIIB (GTF2B), B-TFIID (BTAF1, TBP), TFIID (BTAF1, BTF3, BTF3L4, EDF1, TAF1-15, 16 total), TFIIE, TFIIF, TFIIH and TFIIJ.
The construction of the polymerase complex takes place on the gene promoter. The TATA box is one well-studied example of a promoter element that occurs in approximately 10% of genes. It is conserved in many (though not all) model eukaryotes and is found in a fraction of the promoters in these organisms. The sequence TATA (or variations) is located at approximately 25 nucleotides upstream of the Transcription Start Point (TSP). In addition, there are also some weakly conserved features including the TFIIB-Recognition Element (BRE), approximately 5 nucleotides upstream (BREu) and 5 nucleotides downstream (BREd) of the TATA box.
Assembly of the PIC.
Although the sequence of steps involved in the assembly of the PIC can vary, in general, they follow step 1, binding to the promoter.
The formation of the preinitiation complex (PIC) is analogous to the mechanism seen in bacterial initiation. In bacteria, the sigma factor recognizes and binds to the promoter sequence. In eukaryotes, the transcription factors perform this role.
Mediator complex.
Mediator is a multiprotein complex that functions as a transcriptional coactivator. The Mediator complex is required for the successful transcription of nearly all class II gene promoters in yeast. It works in the same manner in mammals.
The mediator functions as a coactivator and binds to the C-terminal domain (CTD) of RNA polymerase II holoenzyme, acting as a bridge between this enzyme and transcription factors.
C-terminal domain (CTD).
The carboxy-terminal domain (CTD) of RNA polymerase II is that portion of the polymerase that is involved in the initiation of DNA transcription, the capping of the RNA transcript, and attachment to the spliceosome for RNA splicing. The CTD typically consists of up to 52 repeats (in humans) of the sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser. The carboxy-terminal repeat domain (CTD) is essential for life. Cells containing only RNAPII with none or only up to one-third of its repeats are inviable.
The CTD is an extension appended to the C terminus of RPB1, the largest subunit of RNA polymerase II. It serves as a flexible binding scaffold for numerous nuclear factors, determined by the phosphorylation patterns on the CTD repeats. Each repeat contains an evolutionary conserved and repeated heptapeptide, Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7, which is subjected to reversible phosphorylations during each transcription cycle. This domain is inherently unstructured yet evolutionarily conserved, and in eukaryotes it comprises from 25 to 52 tandem copies of the consensus repeat heptad. As the CTD is frequently not required for general transcription factor (GTF)-mediated initiation and RNA synthesis, it does not form a part of the catalytic essence of RNAPII, but performs other functions.
CTD phosphorylation.
RNAPII can exist in two forms: RNAPII0, with a highly phosphorylated CTD, and RNAPIIA, with a nonphosphorylated CTD. Phosphorylation occurs principally on Ser2 and Ser5 of the repeats, although these positions are not equivalent. The phosphorylation state changes as RNAPII progresses through the transcription cycle: The initiating RNAPII is form IIA, and the elongating enzyme is form II0. While RNAPII0 does consist of RNAPs with hyperphosphorylated CTDs, the pattern of phosphorylation on individual CTDs can vary due to differential phosphorylation of Ser2 versus Ser5 residues and/or to differential phosphorylation of repeats along the length of the CTD. The PCTD (phosphoCTD of an RNAPII0) physically links pre-mRNA processing to transcription by tethering processing factors to elongating RNAPII, e.g., 5′-end capping, 3′-end cleavage, and polyadenylation.
Ser5 phosphorylation (Ser5PO4) near the 5′ ends of genes depends principally on the kinase activity of TFIIH (Kin28 in yeast; CDK7 in metazoans). The transcription factor TFIIH is a kinase and will hyperphosphorylate the CTD of RNAP, and in doing so, causes the RNAP complex to move away from the initiation site. Subsequent to the action of TFIIH kinase, Ser2 residues are phosphorylated by CTDK-I in yeast (CDK9 kinase in metazoans). Ctk1 (CDK9) acts in complement to phosphorylation of serine 5 and is, thus, seen in middle to late elongation.
CDK8 and cyclin C (CCNC) are components of the RNA polymerase II holoenzyme that phosphorylate the carboxy-terminal domain (CTD). CDK8 regulates transcription by targeting the CDK7/cyclin H subunits of the general transcription initiation factor IIH (TFIIH), thereby providing a link between the mediator and the basal transcription machinery.
The gene CTDP1 encodes a phosphatase that interacts with the carboxy-terminus of transcription initiation factor TFIIF, a transcription factor that regulates elongation as well as initiation by RNA polymerase II.
Also involved in the phosphorylation and regulation of the RPB1 CTD is cyclin T1 (CCNT1). Cyclin T1 tightly associates and forms a complex with CDK9 kinase, both of which are involved in the phosphorylation and regulation.
TFIIF and FCP1 cooperate for RNAPII recycling. FCP1, the CTD phosphatase, interacts with RNA polymerase II. Transcription is regulated by the state of phosphorylation of a heptapeptide repeat. The nonphosphorylated form, RNAPIIA, is recruited to the initiation complex, whereas the elongating polymerase is found with RNAPII0. RNAPII cycles during transcription. CTD phosphatase activity is regulated by two GTFs (TFIIF and TFIIB). The large subunit of TFIIF (RAP74) stimulates the CTD phosphatase activity, whereas TFIIB inhibits TFIIF-mediated stimulation. Dephosphorylation of the CTD alters the migration of the largest subunit of RNAPII (RPB1).
5' capping.
The carboxy-terminal domain is also the binding site of the cap-synthesizing and cap-binding complex. In eukaryotes, after transcription of the 5' end of an RNA transcript, the cap-synthesizing complex on the CTD will remove the gamma-phosphate from the 5'-phosphate and attach a GMP, forming a 5',5'-triphosphate linkage. The synthesizing complex falls off and the cap then binds to the cap-binding complex (CBC), which is bound to the CTD.
The 5'cap of eukaryotic RNA transcripts is important for binding of the mRNA transcript to the ribosome during translation, to the CTD of RNAP, and prevents RNA degradation.
Spliceosome.
The carboxy-terminal domain is also the binding site for spliceosome factors that are part of RNA splicing. These allow for the splicing and removal of introns (in the form of a lariat structure) during RNA transcription.
Mutation in the CTD.
Major studies in which knockout of particular amino acids was achieved in the CTD have been carried out. The results indicate that RNA polymerase II CTD truncation mutations affect the ability to induce transcription of a subset of genes "in vivo", and the lack of response to induction maps to the upstream activating sequences of these genes.
Genome surveillance complex.
Several protein members of the BRCA1-associated genome surveillance complex (BASC) associate with RNA polymerase II and play a role in transcription.
The transcription factor TFIIH is involved in transcription initiation and DNA repair. MAT1 (for 'ménage à trois-1') is involved in the assembly of the CAK complex. CAK is a multisubunit protein that includes CDK7, cyclin H (CCNH), and MAT1. CAK is an essential component of the transcription factor TFIIH that is involved in transcription initiation and DNA repair.
The nucleotide excision repair (NER) pathway is a mechanism to repair damage to DNA. ERCC2 is involved in transcription-coupled NER and is an integral member of the basal transcription factor BTF2/TFIIH complex. ERCC3 is an ATP-dependent DNA helicase that functions in NER. It also is a subunit of basal transcription factor 2 (TFIIH) and, thus, functions in class II transcription. XPG (ERCC5) forms a stable complex with TFIIH, which is active in transcription and NER. ERCC6 encodes a DNA-binding protein that is important in transcription-coupled excision repair. ERCC8 interacts with Cockayne syndrome type B (CSB) protein, with p44 (GTF2H2), a subunit of the RNA polymerase II transcription factor IIH, and ERCC6. It is involved in transcription-coupled excision repair.
Higher error ratios in transcription by RNA polymerase II are observed in the presence of Mn2+ compared to Mg2+.
Transcription coactivators.
The EDF1 gene encodes a protein that acts as a transcriptional coactivator by interconnecting the general transcription factor TATA element-binding protein (TBP) and gene-specific activators.
TFIID and human mediator coactivator (THRAP3) complexes (mediator complex, plus THRAP3 protein) assemble cooperatively on promoter DNA, from which they become part of the RNAPII holoenzyme.
Transcription initiation.
The completed assembly of the holoenzyme with transcription factors and RNA polymerase II bound to the promoter forms the eukaryotic transcription initiation complex. Transcription in the archaea domain is similar to transcription in eukaryotes.
Transcription begins with matching of NTPs to the first and second in the DNA sequence. This, like most of the remainder of transcription, is an energy-dependent process, consuming adenosine triphosphate (ATP) or other NTP.
Promoter clearance.
After the first bond is synthesized, the RNA polymerase must clear the promoter. During this time, there is a tendency to release the RNA transcript and produce truncated transcripts. This is called "abortive initiation" and is common for both eukaryotes and prokaryotes. Abortive initiation continues to occur until the σ factor rearranges, resulting in the transcription elongation complex (which gives a 35 bp-moving footprint). The σ factor is released before 80 nucleotides of mRNA are synthesized. Once the transcript reaches approximately 23 nucleotides, it no longer slips and elongation can occur.
Initiation regulation.
Due to the range of genes that Pol II transcribes, this is the polymerase that experiences the most regulation by a range of factors at each stage of transcription. It is also one of the most complex in terms of polymerase cofactors involved.
Initiation is regulated by many mechanisms. These can be separated into two main categories:
Regulation by protein interference.
Protein interference is the process where in some signaling protein interacts, either with the promoter or with some stage of the partially constructed complex, to prevent further construction of the polymerase complex, so preventing initiation. In general, this is a very rapid response and is used for fine level, individual gene control and for 'cascade' processes for a group of genes useful under a specific conditions (for example, DNA repair genes or heat shock genes).
Chromatin structure inhibition is the process wherein the promoter is hidden by chromatin structure. Chromatin structure is controlled by post-translational modification of the histones involved and leads to gross levels of high or low transcription levels. See: chromatin, histone, and nucleosome.
These methods of control can be combined in a modular method, allowing very high specificity in transcription initiation control.
Regulation by phosphorylation.
The largest subunit of Pol II (Rpb1) has a domain at its C-terminus called the CTD (C-terminal domain). This is the target of kinases and phosphatases. The phosphorylation of the CTD is an important regulation mechanism, as this allows attraction and rejection of factors that have a function in the transcription process. The CTD can be considered as a platform for transcription factors.
The CTD consists of repetitions of an amino acid motif, YSPTSPS, of which Serines and Threonines can be phosphorylated. The number of these repeats varies; the mammalian protein contains 52, while the yeast protein contains 26. Site-directed-mutagenesis of the yeast protein has found at least 10 repeats are needed for viability. There are many different combinations of phosphorylations possible on these repeats and these can change rapidly during transcription. The regulation of these phosphorylations and the consequences for the association of transcription factors plays a major role in the regulation of transcription.
During the transcription cycle, the CTD of the large subunit of RNAP II is reversibly phosphorylated. RNAP II containing unphosphorylated CTD is recruited to the promoter, whereas the hyperphosphorylated CTD form is involved in active transcription. Phosphorylation occurs at two sites within the heptapeptide repeat, at Serine 5 and Serine 2. Serine 5 phosphorylation is confined to promoter regions and is necessary for the initiation of transcription, whereas Serine 2 phosphorylation is important for mRNA elongation and 3'-end processing.
Elongation.
The process of elongation is the synthesis of a copy of the DNA into messenger RNA. RNA Pol II matches complementary RNA nucleotides to the template DNA by Watson-Crick base pairing. These RNA nucleotides are ligated, resulting in a strand of messenger RNA.
Unlike DNA replication, mRNA transcription can involve multiple RNA polymerases on a single DNA template and multiple rounds of transcription (amplification of particular mRNA), so many mRNA molecules can be rapidly produced from a single copy of a gene.
Elongation also involves a proofreading mechanism that can replace incorrectly incorporated bases. In eukaryotes, this may correspond with short pauses during transcription that allow appropriate RNA editing factors to bind. These pauses may be intrinsic to the RNA polymerase or due to chromatin structure.
Elongation regulation.
RNA Pol II elongation promoters can be summarised in 3 classes:
As for initiation, protein interference, seen as the "drug/sequence-dependent arrest affected factors" and "RNA Pol II catalysis improving factors" provide a very rapid response and is used for fine level individual gene control. Elongation downregulation is also possible, in this case usually by blocking polymerase progress or by deactivating the polymerase.
Chromatin structure-oriented factors are more complex than for initiation control. Often the chromatin-altering factor becomes bound to the polymerase complex, altering the histones as they are encountered and providing a semi-permanent 'memory' of previous promotion and transcription.
Termination.
Termination is the process of breaking up the polymerase complex and ending the RNA strand. In eukaryotes using RNA Pol II, this termination is very variable (up to 2000 bases), relying on post transcriptional modification.
Little regulation occurs at termination, although it has been proposed newly transcribed RNA is held in place if proper termination is inhibited, allowing very fast expression of genes given a stimulus. This has not yet been demonstrated in eukaryotes.
Transcription factory.
Active RNA Pol II transcription holoenzymes can be clustered in the nucleus, in discrete sites called "transcription factories". There are ~8,000 such factories in the nucleoplasm of a HeLa cell, but only 100–300 RNAP II foci per nucleus in erythroid cells, as in many other tissue types. The number of transcription factories in tissues is far more restricted than indicated by previous estimates from cultured cells. As an active transcription unit is usually associated with only one Pol II holoenzyme, a polymerase II factory may contain on average ~8 holoenzymes. Colocalization of transcribed genes has not been observed when using cultured fibroblast-like cells. Differentiated or committed tissue types have a limited number of available transcription sites. Estimates show that erythroid cells express at least 4,000 genes, so many genes are obliged to seek out and share the same factory.
The intranuclear position of many genes is correlated with their activity state. During transcription "in vivo", distal active genes are dynamically organized into shared nuclear subcompartments and colocalize to the same transcription factory at high frequencies. Movement into or out of these factories results in activation (On) or abatement (Off) of transcription, rather than by recruiting and assembling a transcription complex. Usually, genes migrate to preassembled factories for transcription.
An expressed gene is preferentially located outside of its chromosome territory, but a closely linked, inactive gene is located inside.
Holoenzyme stability.
RNA polymerase II holoenzyme stability determines the number of base pairs that can be transcribed before the holoenzyme loses its ability to transcribe. The length of the CTD is essential for RNA polymerase II stability. RNA polymerase II stability has been shown to be regulated by post-translation proline hydroxylation. The von Hippel–Lindau tumor suppressor protein (pVHL, human GeneID: 7428) complex binds the hyperphosphorylated large subunit of the RNA polymerase II complex, in a proline hydroxylation- and CTD phosphorylation-dependent manner, targeting it for ubiquitination.


Pyruvate dehydrogenase (lipoamide) beta

Pyruvate dehydrogenase (lipoamide) beta, also known as pyruvate dehydrogenase E1 component subunit beta, mitochondrial or PDHE1-B is an enzyme that in humans is encoded by the "PDHB" gene. The pyruvate dehydrogenase (PDH) complex is a nuclear-encoded mitochondrial multienzyme complex that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO2, and provides the primary link between glycolysis and the tricarboxylic acid (TCA) cycle. The PDH complex is composed of multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3). The E1 enzyme is a heterotetramer of two alpha and two beta subunits. This gene encodes the E1 beta subunit. Mutations in this gene are associated with pyruvate dehydrogenase E1-beta deficiency.
Structure.
The PDH genes that comprise the E1 subunit are 1.36 kilobases long (alpha) and 1.69 kb long (beta). The PDHB gene has a total of 10 exons and 9 introns. All intron-exon splice junctions follow the standard GT/AG rule. There was an Alu family found in introns 2 and 8. The 5' flanking region gene contains a "CAAT" consensus promoter sequence but no "TATA" sequence. The transcription start site is an adenine residue located 132 bases upstream from the initiation codon in exon 1. The mRNA species that results from transcription of PDHB has been experimentally determined, via Northern blotting, to be 1.6 kb in length, although another fragment 5.5 kb long was also identified.
The PDHB gene encodes a precursor protein that has 359 amino acid residues and a final mature protein that has 329 amino acids, and is part of the pyruvate dehydrogenase multienzyme complex. Two of the mature PDHB proteins come together with two PDHA proteins to form a heterotetrameric E1 subunit. Crystal Structures allowed for a model in which the enzyme undergoes a 2-A shuttle-like motion of its heterodimers to perform the catalysis. Specifically, the catalytic residue has been identified on the PDHB subunit, the 89th residue, which is a glutamate. In forming the entire PDH complex, the 289th beta residue, aspartic acid, interacts with the 276th residue of the E2 complex, a lysine. The entire human complex is 9.5 MDa in size, and has been described as 60-meric, meaning there are over 60 components that are assembled to make the entire complex. These subunits are conserved across many species, as the function of this complex is essential for the generation of ATP for all eukaryotes. Each component is responsible for the catalysis of one step in this pathway; this complex exists for the purpose of channeling the intermediates of each reaction to the next enzyme, thus greatly increasing the rate of reaction.
Function.
The pyruvate dehydrogenase complex is responsible for the oxidative decarboxylation of pyruvate, with the final product being Acetyl CoA. Overall the complex catalyzes five reactions, with the overall reaction being:
Pyruvate + CoA + NAD+ → acetyl-CoA + CO2
There are three different coenzymes required throughout the 5 steps that this complex carries out: thiamine pyrophosphate (TPP), lipoamide, and coenzyme A. This step is only one of the central metabolic pathway carried out by eukaryotes, in which glucose is oxidized to form carbon dioxide, water, and ATP. The E1 complex specifically uses the TPP cofactor to cleave the Calpha-C(=O) bond of pyruvate, and then transfer the acetyl group to the TPP coenzyme, thus resulting in an intermediate, hydroxylethyl-Tpp*E1, and producing CO2. The thiazolium ring on the TPP is ideal for adding to carbonyl groups and acting as an electron sink, or a group that can pull electrons from a reaction and stabilize an electron-deficient intermediate. Additionally, PDHB interacts with Prolyl-hydroxylase PHD3 to regulate the cellular PDH activity.
Clinical significance.
Mutations in the PDHB gene have been known to cause one form of pyruvate dehydrogenase deficiency. Pyruvate dehydrogenase deficiency is characterized by the buildup of a chemical called lactic acid in the body and a variety of neurological problems. Signs and symptoms of this condition usually first appear shortly after birth, and they can vary widely among affected individuals. The most common feature is a potentially life-threatening buildup of lactic acid (lactic acidosis), which can cause nausea, vomiting, severe breathing problems, and an abnormal heartbeat. People with pyruvate dehydrogenase deficiency usually have neurological problems as well. Most have delayed development of mental abilities and motor skills such as sitting and walking. Other neurological problems can include intellectual disability, seizures, weak muscle tone (hypotonia), poor coordination, and difficulty walking. Some affected individuals have abnormal brain structures, such as underdevelopment of the tissue connecting the left and right halves of the brain (corpus callosum), wasting away (atrophy) of the exterior part of the brain known as the cerebral cortex, or patches of damaged tissue (lesions) on some parts of the brain. Because of the severe health effects, many individuals with pyruvate dehydrogenase deficiency do not survive past childhood, although some may live into adolescence or adulthood.
Most cases of pyruvate dehydrogenase complex (PDHc) deficiency are attributable to mutations in the PDHA1 gene which encodes the E(1)α subunit, with few cases of mutations in the genes for E3, E3BP, and E2 being described. However, there are a few cases in which mutations in the beta subunit gene have resulted in patients with Leigh syndrome. Many pathological mutations have been described, including: R36C, which results in conformational change due to increased amino acid interactions; C306R, overall affecting interaction of the two beta subunits; I142M, affecting conformation around a potassium ion, thereby reducing PDHB stability; W165S, which also affects hydrophobic interaction between the beta subunits; and Y132C. Other cases have been described in which there are no pathological mutations, but inborn errors of metabolism, specifically related to ubiquitination and proteasome machineries, resulted in a PDHB deficiency. This was demonstrated by PDH activity being restored in cells that were treated with MG132, which is known as proteasome inhibitor. The clinical manifestations of this deficiency are similar to those of PDHA1 deficiency, with the exception being that ataxia is less frequent in these cases, and that consanguinity was found only in families with the PDHB deficiency.


Glycoside hydrolase family 30

In molecular biology, glycoside hydrolase family 30 is a family of glycoside hydrolases.
Glycoside hydrolases 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 30 CAZY GH_30 includes the mammalian glucosylceramidases. Human acid beta-glucosidase (D-glucosyl-N-acylsphingosine glucohydrolase), cleaves the glucosidic bonds of glucosylceramide and synthetic beta-glucosides. Any one of over 50 different mutations in the gene of glucocerebrosidase have been found to affect activity of this hydrolase, producing variants of Gaucher disease, the most prevalent lysosomal storage disease.


Arabinose isomerase

In enzymology, an arabinose isomerase () is an enzyme that catalyzes the chemical reaction
Hence, this enzyme has one substrate, D-arabinose, and one product, D-ribulose.
This enzyme belongs to the family of isomerases, specifically those intramolecular oxidoreductases interconverting aldoses and ketoses. The systematic name of this enzyme class is D-arabinose aldose-ketose-isomerase. Other names in common use include D-arabinose(L-fucose) isomerase, D-arabinose isomerase, L-fucose isomerase, and D-arabinose ketol-isomerase.
Structural studies.
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code .


ERp27

ERp27 (Endoplasmic Reticulum protein 27.7 kDa) is a homologue of PDI (protein disulfide-isomerase), localised to the Endoplasmic Reticulum. The structure of ERp27 has been solved by both X-ray crystallography and NMR spectroscopy, showing it to be composed of two thioredoxin-like domains with homology to the non-catalytic b and b' domains of PDI. The function of ERp27 is unknown, but on the basis of its homology with PDI it is thought to possess chaperone activity.


Heparinoid

Heparinoids are glycosaminoglycans which are derivatives of heparin. They include oligosaccharides and sulfated polysaccharides of plant, animal, or synthetic origin. One study has been conducted on heparinoids.
Heparinoids, like heparin, act by interacting with heparin binding proteins, generally through ionic interactions or hydrogen bonding. Some examples of heparin binding proteins include antithrombin III. It is thought that much protein interaction with heparin is not direct, and instead heparin binding protein actually interact with glycosaminoglycan (GAG) side chains or mucins bound to the heparin polymer, so it is possible that heparinoids interact with these proteins in a similar way, acquiring GAG side chains in vivo. One counter example is the protein chymase, which directly binds to heparin.
Sulfated polysaccharides.
From animal tissues.
Dermatan sulfate is one example of a compound that is classified as a heparinoid. It is a naturally-occurring polysaccharide of "O"-sulfated "N"-acetyl--galatosamine, -iduronic acid, and -glucuronic acid that has been clinically used as an antithrombotic agent.
Chondroitin sulfate shows slightly less biological activity than dermatan sulfate, and is composed of O-sulfated "N"-acetyl--galatosamine and -glucuronic acid. It is theorized that this change in efficacy is related to the absence of -induronic acid, which affects the flexibility of the polymer chain.
Acharan sulfate is a heparinoid that is naturally produced by the giant African land snail, Achatina fulica. Keratan sulfate is a heparinoid that is a component of cartilage. It is found in the cornea.
Chitin, a component of insect shells and fungal structures, can be de-"N"-acetylated to form chitosan, which when sulfated has a significant chemical similarity to heparin. In fact, it inhibits thrombin by affecting ATIII.
Lepirudin is a recombinant preparation of the polypeptide anticoagulant secreted by leeches and is used in patients with heparin induced thrombocytopenia.
From plant sources.
Fucoidan is a polymer composed of sulfated -fucose.
Carrageenans are isolated from algae.
Hyaluronan functions as a heparinoid when it is sulfated. Intra-articular injections of hyaluronic acid are used to mitigate pain and treat symptoms of osteoarthritis in the knee, but such injections are correlated with increased risk of serious side effects.
Alginic acid functions as a heparinoid when it is sulfated.
Pentosan from the bark of "Fagus sylvatica", when sulfated, acts with 1/10th of the efficacy of heparin.
From microbial sources.
K5 polysaccharide from E. coli acts as a heparinoid when it is sulfated.
History.
Heparin was first isolated from dog liver by medical student Jay McClean in 1916. Jorpes discovered the structure of the heparin polysaccharide in 1935, identifying that it is a highly sulfated polymer of glycosaminoglycoglycan (GAG) and uronic acid. Around that time, heparin began to be used in the prophylaxis and treatment of post-operative thrombosis.
Production.
There is no industrial process for the complete synthesis of heparin; Heparin is isolated from animal tissue - generally bovine lung, porcine, and intestinal mucosa. Heparinoids generally are also naturally-occurring polysaccharides, and similarly need to be purified from the plant or animal tissue that produces them.
Regulation.
There is no internationally accepted molecular standard for the composition of heparin, as it is a complex polymer of GAG units and uronic acids (including D-glucuronic acid, L-iduronic acid, and D-glucosamine). Position of N-acetyl, N-sulfate, and O-sulfate groups in these uronic acids can vary, as can the branching patterns of the chain. This generates an extraordinary amount of variability between molecules of heparin. Current USP standards for heparin limit levels of contamination with dermatan, chondroitin, and over-sulfated chondroitin sulfate, as well as galactosamine levels in the sample, as determined by HPLC, H-NMR, and Strong Anion Exchange Chromatography.


Dihydroorotate dehydrogenase (quinone)

Class 2 dihydroorotate dehydrogenases (DHOQO, ) is an enzyme with systematic name "(S)-dihydroorotate:quinone oxidoreductase". This enzyme catalyses the electron transfer from dihydroorotate (electron donor) to a quinone (electron acceptor):
These enzymes differ from class 1 dihydroorotate dehydrogenases (DHODH) on the electron acceptor, on their structure, and on their cellular localization. Since the reaction catalyzed by DHOQOs is both part of the electron transport chain and the pyrimidine de novo synthesis, it has been explored as a possible target for cancer treatment, immunological disorders and bacterial/viral infections.
Structure.
Structurally, DHOQOs are organized in monomers which adopt a (βα)8 (eightfold beta alpha barrel) fold. The enzyme can be separated in its N-terminal domain (blue in the figure) and in its C-terminal domain (green in the figure).
The N-terminal domain is composed of two amphipathic α-helices (αA – αB) which are responsible for the lipid membrane interaction. This region of the protein is also thought to mediate quinone binding.
Regarding the C-terminal domain, much of its structural elements are shared with the soluble counterparts of DHOQOs. This domain is responsible for the binding of the cofactor FMN (making these enzymes part of the Flavoprotein super-family) and the electron donor dihydroorotate, close to the 8 β-strand core.
There are currently crystallographic structures of DHOQOs from 5 different organisms:


Wortmannin

Wortmannin, a steroid metabolite of the fungi "Penicillium funiculosum", "Talaromyces wortmannii", is a non-specific, covalent inhibitor of phosphoinositide 3-kinases (PI3Ks). It has an "in vitro" inhibitory concentration ("IC"50) of around 5 nM, making it a more potent inhibitor than LY294002, another commonly used PI3K inhibitor. It displays a similar potency "in vitro" for the class I, II, and III PI3K members although it can also inhibit other PI3K-related enzymes such as mTOR, DNA-PKcs, some phosphatidylinositol 4-kinases, myosin light chain kinase (MLCK) and mitogen-activated protein kinase (MAPK) at high concentrations Wortmannin has also been reported to inhibit members of the polo-like kinase family with "IC"50 in the same range as for PI3K. The half-life of wortmannin in tissue culture is about 10 minutes due to the presence of the highly reactive C20 carbon that is also responsible for its ability to covalently inactivate PI3K. Wortmannin is a commonly used cell biology reagent that has been used previously in research to inhibit DNA repair, receptor-mediated endocytosis and cell proliferation.
Phosphoinositide-3-kinase.
Phosphoinositide-3-kinase (PI3K) activates an important cell survival signaling pathway, and constitutive activation is seen in ovarian, head and neck, urinary tract, cervical and small cell lung cancer. PI-3-K signaling is attenuated by the phosphatase activity of the tumor suppressor PTEN that is absent in a number of human cancers. Inhibiting PI-3-K presents the opportunity to inhibit a major cancer cell survival signaling pathway and to overcome the action of an important deleted tumor suppressor, providing antitumor activity and increased tumor sensitivity to a wide variety of drugs.
Wortmannin is a known and potent PI3K inhibitor; as such, it was shown to have detrimental influence on memory and impair spatial learning abilities.
Derivatives.
In order to stabilize the Wortmannin molecule while not losing its therapeutic effect, numerous derivatives were synthesized from Wortmannin.
PX-866.
One of these, PX-866 (now Sonolisib), has been shown to be a novel, potent, irreversible, inhibitor of PI-3 kinase with efficacy when delivered orally. PX-866 was put in a phase 1 clinical trial by Oncothyreon company. The clinical development plan for PX-866 includes both standalone and combination therapy in major human cancers. In 2010 PX-866 was starting 4 phase II trials for solid tumours. The company gave an update on its phase 2 trials in Jun 2012. Phase 1 results (with docetaxel) published Aug 2013. In July 2014 published results of a phase 2 trial (for NSCLC) concluded : "The addition of PX-866 to docetaxel did not improve PFS, response rate, or OS in patients with advanced, refractory NSCLC without molecular preselection". In Sept 2015 as Phase 2 trial for recurrent glioblastoma reported not meeting its primary endpoint.


Psicose

-Psicose (C6H12O6), also known as -allulose, or simply allulose, is a low-calorie epimer of the monosaccharide sugar fructose, used by some major commercial food and beverage manufacturers as a low-calorie sweetener. First identified in wheat in the 1940s, allulose is naturally present in small quantities in certain foods.
The U.S. Food and Drug Administration (FDA) has accepted a petition for Generally Recognized As Safe (GRAS) for allulose as a sugar substitute in various specified food categories. Because it is absorbed and metabolized differently from other sugars, FDA has exempted allulose from the listing of total and added sugars on the Nutrition and Supplement Facts labels, but requires the labeling of 0.4kcal/g as carbohydrate.
A meta-analysis was conducted of the effect on postprandial glucose and insulin responses of adding a median of 5 grams of allulose (range, 2.5-10 g) to a fixed carbohydrate-containing drink or meal, versus the same meal alone. Five studies were included, with a median of 18 largely middle-aged participants, including nondiabetic subjects in three studies and subjects with pre-diabetes and/or Type II diabetes in the other two. Three of the 5 studies used a reference 75 gram oral glucose tolerance test (OGTT) for at least one comparison; some studies used other glucose-containing foods either as the sole comparison or as an additional arm along with the OGTT, for a total of ten comparisons. To control for sweetness, aspartame was added to the control preparation in two of the five studies. Overall, compared to the carbohydrate-containing meal alone, the same meal with a small dose of added allulose resulted in a 10% lower integrated area under the curve (iAUC) of postprandial glucose. The quality of the evidence was rated as moderate.
Biochemistry.
The sweetness of allulose is estimated to be 70% of the sweetness of sucrose. It has some cooling sensation and no bitterness. Its taste is said to be sugar-like, in contrast to certain other sweeteners, like the high-intensity artificial sweeteners aspartame and saccharine. The caloric value of allulose in humans is about 0.2 to 0.4 kcal/g, relative to about 4 kcal/g for typical carbohydrates. In rats, the relative energy value of allulose was found to be 0.007 kcal/g, or approximately 0.3% of that of sucrose. Similar to the sugar alcohol erythritol, allulose is minimally metabolized and is excreted largely unchanged. The glycemic index of allulose is very low or negligible.
Allulose is a weak inhibitor of the enzymes α-glucosidase, α-amylase, maltase, and sucrase. Because of this, it can inhibit the metabolism of starch and disaccharides into monosaccharides in the gastrointestinal tract. Additionally, allulose inhibits the absorption of glucose via transporters in the intestines. For these reasons, allulose has potential antihyperglycemic effects, and has been found to reduce postprandial hyperglycemia in humans. Through modulation of lipogenic enzymes in the liver, allulose may also have antihyperlipidemic effects.
Due to its effect of causing incomplete absorption of carbohydrates from the gastrointestinal tract, and subsequent fermentation of these carbohydrates by intestinal bacteria, allulose can result in unpleasant symptoms such as flatulence, abdominal discomfort, and diarrhea. The maximum non-effect dose of allulose in causing diarrhea in humans has been found to be 0.55 g/kg of body weight. This is higher than that of most sugar alcohols (0.17–0.42 g/kg), but is less than that of erythritol (0.66–1.0+ g/kg).
Chemistry.
Allulose, also known by its systematic name -ribo-2-hexulose as well as by the name -psicose, is a monosaccharide and a ketohexose. It is a C3 epimer of fructose. Fructose can be converted to allulose by the enzyme -tagatose 3-epimerase, which has allowed for mass production of allulose. The compound is found naturally in trace amounts in wheat, figs, raisins, maple syrup, and molasses. Allulose has similar physical properties to those of regular sugar, such as bulk, mouthfeel, browning capability, and freeze point. This makes it favorable for use as a sugar replacement in food products, including ice cream.
History.
Allulose was first discovered in the 1940s. The first mass-production method for allulose was established when Ken Izumori at Kagawa University in Japan discovered the key enzyme, -tagatose 3-epimerase, to convert fructose to allulose in 1994. This method of production has a high yield, but suffers from a very high production cost.
In June 2012, the U.S. Food and Drug Administration (FDA) accepted the assertion of CJ CheilJedang, Inc. that allulose is Generally Recognized As Safe (GRAS) as a sugar substitute in various specified food categories. In June 2014, a similar GRAS letter was issued to Matustani Chemical Industry Company, Ltd. The first Non-GMO allulose was manufactured by Samyang Corporation. Allulose is not approved for use in the European Union.
Oct 2019, FDA announced exemption of allulose from total and added sugars on nutritional label but adding 0.4kcal/g as carbohydrate.
Studies have shown the commercial product is not absorbed in the human body the way common sugars are and does not raise insulin levels, but more testing may be needed to evaluate any other potential side effects.
Manufacturing.
As of 2018, most commercially available allulose was produced from corn. Alluose is also produced from beet sugar.
Commercial application.
Commercial manufacturers and food laboratories are looking into properties of allulose that may differentiate it from sucrose and fructose sweeteners, including an ability to induce the high foaming property of egg white protein and the production of antioxidant substances produced through the Maillard reaction.
Commercial uses of allulose include low-calorie sweeteners in beverages, yogurt, ice cream, baked goods, and other typically high-calorie items. London-based Tate & Lyle released its proprietary variant of allulose, known as Dolcia Prima allulose, and U.S.-based Anderson Global Group released its own proprietary variant into the North American market in 2015. The first major food company to adopt allulose as a sweetener was Quest Nutrition in some of their protein bar products.
On April 16, 2019, US Food and Drug Administration (FDA) issued a draft guidance, allowing food manufacturers to exclude allulose from total and added sugar counts on Nutrition and Supplement Facts labels. Like sugar alcohols and dietary fiber, allulose will still count towards total carbohydrates on nutrition labels. This, combined with the GRAS designation, has increased interest in including allulose in food products instead of sucrose.


Lychee Mini Fruity Gels

Lychee Mini Fruity Gels are a type of sweet or candy made with konjac, a gummy binding agent made from the tubers of the konnyaku root. The product is made by AP Frozen Foods Ltd, Thailand.
Deaths and injury.
Lychee Mini Fruity Gels have been implicated in a number of deaths and choking injuries in the US and Pacific Rim countries. While choking on candy and other foodstuffs is not uncommon, the gel nature means that these candies totally block the airway and the konnyaku gel is "ten times stronger" than gelatin. Research shows that "hard, round foods with high elasticity or lubricity properties, or both, pose a significant level of risk," especially to children under three years old. The candies can resist attempts to dislodge with the Heimlich manoeuvre.
Legal status.
Lychee Mini Fruit Gels have been banned due to choking hazards in the US (by the FDA) and the European Union.