ACT domain

In molecular biology, the ACT domain is a protein domain that is found in a variety of proteins involved in metabolism. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The ACT domain is named after three of the proteins that contain it: aspartate kinase, chorismate mutase and TyrA. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure.
The ACT domain was discovered by Aravind and Koonin using iterative sequence searches.


Thymidine

Thymidine (deoxythymidine; other names deoxyribosylthymine, thymine deoxyriboside) is a pyrimidine deoxynucleoside. Deoxythymidine is the DNA nucleoside T, which pairs with deoxyadenosine (A) in double-stranded DNA. In cell biology it is used to synchronize the cells in G1/early S phase.
Before the boom in thymidine use caused by the need for thymidine in the production of the antiretroviral drug azidothymidine (AZT), much of the world's thymidine production came from herring sperm. Thymidine occurs almost exclusively in DNA but it also occurs in the T-loop of tRNA.
Structure and properties.
In its composition, deoxythymidine is a nucleoside composed of deoxyribose (a pentose sugar) joined to the pyrimidine base thymine.
Deoxythymidine can be phosphorylated with one, two or three phosphoric acid groups, creating dTMP (deoxythymidine monophosphate), dTDP, or dTTP (for the di- and tri- phosphates, respectively).
It exists in solid form as small white crystals or white crystalline powder. It has a molecular weight of 242.229 u and a melting point of 185 °C. The stability of deoxythymidine under standard temperature and pressure (STP) is very high.
Deoxythymidine is non-toxic and as part of one of the four nucleosides in DNA it is a naturally occurring compound that exists in all living organisms and DNA viruses. Instead of thymidine, RNA contains uridine (uracil joined to ribose). Uracil is chemically very similar to thymine, which is also known as 5-methyluracil. Since thymine nucleotides are precursors of DNA (but not RNA), the prefix "deoxy" is often left out, i.e., deoxythymidine is often just called thymidine.
Thymidine is listed as a chemical teratogen.
Modified analogs.
Iododeoxyuridine is a radiosensitizer and increases the amount of DNA damage received from ionizing radiation.
Azidothymidine (AZT) – used in the treatment of HIV infection. AZT inhibits the process of reverse transcription, a critical step in the viral life cycle.
Radiolabeled thymidine (TdR), such as tritiated thymidine (3H-TdR), is commonly used in cell proliferation assays. The thymidine is incorporated into dividing cells and the level of this incorporation, measured using a liquid scintillation counter, is proportional to the amount of cell proliferation. For example, lymphocyte proliferation can be measured this way in lymphoproliferative disorders.
Bromodeoxyuridine (BrdU) is another thymidine analog that is often used for the detection of proliferating cells in living tissues.
5-Ethynyl-2´-deoxyuridine (EdU) is a thymidine analog which is incorporated into the DNA of dividing cells and is used to assay DNA synthesis in cell culture or living tissues. It can be visualized by covalently binding a fluorescent azide using click chemistry, which is less harsh than the conditions used to expose the epitope for BrdU antibodies.
Edoxudine is an antiviral drug.
Thymidine imbalance induces mutation and recombination.
During growth of bacteriophage T4, an excess of thymidine availability increases mutation. A deficiency of thymidine during growth also increases mutation. A thymidylate auxotroph of the diploid yeast "Saccharomyces cerevisiae" was grown under conditions in which thymidyate levels varied from excess to depletion. High levels of thymidylate were observed to be mutagenic and recombinogenic, whereas starvation for thymidylate was recombinogenic but only slightly mutagenic.


3-methyl-2-oxobutanoate hydroxymethyltransferase

In enzymology, a 3-methyl-2-oxobutanoate hydroxymethyltransferase () is an enzyme that catalyzes the chemical reaction
The 3 substrates of this enzyme are 5,10-methylenetetrahydrofolate, 3-methyl-2-oxobutanoate, and H2O, whereas its two products are tetrahydrofolate and 2-dehydropantoate.
This enzyme belongs to the family of transferases that transfer one-carbon groups, specifically the hydroxymethyl-, formyl- and related transferases. The systematic name of this enzyme class is 5,10-methylenetetrahydrofolate:3-methyl-2-oxobutanoate hydroxymethyltransferase. Other names in common use include alpha-ketoisovalerate hydroxymethyltransferase, dehydropantoate hydroxymethyltransferase, ketopantoate hydroxymethyltransferase, oxopantoate hydroxymethyltransferase, 5,10-methylene tetrahydrofolate:alpha-ketoisovalerate, and hydroxymethyltransferase. This enzyme participates in pantothenate and coa biosynthesis.
Structural studies.
As of late 2007, 4 structures have been solved for this class of enzymes, with PDB accession codes , , , and .


Apiose

 Apiose is a branched-chain sugar found as residues in galacturonans-type pectins; that occurs in parsley and many other plants. Apiose is a component of cell wall polysaccharides.
Apiose 1-reductase uses -apiitol and NAD+ to produce apiitol-apiose, NADH, and H+.
Flavone apiosyltransferase uses UDP-apiose and 5,7,4'-trihydroxyflavone 7-"O"-β--glucoside to produce UDP, 5,7,4'-trihydroxyflavone (apigenin), and 7-O-β--apiosyl-(1->2)-β-apiitol-glucoside.


Xylenol

Xylenols are organic compounds with the formula (CH3)2C6H3OH. They are volatile colorless solids or oily liquids. They are derivatives of phenol with two methyl groups at various positions relative to the hydroxyl group. Six isomers exist, of which 2,6-xylenol with both methyl groups in an ortho position with respect to the hydroxyl group is the most important. The name "xylenol" is a portmanteau of the words xylene and phenol.
2,4-Dimethylphenol together with other xylenols and many other compounds are traditionally extracted from coal tar, the volatile materials obtained in the production of coke from coal. These residue contains a few percent by weight of xylenols as well as cresols and phenol. The main xylenols in such tar are the 3,5-, 2,4, and 2,3- isomers. 2,6-Xylenol is produced by methylation of phenol using methanol in the presence of metal oxide catalysts:
Properties.
The physical properties of the six isomeric xylenols are similar.
Uses.
Together with cresols and cresylic acid, xylenols are an important class of phenolics with great industrial importance. They are used in the manufacture of antioxidants. Xylenol orange is a redox indicator built on a xylenol skeleton. 2,6-Xylenol is a monomer for poly(p-phenylene oxide) (PEO) engineering resins through carbon-oxygen oxidative coupling.


Alkanal monooxygenase (FMN-linked)

In enzymology, an alkanal monooxygenase (FMN-linked) () is an enzyme that catalyzes the chemical reaction
The 3 substrates of this enzyme are RCHO, reduced FMN, and O2, whereas its 4 products are RCOOH, FMN, H2O, and hn.
This enzyme belongs to the family of oxidoreductases, specifically those acting on paired donors, with O2 as oxidant and incorporation or reduction of oxygen. The oxygen incorporated need not be derived from O2 with reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor. The systematic name of this enzyme class is alkanal, reduced-FMN:oxygen oxidoreductase (1-hydroxylating, luminescing). Other names in common use include bacterial luciferase, aldehyde monooxygenase, luciferase, and Vibrio fischeri luciferase.
Structural studies.
As of late 2007, 4 structures have been solved for this class of enzymes, with PDB accession codes , , , and .


Pseudouridine

Pseudouridine (abbreviated by the Greek letter psi- Ψ or the letter Q) is an isomer of the nucleoside uridine in which the uracil is attached via a carbon-carbon instead of a nitrogen-carbon glycosidic bond. (In this configuration, uracil is sometimes referred to as 'pseudouracil'.)
Pseudouridine is the most abundant RNA modification in cellular RNA. After transcription and following synthesis, RNA can be modified with over 100 chemically distinct modifications. These can potentially regulate RNA expression post-transcriptionally, in addition to the four standard nucleotides and play a variety of roles in the cell including translation, localization and stabilization of RNA. Pseudouridine, being one of them, is the C5-glycoside isomer of uridine that contains a C-C bond between C1 of the ribose sugar and C5 of uracil, rather than usual C1-N1 bond found in uridine. The C-C bond gives it more rotational freedom and conformational flexibility. In addition, pseudouridine has an extra hydrogen bond donor at the N1 position.
Also known as 5-ribosyluracil, pseudouridine is a ubiquitous yet enigmatic constituent of structural RNAs (transfer, ribosomal, small nuclear (snRNA) and small nucleolar). Recently it has also been discovered in coding RNA. Being the most abundant, it is found in all 3 phylogenetic domains of life and was the first to be discovered. Pseudouridine accounts for 4% of the nucleotides in the yeast tRNA . This base modification is able to stabilize RNA and improve base-stacking by forming additional hydrogen bonds with water through its extra imino group . There are 11 pseudouridines in the "Escherichia coli" rRNA, 30 in yeast cytoplasmic rRNA and a single modification in mitochondrial 21S rRNA and about 100 pseudouridines in human rRNA indicating that the extent of pseudouridylation increases with the complexity of an organism .
Pseudouridine in rRNA and tRNA has been shown to fine-tune and stabilize the regional structure and help maintain their functions in mRNA decoding, ribosome assembly, processing and translation. Pseudouridine in snRNA has been shown to enhance spliceosomal RNA-pre-mRNA interaction to facilitate splicing regulation.
Effects and modification on different RNA.
tRNA.
Ψ is ubiquitous in this class of RNAs and facilitates common tRNA structural motifs. One such structural motif is the TΨC stem loop which incorporates Ψ55. Ψ is commonly found in the D stem and anticodon stem and loop of tRNAs from each domain. In each structural motif the unique physicochemical properties of Ψ stabilize structures that would not be possible with the standard U.
During translation Ψ modulates interactions of tRNA molecules with rRNAs and mRNAs. Ψ and other modified nucleotides affect the local structure of the tRNA domains they are found in without impacting the overall fold of the RNA. In the anticodon stem-loop (ASL) Ψ seems critical for proper binding of tRNAs to the ribosome. Ψ stabilizes the dynamic structure of the ASL and promotes stronger binding to the 30S ribosome. The stabilized conformation of the ASL helps maintain correct anticodon-codon pairings during translation. This stability may increase translational accuracy by decreasing the rate of peptide bond formation and allowing for more time for incorrect codon-anticodon pairs to be rejected. Despite Ψ’s role in local structure stabilization, pseudouridylation of tRNA is not essential for cell viability and is not usually required for aminoacylation.
mRNA.
Ψ is also found in mRNAs which are the template for protein synthesis. Ψ residues in mRNA can affect the coding specificity of stop codons UAA, UGA, and UAG. In these stop codons both a U→Ψ modification and a U→C mutation both promote nonsense suppression. In the SARS-CoV2 vaccine from BioNTech/Pfizer, also known as BNT162b2, Tozinameran or Comirnaty, all U's have been substituted with N1-methyl-pseudouridine, a nucleoside related to Ψ that contains a methyl group added to N1 atom.
rRNA.
Ψ is found in the large and small ribosomal subunits of all domains of life and their organelles. In the ribosome Ψ residues cluster in domains II, IV, and V and stabilize RNA-RNA and/or RNA-protein interactions. The stability afforded by Ψ may assist rRNA folding and ribosome assembly. Ψ may also influence the stability of local structures which impact the speed and accuracy of decoding and proofreading during translation.
snRNA.
Ψ is found in the major spliceosomal snRNAs of eukaryotes. Ψ residues in snRNA are often phylogenetically conserved, but have some variations across taxa and organisms. The Ψ residues in snRNAs are normally located in regions that participate in RNA-RNA and/or RNA-protein interactions involved in the assembly and function of the spliceosome. Ψ residues in snRNAS contribute to the proper folding and assembly of the spliceosome which is essential for pre-mRNA processing.
Pseudouridine synthase proteins.
Pseudouridine are RNA modifications that are done post-transcription, so after the RNA is formed. The proteins that do this modification are called Pseudouridine Synthases or PUS. PUS proteins are found in all kingdoms of life. Most research has been done on how PUS protein modify tRNA, so mechanism involving snRNA, and mRNA are not clearly defined. PUS proteins can vary on RNA specificity, structure , and isomerization mechanisms. The different structures of PUS are divided into 5 families. The families share the active sequence and important structural motifs.
TruA.
TruA domain modifies a variety of different places in tRNA, snRNA, and mRNA. The mechanism of isomerization of uridine is still being talked about in this family.
PUS 1 is located in the nucleus and modifies tRNA at different locations, U44 of U2 snRNA, and U28 of U6 snRNA. Studies found that PUS 1 expression increased during environmental stress and is important for regulating the splicing of RNA. Also that PUS 1 is necessary for taking the tRNA made in the nucleus and sending them to the cytoplasm.
PUS 2 is very similar to PUS 1, but located in the mitochondria and only modifies U27 and U28 of mito-tRNA. This protein modifies the mitochondrial tRNA, which have a lesser amount of pseudouridine modifications compared to other tRNA. Unlike most mitochondria located protein, PUS 2 has not been found to have a mitochondrial targeting signal or MTS.
PUS 3 is a homolog to PUS 1, but modifies different places of the tRNA (U38/39) in the cytoplasm and mitochondrial. This protein is the most conserved of the TruA family. A decrease in modifications made by PUS 3 was found when the tRNA structure of improperly folded. Along with tRNA the protein targets ncRNA and mRNA, further research is still needed as to the importance of this modification. PUS 3 along with PUS 1 modify steroid activator receptor in humans.
TruB.
The TruB family only contains PUS 4 located in the mitochondrial and nucleus. PUS 4 modification is heavily conserved located in the U55 in the elbow of the tRNA. The human form of PUS 4 is actually missing a binding domain called PUA or pseudouridine synthase and archaeosine trans-glycosylase. PUS 4 has a sequence specificity for T-loop part of the tRNA. Preliminary data of PUS4 modifying mRNA, but more research is needed to confirm. Also binds to a specific Brome Mosaic Virus, which is a plant-infecting RNA virus.
TruD.
TruD is able to modify a variety of RNA, and it is unclear how these different RNA substrates are recognized. PUS 7 modifies U2 snRNA at the position 35 and this modification will increase when the cells are in high shock. Another modification is cytoplasmic tRNA in position 13, and position 35 in pre-tRNATyr. PUS 7 modifies almost specificity does not depend on the type of RNA as mRNA show pseudouridylated by PUS 7. Recognize this the sequence of the RNA, UGUAR with the second U being the nucleotide that will be modified. The pseudouridylation of mRNA by PUS 7 increases during heat shock, because the protein moves from the nucleus to the cytoplasm. The modification is thought to increase the stability of mRNA during heat shock before the RNA goes to the nucleus or mitochondria, but more studies are needed.
RluA.
The RluA domain of these proteins can identify the substrate through a different protein binding to the substrate and then particular bonds to the RluA domain.
PUS 5 is not well studied and located pseudouridine synthase and similar to Pus 2 does not have a mitochondrial signal targeting sequence. The protein modifies U2819 of mitochondrial 21S rRNA. Also suspected that Pus 5 modifies some Uridines in the mRNA, but again more data is needed to confirm.
PUS 6 has one that only modifies U31 of cytoplasmic and mitochondrial tRNA. Pus 6 is also known to modify mRNA.
PUS 8 also known as Rib2 modifies cytoplasmic tRNA at position U32. On the C-terminus there is a DRAP-deaminase domain related to the biosynthesis of riboflavin. The RluA and DRAP or deaminase domain related to riboflavin synthase have completely separate functions in the protein and it is not known whether they interact with each other. PUS 8 is necessary in yeast, but that is suspected to be related to the riboflavin synthesis and not the pseudouridine modification.
PUS 9 and PUS 8 catalyze the same position in mitochondrial tRNA instead of cytoplasmic. It is the only PUS protein that contains a mitochondrial targeting signal domain on the N-terminus. Studies suspect that PUS 9 can modify mRNAs, which would mean less substrate specificity.
Techniques in genome sequencing for pseudouridine.
Pseudouridine can be identified through a multitude of different techniques. A common technique to identify modifications in RNA and DNA is Liquid Chromatography with Mass Spectrometry or LC-MS. Mass spectrometry separates molecules by the mass and charge. While uridine and pseudouridine have the same mass, but have different charges. Liquid chromatography works by retention time, which has to do with leaving the column. A chemical way to identify pseudouridine uses a compound called CMC or N-cyclohexyl-N′-β-(4-methylmorpholinium) ethylcarbodiimide to specifically label and distinguish Uridine from Pseudouridine. CMC will bond both with Pseudouridine and Uridine, but holds tighter to the former, because of the third nitrogen able to form hydrogen bond. CMC bound to pseudouridine can then be imaged by tagging a signaling molecule. This method is still being worked on to become high-throughput.
Medical relevance of pseudouridine.
Pseudouridine exerts a subtle but significant influence on the nearby sugar-phosphate backbone and also enhances base stacking. These effects may underlie the biological role of most, but perhaps not all of the pseudouridine residues in RNA. Certain genetic mutants lacking specific pseudouridine residues in tRNA or rRNA exhibit difficulties in translation, display slow growth rates, and fail to compete effectively with wild-type strains in mixed culture. Pseudouridine modifications are also implicated in human diseases such as mitochondrial myopathy and sideroblastic anemia (MLASA) and Dyskeratosis congenita. Dyskeratosis congenita and Hoyeraal-Hreidarsson syndrome are two rare inherited syndromes caused by mutations in DKC1, the gene encoding for the pseudouridine synthase dyskerin. Pseudouridines have been recognized as regulators of viral latency processes in human immunodeficiency virus (HIV) infections. Pseudouridylation has also been associated with the pathogenesis of maternally inherited diabetes and deafness (MIDD). In particular, a point mutation in a mitochondrial tRNA seems to prevent the pseudouridylation of one nucleotide, thus altering the tRNA tertiary structure. This may lead to higher tRNA instability, causing deficiencies in mitochondrial translation and respiration.


Karyopherin

Karyopherins are proteins involved in transporting molecules between the cytoplasm and the nucleus of a eukaryotic cell. The inside of the nucleus is called the karyoplasm (or nucleoplasm). Generally, karyopherin-mediated transport occurs through nuclear pores which acts as a gateway into and out of the nucleus. Most proteins require karyopherins to traverse the nuclear pore.
Karyopherins can act as "importins" (i.e. helping proteins get into the nucleus) or "exportins" (i.e. helping proteins get out of the nucleus). They belong to the nuclear pore complex family in the transporter classification database (TCDB). Energy for transport is derived from the Ran gradient.
Upon stress, several karyopherins stop shuttling between the nucleus and the cytoplasm and are sequestered in stress granules, cytoplasmic aggregates of ribonucleoprotein complexes.
Importin beta.
Importin beta is a of karyopherin that facilitates the transport of cargo proteins into the nucleus. First, it is binding importin alpha – another type of karyopherin that binds the cargo protein in the cytoplasm—before the cargo protein is imported into the nucleus through the nuclear pore using energy derived from the Ran gradient. Once inside the nucleus, the cargo dissociates from the karyopherins.
Importin beta can also carry proteins into the nucleus without the aid of the importin alpha adapter protein.


Lactose permease

Lactose permease is a membrane protein which is a member of the major facilitator superfamily. Lactose permease can be classified as a symporter, which uses the proton gradient towards the cell to transport β-galactosides such as lactose in the same direction into the cell.
The protein has twelve transmembrane alpha-helices and its molecular weight is 45,000 Daltons. It exhibits an internal two-fold symmetry, relating the N-terminal six helices onto the C-terminal helices. It is encoded by the "lacY" gene in the "lac" operon.
The sugar lies in the hydrophilic core of the protein which is accessible from the periplasm. On binding, a large conformational change takes place which makes the sugar binding site accessible from the cytoplasm.
Mechanism: hydronium ions from the outside of the cell binds to a carboxyl group on the enzyme that allows it to undergo a conformational change. This form of lactose permease can bind lactose from outside the cell. The enzyme then everts and lactose is transported inward.
The X-ray crystal structure was first solved in 2003 by J. Abramson "et al."


Delta24-sterol reductase

In enzymology, a Delta24-sterol reductase () is an enzyme that catalyzes the chemical reaction
Thus, the two substrates of this enzyme are 5alpha-cholest-7-en-3beta-ol and NADP+, whereas its 3 products are 5alpha-cholesta-7,24-dien-3beta-ol, NADPH, and H+.
This enzyme belongs to the family of oxidoreductases, specifically those acting on the CH-CH group of donor with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is sterol:NADP+ Delta24-oxidoreductase. This enzyme is also called lanosterol Delta24-reductase. This enzyme participates in biosynthesis of steroids.


Rosiridin

Rosiridin is a chemical compound that has been isolated from "Rhodiola sachalinensis". Rosiridin can inhibit monoamine oxidases A and B, possibly meaning that the compound could help in the treatment of depression and senile dementia.


Hydroxy alpha sanshool

Hydroxy-alpha sanshool is a molecule found in plants from the genus "Zanthoxylum".
It is believed to be responsible for the numbing and tingling sensation caused by eating food cooked with Sichuan peppercorns and Uzazi.
The term "sanshool" in the compound's name is derived from the Japanese term for the Japanese pepper, (literally, mountain pepper), to which was appended the suffix -ol, indicating an alcohol.
Mechanism.
The chemical structure of hydroxy-alpha sanshool is similar to that of capsaicin, but the mechanism of action by which it induces nerve sensations has been a matter of debate. Although the compound is an agonist at the pain integration channels TRPV1 and TRPA1 like capsaicin, newer evidence suggests that the tandem pore domain potassium channels KCNK3, KCNK9, and KCNK18 are primarily responsible for sanshool's effects.
Hydroxy-alpha sanshool excites D-hair afferent nerve fibers, a distinct subset of the sensitive light touch receptors in the skin, and targets novel populations of Aβ and C-fiber nerve fibers.
Extraction.
To isolate the molecule from the pepper in form of an extract, steam distillation can be used: Dried peels
of the fruit are immersed in a mixture of lower alcohols (for example ethanol) and water with a mass
percentage between 35-65% of the alcohol. The solution gets heated up in the process of steam
distillation where the aqueous part evaporates and takes parts of the hydroxy-alpha- sanshool up, too.
The distillate separates in two phases: the aqueous ethanol phase and the oil phase which contains the
desired molecule.
A problem with this extraction method is the low yield which is most times below 60%.


Alliinase

In enzymology, an alliin lyase () is an enzyme that catalyzes the chemical reaction
Hence, this enzyme has one substrate, "S"-alkyl--cysteine "S"-oxide, and two products, alkyl sulfenate and 2-aminoacrylate.
This enzyme belongs to the family of lyases, specifically the class of carbon-sulfur lyases. The systematic name of this enzyme class is S"-alkyl--cysteine "S"-oxide alkyl-sulfenate-lyase (2-aminoacrylate-forming). Other names in common use include alliinase, cysteine sulfoxide lyase, alkylcysteine sulfoxide lyase, S"-alkylcysteine sulfoxide lyase, -cysteine sulfoxide lyase, "S"-alkyl--cysteine sulfoxide lyase, and alliin alkyl-sulfenate-lyase. It employs one cofactor, pyridoxal phosphate.
Many alliinases contain a novel N-terminal epidermal growth factor-like domain (EGF-like domain).
Occurrence.
These enzymes are found in plants of the genus "Allium", such as garlic and onions. Alliinase is responsible for catalyzing chemical reactions that produce the volatile chemicals that give these foods their flavors, odors, and tear-inducing properties. Alliinases are part of the plant's defense against herbivores. Alliinase is normally sequestered within a plant cell, but, when the plant is damaged by a feeding animal, the alliinase is released to catalyze the production of the pungent chemicals. This tends to have a deterrent effect on the animal. The same reaction occurs when onion or garlic is cut with a knife in the kitchen.
Chemistry.
In garlic, an alliinase enzyme acts on the chemical alliin converting it into allicin. The process involves two stages: elimination of 2-propenesulfenic acid from the amino acid unit (with α-aminoacrylic acid as a byproduct), and then condensation of two of the sulfenic acid molecules.
Alliin and related substrates found in nature are chiral at the sulfoxide position (usually having the "S" , and alliin itself was the first natural product found to have both carbon- and sulfur-centered stereochemistry. However, the sulfenic acid intermediate is not chiral, and the final product's stereochemistry is not controlled.
There are a range of similar enzymes that can react with the cysteine-derived sulfoxides present in different species. In onions, an isomer of alliin, isoalliin, is converted to 1-propenesulfenic acid. A separate enzyme, the lachrymatory factor synthase or LFS, then converts this chemical to "syn"-propanethial-"S"-oxide, a potent lachrymator. The analogous butyl compound, "syn"-butanethial-"S"-oxide, is found in "Allium siculum" species.
Structural studies.
As of late 2007, 3 structures have been solved for this class of enzymes, using X-ray crystallography. The PDB accession codes are , , and .


4-Hydroxyphenylacetate 3-monooxygenase

4-hydroxyphenylacetate 3-monooxygenase () is an enzyme that catalyzes the chemical reaction
This reaction is the first step in a pathway found in enteric bacteria such as Escherichia coli and soil bacteria such as Pseudomonas putida which degrades 4-hydroxyphenylacetate (4-HPA), allowing these bacteria to use 4-HPA and other aromatic compounds found in mammalian digestive tracts or in soil as a carbon source. While most known flavin monooxygenases use NADH or NADPH as substrates (and use the flavins FAD or FMN as prosthetic groups ), this enzyme is part of a two-component system, in which a flavin oxidoreductase partner () regenerates FADH2 by oxidizing NADH to NAD+. hpaB and hpaC, the 4-HPA oxygenase and reductase partner proteins (respectively) of "E. coli" strain W, were the first two-component flavin monoxygenase system identified. While known examples of this enzyme share a common catalytic mechanism and likely evolutionary origin, they differ with respect to regulation and ability to substitute FMNH2 for FADH2 as a substrate.
Structure.
This enzyme is a tetramer which forms as a dimer of dimers. Sequence alignments of the Thermus thermophilus and "E. coli" hpaB enzymes show structural similarity to each other and to the oxygenase components of other bacterial two-component monooxygenases for compounds such as phenol and chlorophenol. Each monomer of this protein consists of an N-terminal alpha-helical domain, a middle beta barrel domain, and a C-terminal "tail" helix. FADH2 is bound by a groove between these domains; this binding event causes a loop in the middle domain to change position, preforming a binding site for 4-HPA. At this point, multiple residues act to stabilize catalytic intermediates by hydrogen-bonding to the peroxide bound to FAD, as well as to the hydroxyl group of 4-HPA's phenol moiety (stabilizing its dienone transition state - see Mechanism). The loop which moves to form the 4-HPA binding site when FADH2 binds provides catalytic specificity by hydrogen-bonding to 4-HPA's carboxylic acid moiety.
Mechanism.
While many flavin-dependent monooxygenases retain FMN or FAD in their active sites throughout their catalytic cycle, this enzyme binds FADH2 at the start of its catalytic cycle and releases FAD at the end. After FADH2 binds, dioxygen attacks it at the C4a carbon, leading to a C4a-hydroperoxyflavin intermediate. 4-HPA then binds, and a conformational change sequesters the enzyme's active site from solution, preventing the oxygen from escaping as toxic hydrogen peroxide. 4-HPA is then hydoxylated via a dienone intermediate and released as 3,4-DHPA; with the peroxide bond broken, C4a-hydroxyflavin releases the remaining oxygen atom by eliminating water and is released from the enzyme as FAD.
Biological Function.
To cope with the wide variety of phenolic compounds found in nature, bacterial pathways for degradation of aromatic compounds generally begin by channeling these diverse substrates towards a few common intermediates, which are then further degraded. Pathways for catabolizing aromatic compounds generally begin by adding two hydroxyl groups to the benzene ring, most often on adjacent carbons. This product then undergoes ring cleavage to produce a linear molecule which is ultimately degraded to intermediates of central metabolism, such as succinate, pyruvate, and carbon dioxide. In the case of 4-hydroxyphenylacetate, which only needs one hydroxyl group to be added, a monooxygenase is required.
Among common "E. coli" laboratory strains, the 4-HPA degradation pathway is not found in the commonly used K-12 strain, but it does appear in strains B, C, and W (the strain in which most research into the pathway has been done). Only strains containing this pathway are able to survive by metabolizing 4-HPA as the sole carbon source, showing that this pathway is required for catabolism of this compound, and likely for similar phenolic compounds as well.
Evolution.
In addition to the exclusively FADH2-dependent monooxygenase found in species such as "E. coli" and "T. thermophilus", a version of the enzyme which can use either reduced FAD or reduced FMN has been described in Acinetobacter baumannii. Although these enzymes catalyze similar reactions and share a similar acyl-CoA dehydrogenase fold, the FMN-dependent enzyme is allosterically regulated by 4-HPA while the FADH2-dependent enzyme is likely regulated by a simpler kinetic mechanism, in which low concentrations of 4-HPA lead the enzyme to bind and sequester FADH2 as part of the normal catalytic cycle, causing the free concentration of FADH2 to drop until the flavin oxidoreductase's reaction is indirectly inhibited as well. Along with other differences in regulation and substrate binding despite a shared fundamental catalytic mechanism, this has led to speculation that these enzymes collectively represent an example of convergent evolution.
Potential Applications.
In addition to 4-HPA, the enzyme has been reported to have activity on a number of other phenolic substrates. Metabolic engineers have demonstrated that microbes expressing the "E. coli" enzyme can catalyze reactions such as hydroxylation of tyrosine to L-dopa and hydroxylation of the pharmacologically interesting phenylpropanoids umbelliferone and resveratrol. However, these approaches are not currently used commercially.


Bisphosphonate

Bisphosphonates are a class of drugs that prevent the loss of bone density, used to treat osteoporosis and similar diseases. They are the most commonly prescribed drugs used to treat osteoporosis. They are called bisphosphonates because they have two phosphonate () groups. They are thus also called diphosphonates ("bis-" or "di-" + "phosphonate").
Evidence shows that they reduce the risk of fracture in post-menopausal women with osteoporosis.
Bone tissue undergoes constant remodeling and is kept in balance (homeostasis) by osteoblasts creating bone and osteoclasts destroying bone. Bisphosphonates inhibit the digestion of bone by encouraging osteoclasts to undergo apoptosis, or cell death, thereby slowing bone loss.
The uses of bisphosphonates include the prevention and treatment of osteoporosis, Paget's disease of bone, bone metastasis (with or without hypercalcemia), multiple myeloma, primary hyperparathyroidism, osteogenesis imperfecta, fibrous dysplasia, and other conditions that exhibit bone fragility.
Medical uses.
Bisphosphonates are used to treat osteoporosis, osteitis deformans (Paget's disease of the bone), bone metastasis (with or without hypercalcaemia), multiple myeloma, and other conditions involving fragile, breakable bone.
In osteoporosis and Paget's, the most popular first-line bisphosphonate drugs are alendronate and risedronate. If these are ineffective or if the person develops digestive tract problems, intravenous pamidronate may be used. Strontium ranelate or teriparatide are used for refractory disease. The use of strontium ranelate is restricted because of increased risk of venous thromboembolism, pulmonary embolism and serious cardiovascular disorders, including myocardial infarction. In postmenopausal women, the selective estrogen receptor modulator raloxifene is occasionally administered instead of bisphosphonates. Bisphosphonates are beneficial in reducing the risk of vertebral fracture in steroid induced osteoporosis.
Post-menopausal osteoporosis.
Bisphosphonates are recommended as a first line treatments for post-menopausal osteoporosis.
Long-term treatment with bisphosphonates produces anti-fracture and bone mineral density effects that persist for 3–5 years after an initial 3–5 years of treatment. The bisphosphonate alendronate reduces the risk of hip, vertebral, and wrist fractures by 35-39%; zoledronate reduces the risk of hip fractures by 38% and of vertebral fractures by 62%. Risedronate has also been shown to reduce the risk of hip fractures.
After five years of medications by mouth or three years of intravenous medication among those at low risk, bisphosphonate treatment can be stopped. In those at higher risk ten years of medication by mouth or six years of intravenous treatment may be used.
Cancer.
Bisphosphonates reduce the risk of fracture and bone pain in people with breast, lung, and other metastatic cancers as well as in people with multiple myeloma. In breast cancer there is mixed evidence regarding whether bisphosphonates improve survival. A 2017 Cochrane review found that for people with early breast cancer, bisphosphonate treatment may reduce the risk of the cancer spreading to the person's bone, however, for people who had advanced breast cancer bisphosphonate treatment did not appear to reduce the risk of the cancer spreading to the bone. Side effects associated with bisphosphonate treatment for people with breast cancer are mild and rare.
Bisphosphonates can also reduce mortality in those with multiple myeloma and prostate cancer.
Other.
Evidence suggests that the use of bisphosphonates would be useful in the treatment of complex regional pain syndrome, a neuro-immune problem with high MPQ scores, low treatment efficacy and symptoms which can include regional osteoporosis. In 2009 bisphosphonates were "among the only class of medications that has survived placebo-controlled studies showing statistically significant improvement (in CRPS) with therapy."
Bisphosphonates have been used to reduce fracture rates in children with the disease osteogenesis imperfecta and to treat otosclerosis by minimizing bone loss.
Other bisphosphonates, including medronate (R1=H, R2=H) and oxidronate (R1=H, R2=OH), are mixed with radioactive technetium and injected, as a way to image bone and detect bone disease.
Adverse effects.
Common.
Oral bisphosphonates can cause upset stomach and inflammation and erosions of the esophagus, which is the main problem of oral "N"-containing preparations. This can be prevented by remaining seated upright for 30 to 60 minutes after taking the medication. Intravenous bisphosphonates can give fever and flu-like symptoms after the first infusion, which is thought to occur because of their potential to activate human γδ T cells.
Bisphosphonates, when administered intravenously for the treatment of cancer, have been associated with osteonecrosis of the jaw (ONJ), with the mandible twice as frequently affected as the maxilla and most cases occurring following high-dose intravenous administration used for some cancer patients. Some 60% of cases are preceded by a dental surgical procedure (that involves the bone), and it has been suggested that bisphosphonate treatment should be postponed until after any dental work to eliminate potential sites of infection (the use of antibiotics may otherwise be indicated prior to any surgery).
A number of cases of severe bone, joint, or musculoskeletal pain have been reported, prompting labeling changes.
Some studies have identified bisphosphonate use as a risk factor for atrial fibrillation (AF), though meta-analysis of them finds conflicting reports. , the US Food and Drug Administration did not recommend any alteration in prescribing of bisphosphonates based on AF concerns. More recent meta-analyses have found strong correlations between bisphosphonate use and development of AF, especially when administered intravenously, but that a significantly increased risk of AF that required hospitalization did not have an attendant increased risk of stroke or cardiovascular mortality.
Long-term risks.
In large studies, women taking bisphosphonates for osteoporosis have had unusual fractures ("bisphosphonate fractures") in the femur (thigh bone) in the shaft (diaphysis or sub-trochanteric region) of the bone, rather than at the femoral neck, which is the most common site of fracture. However, these fractures are rare (12 in 14,195 women) compared to the common hip fractures (272 in 14,195 women), and the overall reduction in hip fractures caused by bisphosphonate is more than the increase in unusual shaft fractures. There are concerns that long-term bisphosphonate use can result in over-suppression of bone turnover. It is hypothesized that micro-cracks in the bone are unable to heal and eventually unite and propagate, resulting in atypical fractures. Such fractures tend to heal poorly and often require some form of bone stimulation, for example bone grafting as a secondary procedure. This complication is not common, and the benefit of overall fracture reduction still holds. In cases where there is concern of such fractures occurring, teriparatide is potentially a good alternative because it does not cause as much damage as a bisphosphonate does by suppressing bone turnover.
Three meta analyses have evaluated whether bisphosphonate use is associated with an increased risk of esophageal cancer. Two studies concluded that there was no evidence of increased risk.
Chemistry and classes.
All bisphosphonate drugs share a common phosphorus-carbon-phosphorus "backbone":
The two (phosphonate) groups covalently linked to carbon determine both the name "bis"phospho"nate" and the function of the drugs. "Bis" refers to the fact that there are two such groups in the molecule.
The long side-chain (R2 in the diagram) determines the chemical properties, the mode of action and the strength of bisphosphonate drugs. The short side-chain (R1), often called the 'hook', mainly influences chemical properties and pharmacokinetics.
Pharmacokinetics.
Of the bisphosphonate that is resorbed (from oral preparation) or infused (for intravenous drugs), about 50% is excreted unchanged by the kidney. The remainder has a very high affinity for bone tissue, and is rapidly adsorbed onto the bone surface. Once bisphosphonates are in bone, they have a very long elimination half-life that can exceed ten years.
Mechanism of action.
Bisphosphonates are structurally similar to pyrophosphate, but with a central carbon that can have up to two substituents (R1 and R2) instead of an oxygen atom. Because a bisphosphonate group mimics the structure of pyrophosphate, it can inhibit activation of enzymes that utilize pyrophosphate.
The specificity of bisphosphonate-based drugs comes from the two phosphonate groups (and possibly a hydroxyl at R1) that work together to coordinate calcium ions. Bisphosphonate molecules preferentially bind to calcium ions. The largest store of calcium in the human body is in bones, so bisphosphonates accumulate to a high concentration only in bones.
Bisphosphonates, when attached to bone tissue, are released by osteoclasts, the bone cells that break down bone tissue. Bisphosphonate molecules then attach to and enter osteoclasts where they disrupt intracellular enzymatic functions needed for bone resorption.
There are two classes of bisphosphonate compounds: non-nitrogenous (no nitrogen in R2) and nitrogenous (R2 contains nitrogen). The two types of bisphosphonates work differently in killing osteoclasts.
Non-nitrogenous.
The non-nitrogenous bisphosphonates (diphosphonates) are metabolised in the cell to compounds that replace the terminal pyrophosphate moiety of ATP, forming a non-functional molecule that competes with adenosine triphosphate (ATP) in the cellular energy metabolism. The osteoclast initiates apoptosis and dies, leading to an overall decrease in the breakdown of bone. This type of bisphosphonate has overall more negative effects than the nitrogen containing group, and is prescribed far less often.
Nitrogenous.
Nitrogenous bisphosphonates act on bone metabolism by binding and blocking the enzyme farnesyl diphosphate synthase (FPPS) in the HMG-CoA reductase pathway (also known as the mevalonate pathway).
Bisphosphonates that contain isoprene chains at the R1 or R2 position can impart specificity for inhibition of GGPS1.
Disruption of the HMG CoA-reductase pathway at the level of FPPS prevents the formation of two metabolites (farnesol and geranylgeraniol) that are essential for connecting some small proteins to the cell membrane. This phenomenon is known as prenylation, and is important for proper sub-cellular protein trafficking (see "lipid-anchored protein" for the principles of this phenomenon).
While inhibition of protein prenylation may affect many proteins found in an osteoclast, disruption to the lipid modification of Ras, Rho, Rac proteins has been speculated to underlie the effects of bisphosphonates. These proteins can affect both osteoclastogenesis, cell survival, and cytoskeletal dynamics. In particular, the cytoskeleton is vital for maintaining the "ruffled border" that is required for contact between a resorbing osteoclast and a bone surface.
Statins are another class of drugs that inhibit the HMG-CoA reductase pathway. Unlike bisphosphonates, statins do not bind to bone surfaces with high affinity, and thus are not specific for bone. Nevertheless, some studies have reported a decreased rate of fracture (an indicator of osteoporosis) and/or an increased bone mineral density in statin users. The overall efficacy of statins in the treatment of osteoporosis remains controversial.
History.
Bisphosphonates were developed in the 19th century but were first investigated in the 1960s for use in disorders of bone metabolism. Their non-medical use was to soften water in irrigation systems used in orange groves. The initial rationale for their use in humans was their potential in preventing the dissolution of hydroxylapatite, the principal bone mineral, thus arresting bone loss. In the 1990s their actual mechanism of action was demonstrated with the initial launch of alendronate by Merck & Co.


Uridine diphosphate N-acetylglucosamine

Uridine diphosphate "N"-acetylglucosamine or UDP-GlcNAc is a nucleotide sugar and a coenzyme in metabolism. It is used by glycosyltransferases to transfer "N"-acetylglucosamine residues to substrates. -Glucosamine is made naturally in the form of glucosamine-6-phosphate, and is the biochemical precursor of all nitrogen-containing sugars. To be specific, glucosamine-6-phosphate is synthesized from fructose 6-phosphate and glutamine as the first step of the hexosamine biosynthesis pathway. The end-product of this pathway is UDP-GlcNAc, which is then used for making glycosaminoglycans, proteoglycans, and glycolipids.
UDP-GlcNAc is extensively involved in intracellular signaling as a substrate for "O"-linked "N"-acetylglucosamine transferases (OGTs) to install the "O"-GlcNAc post-translational modification in a wide range of species. It is also involved in nuclear pore formation and nuclear signalling. OGTs and OG-ases play an important role in the structure of the cytoskeleton. In mammals, there is enrichment of OGT transcripts in the pancreas beta-cells, and UDP-GlcNAc is thought to be part of the glucose sensing mechanism. There is also evidence that it plays a part in insulin sensitivity in other cells. In plants, it is involved in the control of gibberellin production.
"Clostridium novyi" type A alpha-toxin is an "O"-linked "N"-actetylglucosamine transferase acting on Rho proteins and causing the collapse of the cytoskeleton.


Autolysin

Autolysins are a endogenous lytic enzymes that breaks down the peptidoglycan components of biological cells which enables the separation of daughter cells following cell division. They are involved in cell growth, cell wall metabolism, cell division and separation, as well as peptidoglycan turnover and has similar function to lysozymes.
Autolysin is formed from the precursor gene, Atl. Amidases (EC 3.5.1.28), gametolysin (EC 3.4.24.38), and glucosaminidase are considered as types of autolysins.
Function and Mechanisms.
Autolysins exist in all bacteria containing peptidoglycan and are potentially considered as lethal enzymes when uncontrolled. They target the glycosidic bonds as well as the cross-linked peptides of the peptidoglycan matrix. The peptidoglycan matrix functions for cell wall stability to protect from turgor changes and carries out function for immunological defense. These enzymes break down the peptidoglycan matrix in small sections to allow for peptidoglycan biosynthesis. Autolysins breaks down old peptidoglycan which allows for the formation of newer peptidoglycan for cell growth and elongation. This is called cell wall turnover. Autolysins do this by hydrolyzing the β-(1,4) glycosidic bond of the peptidoglycan cell wall and the linkage between N-acetylmuramoyl residues and L-amino acid residues of certain cell-wall glycopeptides . This enzyme catalyses the following chemical reaction:
This glycoprotein is present in "Chlamydomonas reinhardtii" gametes.
Gram-positive bacteria regulate autolysins with teichoic acid molecules attached to the tetrapeptide of the peptidoglycan matrix.
The antibiotics complestatin and corbomycin prevent autolysin from remodeling the cell wall by binding to peptidoglycan, therefore stopping bacterial growth. The amide linkages between stem peptide and lactyl moiety of muramoyl residue are cleaved by N-acetylmuramoyl-l-alanine amidases and partakes in cell separation and the dissociation of the cell septum. There are 5 types of autolysins that contribute to cell separation of daughter cells, LytC, LytD, LytE, and LytF.
In a study conducted with mice, those that were immunized with autolysin were able to survive longer than the infected mice. This study was able to support as evidence autolysin's contribution in virulence and potential for vaccine antigen.
Lysis of Mother Cell.
LytC and CwlC are two amidases from the LytC family that hydrolyze the peptidoglycan of the mother cell wall to allow for the release of the mature endospore. CwlC is directly found in the mother cell wall.
Motility.
Expression of lytC, lytD, and lytF genes together leads to flagellar motility and is controlled by the activity of the chemotaxis sigma factor,  σD. The activity of this sigma factor peaks at the start of the stationary phase.
Potential Lethality.
Autolysins are naturally produced by peptidoglycan containing bacteria, but excessive amounts will degrade the peptidoglycan matrix and cause the cell to burst due to osmotic pressure. Previous studies have found that the byproducts of autolysin during cell wall breakdown are highly immunogenic. When observed in the bacteria, Bacillus subtilis (B. subtilis), there were potentially lethal amounts of autolysin found in the cell walls. In Steptococcus pneumoniae (S. pneumoniae), it was found that N-acetylmuramoyl-l-alanine amidase, a cell wall autolysin, could assist in pathogenesis due to its ability to break down the wall or lyse a portion of the invading pneumococci and release potentially lethal toxins into the cell. Researchers studied the function, structure, and cloning ability through Escherichia coli (E. coli) and also determined its nucleotide sequence.
Families.
LytC amidase Family.
LytC.
LytC as well as LytD are considered as two major autolysins that contribute to vegetative cell wall growth and account for 95% of the autolytic activity in B. subtilis. LytC is found in the cell wall. LytB, a non-autolysin, was found to enhance LytC activity. LytC and LytA interact and function together for lysis and cell death.
CwlC.
CwlC is found in the mother cell wall and functions for the lysis of the mother cell wall. CwlC does not have a signal sequence but participates in late sporulation and is present in the cell wall. It was found in B. subtilis that CwlC is able to hydrolyze both vegetative cell walls and spore peptidoglycan.
LytD glucosaminidase Family.
This family of autolysin consist of only LytD itself. LytD functions for vegetative growth. Autolytic activity is found within the C-terminal region with catalytic domain homologous to the glucosaminidase domain. LytD is found in the cell wall. LytD activity was studied in B. subtilis and glucosaminidase activity was found in mature glycan strands due to the presence of MurNAc at the nonreducing ends.


Type I collagen

Type I collagen is the most abundant collagen of the human body. It forms large, eosinophilic fibers known as collagen fibers.
It is present in scar tissue, the end product when tissue heals by repair, as well as tendons, ligaments, the endomysium of myofibrils, the organic part of bone, the dermis, the dentin, and organ capsules.
Formation.
The COL1A1 gene produces the pro-alpha1(I) chain. This chain combines with another pro-alpha1(I) chain and also with a pro-alpha2(I) chain (produced by the COL1A2 gene) to make a molecule of type I pro-collagen. These triple-stranded, rope-like pro-collagen molecules must be processed by enzymes outside the cell. Once these molecules are processed, they arrange themselves into long, thin fibrils that cross-link to one another in the spaces around cells. The cross-links result in the formation of very strong mature type I collagen fiber.
Clinical significance.
See Collagen, type I, alpha 1#Clinical significance


Extracellular adenylate cyclase

Extracellular adenylate cyclase is an adenylate cyclase produced by "Bordetella pertussis".


M-Cresol

"meta"-Cresol, also 3-methylphenol, is an organic compound with the formula CH3C6H4(OH). It is a colourless, viscous liquid that is used as an intermediate in the production of other chemicals. It is a derivative of phenol and is an isomer of "p"-cresol and "o"-cresol.
Production.
Together with many other compounds, "m"-cresol is traditionally extracted from coal tar, the volatile materials obtained in the production of coke from (bituminous) coal. This residue contains a few percent by weight of phenol and isomeric cresols. In the cymene–cresol process, toluene is alkylated with propylene to give isomers of cymene, which can be oxidatively dealkylated analogous to the cumene process. Another method, involves carbonylation of a mixture of methallyl chloride and acetylene in the presence of nickel carbonyl.
Applications.
"m"-Cresol is a precursor to numerous compounds. Important examples include:
Natural occurrences.
"m"-Cresol is a component found in temporal glands secretions during musth in male African elephants ("Loxodonta africana").
"m"-Cresol is a constituent of tobacco smoke.
"m"-Cresol is a component found in secretions from the ant Colobopsis_saundersi during Autothysis.


2-acetolactate mutase

In enzymology, a 2-acetolactate mutase () is an enzyme that catalyzes the chemical reaction
Hence, this enzyme has one substrate, 2-acetolactate, and one product, 3-hydroxy-3-methyl-2-oxobutanoate.
This enzyme belongs to the family of isomerases, specifically those intramolecular transferases transferring other groups. The systematic name of this enzyme class is 2-acetolactate methylmutase. Other names in common use include acetolactate mutase, and acetohydroxy acid isomerase. This enzyme participates in valine, leucine and isoleucine biosynthesis. It employs one cofactor, ascorbate.


2-nitropropane dioxygenase

In enzymology, a 2-nitropropane dioxygenase () is an enzyme that catalyzes the chemical reaction
Thus, the two substrates of this enzyme are 2-nitropropane and O2, whereas its two products are acetone and nitrite.
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 2-nitropropane:oxygen 2-oxidoreductase. This enzyme participates in nitrogen metabolism. It has 3 cofactors: FAD, Iron, and FMN.
Structural studies.
As of late 2007 Steve Fuhrer from the DHPA solved this very complex formula to find, two structures have been solved for this class of enzymes, with PDB accession codes and .


(Ribulose-bisphosphate carboxylase)-lysine N-methyltransferase

In enzymology, a [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase () is an enzyme that catalyzes the chemical reaction
Thus, the two substrates of this enzyme are S-adenosyl methionine and ribulose-1,5-bisphosphate carboxylase-lysine, whereas its two products are S-adenosylhomocysteine and ribulose-1,5-bisphosphate carboxylase-N6-methyl-L-lysine.
Transferase Family.
This enzyme belongs to the family of transferases, specifically those transferring one-carbon group methyltransferases.
The systematic name of this enzyme class is S-adenosyl-L-methionine:[3-phospho-D-glycerate-carboxy-lyase (dimerizing)]-lysine N6-methyltransferase.
Other names in common use include rubisco methyltransferase, ribulose-bisphosphate-carboxylase/oxygenase N-methyltransferase, ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, epsilonN-methyltransferase, S-adenosyl-L-methionine:[3-phospho-D-glycerate-carboxy-lyase, and (dimerizing)]-lysine 6-N-methyltransferase.
Structural studies.
As of late 2007, 7 structures have been solved for this class of enzymes, with PDB accession codes , , , , , , and .


Cis-2-enoyl-CoA reductase (NADPH)

In enzymology, a cis-2-enoyl-CoA reductase (NADPH) () is an enzyme that catalyzes the chemical reaction
Thus, the two substrates of this enzyme are acyl-CoA and NADP+, whereas its 3 products are cis-2,3-dehydroacyl-CoA, NADPH, and H+.
Nomenclature.
This enzyme belongs to the family of oxidoreductases, specifically those acting on the CH-CH group of donor with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is acyl-CoA:NADP+ cis-2-oxidoreductase. Other names in common use include NADPH-dependent cis-enoyl-CoA reductase, reductase, cis-2-enoyl coenzyme A, cis-2-enoyl-coenzyme A reductase, and cis-2-enoyl-CoA reductase (NADPH).


Endogalactosaminidase

Endogalactosaminidase () is an enzyme with systematic name "galactosaminoglycan glycanohydrolase". This enzyme catalyses the following chemical reaction


Nicotinamide adenine dinucleotide phosphate

Nicotinamide adenine dinucleotide phosphate, abbreviated NADP or, in older notation, TPN (triphosphopyridine nucleotide), is a cofactor used in anabolic reactions, such as the Calvin cycle and lipid and nucleic acid syntheses, which require NADPH as a reducing agent. It is used by all forms of cellular life.
NADPH is the reduced form of NADP. NADP differs from NAD by the presence of an additional phosphate group on the 2' position of the ribose ring that carries the adenine moiety. This extra phosphate is added by NAD+ kinase and removed by NADP+ phosphatase.
Biosynthesis.
NADP.
In general, NADP+ is synthesized before NADPH is. Such a reaction usually starts with NAD+ from either the de-novo or the salvage pathway, with NAD+ kinase adding the extra phosphate group. NAD(P)+ nucleosidase allows for synthesis from nicotinamide in the salvage pathway, and NADP+ phosphatase can convert NADPH back to NADH to maintain a balance. Some forms of the NAD+ kinase, notably the one in mitochondria, can also accept NADH to turn it directly into NADPH. The prokaryotic pathway is less well understood, but with all the similar proteins the process should work in a similar way.
NADPH.
NADPH is produced from NADP+. The major source of NADPH in animals and other non-photosynthetic organisms is the pentose phosphate pathway, by glucose-6-phosphate dehydrogenase (G6PDH) in the first step. The pentose phosphate pathway also produces pentose, another important part of NAD(P)H, from glucose. Some bacteria also use G6PDH for the Entner–Doudoroff pathway, but NADPH production remains the same.
Ferredoxin-NADP reductase, present in all domains of life, is a major source of NADPH in photosynthetic organisms including plants and cyanobacteria. It appears in the last step of the electron chain of the light reactions of photosynthesis. It is used as reducing power for the biosynthetic reactions in the Calvin cycle to assimilate carbon dioxide and help turn the carbon dioxide into glucose. It has functions in accepting electrons in other non-photosynthetic pathways as well: it is needed in the reduction of nitrate into ammonia for plant assimilation in nitrogen cycle and in the production of oils.
There are several other lesser-known mechanisms of generating NADPH, all of which depend on the presence of mitochondria in eukaryotes. The key enzymes in these carbon-metabolism-related processes are NADP-linked isoforms of malic enzyme, isocitrate dehydrogenase (IDH), and glutamate dehydrogenase. In these reactions, NADP+ acts like NAD+ in other enzymes as an oxidizing agent. The isocitrate dehydrogenase mechanism appears to be the major source of NADPH in fat and possibly also liver cells. These processes are also found in bacteria. Bacteria can also use a NADP-dependent glyceraldehyde 3-phosphate dehydrogenase for the same purpose. Like the pentose phosphate pathway, these pathways are related to parts of glycolysis.
NADPH can also be generated through pathways unrelated to carbon metabolism. The ferredoxin reductase is such an example. Nicotinamide nucleotide transhydrogenase transfers the hydrogen between NAD(P)H and NAD(P)+, and is found in eukaryotic mitochondria and many bacteria. There are versions that depend on a proton gradient to work and ones that do not. Some anaerobic organisms use NADP+-linked hydrogenase, ripping a hydride from hydrogen gas to produce a proton and NADPH.
Like NADH, NADPH is fluorescent. NADPH in aqueous solution excited at the nicotinamide absorbance of ~335 nm (near UV) has a fluorescence emission which peaks at 445-460 nm (violet to blue). NADP has no appreciable fluorescence.
Function.
NADPH provides the reducing equivalents for biosynthetic reactions and the oxidation-reduction involved in protecting against the toxicity of reactive oxygen species (ROS), allowing the regeneration of glutathione (GSH). NADPH is also used for anabolic pathways, such as cholesterol synthesis, steroid synthesis, ascorbic acid synthesis, xylitol synthesis, cytosolic fatty acid synthesis and microsomal fatty acid chain elongation.
The NADPH system is also responsible for generating free radicals in immune cells by NADPH oxidase. These radicals are used to destroy pathogens in a process termed the respiratory burst.
It is the source of reducing equivalents for cytochrome P450 hydroxylation of aromatic compounds, steroids, alcohols, and drugs.
Stability.
NADH and NADPH are very stabile in basic solutions, but NAD+ and NADP+ are degraded in basic solutions into a fluorescent product which conveniently can be used for quantitation. Conversely, NADPH and NADH are degraded by acidic solutions while NAD+/NADP+ are fairly stable to acid.
Enzymes that use NADP(H) as a substrate.
In 2018 and 2019, the first two reports of enzymes that catalyze the removal of the 2' phosphate of NADP(H) in eukaryotes emerged. First, the cytoplasmic protein MESH1 (), then the mitochondrial protein nocturnin were reported. Of note, the structures and NADPH binding of MESH1 (5VXA) and nocturnin (6NF0) are not related.


Calponin homology domain

Calponin homology domain (or CH domain) is a family of actin binding domains found in both cytoskeletal proteins and signal transduction proteins. The domain is about 100 amino acids in length and is composed of four alpha helices. It comprises the following groups of actin-binding domains:
A comprehensive review of proteins containing this type of actin-binding domains is given in.
The CH domain is involved in actin binding in some members of the family. However, in calponins there is evidence that the CH domain is not involved in its actin binding activity. Most proteins have two copies of the CH domain, however some proteins such as calponin and the human vav proto-oncogene () have only a single copy. The structure of an example CH domain has been determined using X-ray crystallography.
Examples.
Human genes encoding calponin homology domain-containing proteins include:


CUT domain

In molecular biology, the CUT domain (also known as ONECUT) is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, which is often found downstream of the CUT domain. Proteins display two modes of DNA binding, which hinge on the homeodomain and on the linker that separates it from the CUT domain, and two modes of transcriptional stimulation, which hinge on the homeodomain.


5-Methyluridine

The chemical compound 5-methyluridine, also called ribothymidine, is a pyrimidine nucleoside. Abbreviated m5U, it is the ribonucleoside counterpart to the deoxyribonucleoside thymidine, which lacks a hydroxyl group at the 2' position. 5-Methyluridine contains a thymine base joined to a ribose pentose sugar. It is a white solid.


Cytidine

Cytidine is a nucleoside molecule that is formed when cytosine is attached to a ribose ring (also known as a ribofuranose) via a β-N1-glycosidic bond. Cytidine is a component of RNA.
If cytosine is attached to a deoxyribose ring, it is known as a deoxycytidine.
Properties.
Cytidine is a white, crystalline powder. It is very soluble in water, but only slightly soluble in ethanol.
Dietary sources.
Dietary sources of cytidine include foods with high RNA (ribonucleic acid) content, such as organ meats, Brewer's yeast, as well as pyrimidine-rich foods such as beer. During digestion, RNA-rich foods are broken-down into ribosyl pyrimidines (cytidine and uridine), which are absorbed intact. In humans, dietary cytidine is converted into uridine, which is probably the compound behind cytidine's metabolic effects.
Cytidine analogues.
There are a variety of cytidine analogues with potentially useful pharmacology. For example, KP-1461 is an anti-HIV agent that works as a viral mutagen, and zebularine exists in "E. coli" and is being examined for chemotherapy. Low doses of azacitidine and its analog decitabine have shown results against cancer through epigenetic demethylation.
Biological actions.
In addition to its role as a pyrimidine component of RNA, cytidine has been found to control neuronal-glial glutamate cycling, with supplementation decreasing midfrontal/cerebral glutamate/glutamine levels. As such, cytidine has generated interest as a potential glutamatergic antidepressant drug.


Steroidal alkaloid

Steroidal alkaloids have organic ring backbones which feature nitrogen-based functional groups. More specifically, they are distinguished by their tetracyclic cyclopentanophenanthrene backbone that marks their close relationship with sterols. They fall in two major categories: Solanum alkaloids and Veratrum alkaloids. A Steroidal alkaloid has also been found in "Chonemorpha fragrans" (Frangipani vine), 'chonemorphine' was used to treat intestinal infections in Wistar rats. (Chatterjee DK et al (1987) Parasitol Res 74, 1, 30-33).
Solanum alkaloids.
These compounds generally appear as their corresponding glycoside in plants of the genus "Solanum". "Solanum" includes plants like potatoes, tomatoes, and various nightshades Starting with cholesterol, the biosynthesis of these compounds follow a similar general mechanism including hyroxylation, oxidation, and transamination before differentiating. Alkaloids found in these plants include chaconine, solanine, solasodine, tomatidine, tomatine, and solanidine. Typically they are used in plants as a protection mechanism against animals. Due to the typical anti-cholinesterase activity, they can be used as poisons against the plants' predators. They can be used as starting materials for steroidal drugs. There are various tests for identifying these alkaloids. The characteristic test involves dissolving the compound in hot amyl alcohol or ethanol and watching for the formation of a jelly-like product as the mixture cools.
Veratrum alkaloids.
True to their name, Veratrum alkaloids come from plants of the genus "Veratrum". Alkaloids are found in the roots and rhizomes of these plants. They include veratridine, cyclopamine, and jervine. Because of their actions on the cardiovascular, neuromuscular, and respiratory systems, Veratrum alkaloids have been used for the treatment of various conditions like myasthenia gravis, hypotension, and eclampsia.
Bioactivity.
Steroidal alkaloids have been investigated for a wide range of potential bioactivities including antimicrobial, anti-inflammatory, anti-estrogenic, and chemotherapeutic activity. These bioactivities are the result of a wide array of mechanisms across different compounds. For example, solasodine antimicrobial bioactivity is accomplished by interfering with the synthesis of genetic substances in "Saccharomyces cerevisiae" and "Prototheca wickerhamii". Solasodine inhibits growth signaling in "Geim original algal". On the other hand, tomatidine synergistically works with aminoglycosides as antibiotics against "S. aureus".
Antiinflammation is similarly accomplished with a variety of mechanisms. Solasodine, for example, reduces interleukin-2 and -8 production whereas tomatidine inhibits specific nuclear translocation, JNK activation, as well as induce nitrous oxide synthase. Lastly, nine steroidal alkaloids have significant antiestrogenic activity whereas seven inhibit estrone sulfatase.
However, in addition to their therapeutic benefits, steroidal alkaloids, specifically veratrum alkaloids, are potentially deadly.
Veratrum alkaloid compounds act by attaching to voltage-gated sodium ion channels, altering their permeability. Veratrum alkaloids cause affected sodium channels to reactivate 1000x slower than unaffected channels. Furthermore, veratrum alkaloids block inactivation of sodium channels and lower their activation threshold so they remain open even at resting potential. As a result, sodium concentrations within the cell rise, leading to increased nerve and muscle excitability. These biochemical channels cause muscle contractions, repetitive firing of the nerves and an irregular heart rhythm caused by stimulation of vagal nerves which control the parasympathetic functions of the heart, lungs and digestive tract.


Betaine-aldehyde dehydrogenase

In enzymology, a betaine-aldehyde dehydrogenase () is an enzyme that catalyzes the chemical reaction
The 3 substrates of this enzyme are betaine aldehyde, NAD+, and H2O, whereas its 3 products are betaine, NADH, and H+.
This enzyme belongs to the family of oxidoreductases, specifically those acting on the aldehyde or oxo group of donor with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is betaine-aldehyde:NAD+ oxidoreductase. Other names in common use include betaine aldehyde oxidase, BADH, betaine aldehyde dehydrogenase, and BetB. This enzyme participates in glycine, serine and threonine metabolism.
Structural studies.
, 4 structures have been solved for this class of enzymes, with PDB accession codes , , , and .


Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

In enzymology, a glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) () is an enzyme that catalyzes the chemical reaction
The 3 substrates of this enzyme are D-glyceraldehyde 3-phosphate, phosphate, and NAD+, whereas its 3 products are 3-phospho-D-glyceroyl phosphate, NADH, and H+. This enzyme participates in glycolysis / gluconeogenesis.
Nomenclature.
This enzyme belongs to the family of oxidoreductases, specifically those acting on the aldehyde or oxo group of donor with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is D-glyceraldehyde-3-phosphate:NAD+ oxidoreductase (phosphorylating). Other names in common use include triosephosphate dehydrogenase, dehydrogenase, glyceraldehyde phosphate, phosphoglyceraldehyde dehydrogenase, 3-phosphoglyceraldehyde dehydrogenase, NAD+-dependent glyceraldehyde phosphate dehydrogenase, glyceraldehyde phosphate dehydrogenase (NAD+), glyceraldehyde-3-phosphate dehydrogenase (NAD+), NADH-glyceraldehyde phosphate dehydrogenase, and glyceraldehyde-3-P-dehydrogenase.


Tic Tac

Tic Tac (stylized as "tic tac") is a brand of small, hard mint manufactured by the Italian company Ferrero. They were first produced in 1969 and are now available in a variety of flavours in over 100 countries.
Tic Tacs are usually sold in small transparent plastic boxes with a flip-action living hinge lid. Originally, Tic Tacs were dyed specific colours for different flavours, although in many countries the transparent plastic boxes are now coloured and the actual Tic Tacs are white.
Tic Tac has featured advertising that emphasizes the low calorie count of the mints. Most flavours have approximately 1.9 calories per mint.
History.
Tic Tac were first introduced by Ferrero in 1969, under the name "Refreshing Mints". In 1970, the name was changed to Tic Tac, after the distinctive clicking sound made by the pack being opened and closed. Besides the original mint and orange flavours, several new varieties were added, including aniseed, cinnamon (or "Winter Warmer"), an orange and lime mix (in 1976), spearmint, peppermint, Powermint, sour apple, mandarin, tangerine, berry, fresh orange, strawberry, wintergreen, pink grapefruit, orange and lime together (in 1978), cherry, passionfruit (in 2007), pomegranate (in 2010), mango, lime, and popcorn (2014). The grape flavour was eliminated in 1976 because of health concerns about the red dye amaranth (FD&C Red #2), a suspected carcinogen.
Other offerings have included holiday gift packs for Christmas, Easter, St Patricks Day and Valentine's Day.
Since 1980, the Tic Tac slogan has been "The 1½ Calorie Breath Mint." In the UK, France, Ireland, Italy and Australia Tic Tacs are noted as being less than two calories with the slogan "Two hours of Tic Tac freshness in less than two calories." In Canada, New Zealand and Australia, and used once in the United States, the Tic Tac slogan is "it's not just a mint, it's a tic tac." In India, the Tic Tac slogan is "Refreshment to be shared."
During the 1990s, "double packs" were introduced, featuring a regular Tic Tac container with two flavours inside. Available combinations included Tangerine and Lime, Orange and Grape, and Berry and Cherry.
In 2006, Tic Tac introduced a "Bold" edition with more intense flavours of Mint and Fruit.
In 2008, Tic Tac introduced "Tic Tac Chill," which is slightly larger than ordinary Tic Tacs and comes in a dual-opening packaging, using the traditional living hinge or a sliding opening on the front of the case. These come in three flavours: Exotic Cherry, Berry Blast, and Paradise Mint. Tic Tac Chill mints are also sugar-free, the Exotic Cherry ones instead being sweetened with xylitol.
May 2010 Australia Trademark Registrar's office rejected Ferrero application to trademark their Tic Tac container as not being unique enough to distinguish its products from other manufacturers.
Orange, Mint, Spearmint, Mintensity, Peach and Passion, Strawberry Mix, Cherry, Elaichi (cardamom) and Banana are available in India.
Tic Tac sometimes provides limited editions to promote films, such as a banana and mandarin flavour for the 2015 movie "Minions". Orange Tic Tacs featured prominently in the 2007 film "Juno", in an orange box with white colour mints as sold in Canada and Brazil. Film promoters distributed boxes of the mints prior to the film's release.
Manufacturing.
Forty-five percent of the world's Tic Tacs are manufactured in the Ferrero factory in Cork, Ireland.
Tic Tacs are also manufactured in Australia, Canada, India and Ecuador.
Nutrition facts.
For Fresh mint (Europe/US/Canada); Peppermint (Australia)
Nutritional information.
Per 100 g – Energy 1663 kJ (391 kcal), Protein 0.1 g, Carbohydrate 97.5 g, Fat 0.4 g.
Per Tic Tac – Energy 8 kJ (2 kcal), Protein 0 g, Carbohydrate 0.5 g, Fat 0 g.
Ingredients.
Sugar, fructose, maltodextrin, peppermint essential oil, rice starch, gum arabic, filling agent (magnesium salts of fatty acids), glazing agent (carnauba wax).
Each pack weighs and contains about 38 Tic Tacs. New packs in Australia and Canada weigh 24g and contain 50 Tic Tacs, and the Tic Tac "100 pack" weighs 49g and contains 100 Tic Tacs. The "Big Pack" weighs 29g and contains 60 Tic Tacs. The "Bottle Pack" weighs 98g and contains 200 Tic Tacs.
In the United States, Tic Tac list the sugar content as 0g despite the mints being approximately 90% sugar (depending on the flavour). This stems from the fact that a serving size is one 0.49g mint, and the American Food and Drug Administration permits manufacturers to list sugar (or other nutritional components) as 0g if they contain less than 0.5g. In at least some jurisdictions, the 0g now features a footnote that clarifies "less than 0.5g".


Diclofenamide

Diclofenamide (or dichlorphenamide) is a sulfonamide and a carbonic anhydrase inhibitor of the "meta"-disulfamoylbenzene class.
Uses.
Diclofenamide was approved in the United States in 1958 as "Daranide" to treat glaucoma, Subsequently, it was found effective in cases of therapy-resistant epilepsy. In 2015, the medication was approved in the US under the name "Keveyis" as an orphan drug for the treatment of primary hypokalemic and hyperkalemic periodic paralysis.
Cost.
In 2001, diclofenamide had a U.S. list price of $50 for a bottle of 100 pills, and was approved for glaucoma. Merck discontinued diclofenamide when better glaucoma drugs were developed. In 2010, Sun Pharmaceutical Industries bought the rights. In 2015, the F.D.A. approved it as an orphan drug, with 7-year exclusive marketing rights, for periodic paralysis, which the company estimates affects 5,000 people in the U.S. In 2016, Strongbridge Biopharma acquired Sun, which raised the price to $15,001 for 100 pills. The cost of treatment would range from $109,500 to $219,000 a year. Sun gives the drug free to patients who don't have insurance.


Cellobiose

Cellobiose is a disaccharide with the formula (C6H7(OH)4O)2O. It is classified as a reducing sugar. In terms of its chemical structure, it is derived from the condensation of a pair β-glucose molecules forging a β(1→4) bond. It can be hydrolyzed to glucose enzymatically or with acid. Cellobiose has eight free alcohol (OH) groups, one acetal linkage and one hemiacetal linkage, which give rise to strong inter- and intramolecular hydrogen bonds. It is a white solid.
It can be obtained by enzymatic or acidic hydrolysis of cellulose and cellulose-rich materials such as cotton, jute, or paper. Cellobiose can be used as an indicator carbohydrate for Crohn's disease and malabsorption syndrome.
Treatment of cellulose with acetic anhydride and sulfuric acid, gives cellobiose octoacetate, which is no longer a hydrogen bond donor (though it is still a hydrogen bond acceptor) and is soluble in nonpolar organic solvents.


Sophorose

Sophorose is a disaccharide, a dimer of glucose. It differs from other glucose dimers such as maltose in having an unusual β-1,2 bond. It was isolated in 1938 from pods of "Sophora japonica". It is a component of sophorolipids. It is a product of the caramelization of glucose.


NLRP9

NLRP9, short for NOD-like receptor family pyrin domain containing 9, is an intracellular protein that is expressed in the ovaries, testes, oocytes, and preimplantation embryos of mammals that is likely involved in reproductive processes. It is also known as NALP9, NOD6, PAN12, and CLR19.1, and is one of 14 pyrin domain containing members of the NOD-like receptor family of cytoplasmic receptors.


6-endo-hydroxycineole dehydrogenase

In enzymology, a 6-endo-hydroxycineole dehydrogenase () is an enzyme that catalyzes the chemical reaction
Thus, the two substrates of this enzyme are 6-endo-hydroxycineole and NAD+, whereas its 3 products are 6-oxocineole, NADH, 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 6-endo-hydroxycineole:NAD+ 6-oxidoreductase. This enzyme participates in terpenoid biosynthesis.


Aryl-alcohol dehydrogenase

In enzymology, an aryl-alcohol dehydrogenase () is an enzyme that catalyzes the chemical reaction
Thus, the two substrates of this enzyme are aromatic alcohol and NAD+, whereas its 3 products are aromatic aldehyde, NADH, 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 aryl-alcohol:NAD+ oxidoreductase. Other names in common use include p-hydroxybenzyl alcohol dehydrogenase, benzyl alcohol dehydrogenase, and coniferyl alcohol dehydrogenase. This enzyme participates in 5 metabolic pathways: tyrosine metabolism, phenylalanine metabolism, biphenyl degradation, toluene and xylene degradation, and caprolactam degradation.
Structural studies.
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code .


OPA anhydrase

OPA anhydrase may refer to:


C-5 sterol desaturase

C-5 sterol desaturase (also known as sterol C-5 desaturase and C5SD) is an enzyme that is highly conserved among eukaryotes and catalyzes the dehydrogenation of a C-5(6) bond in a sterol intermediate compound as a step in the biosynthesis of major sterols. The precise structure of the enzyme’s substrate varies by species. For example, the human C-5 sterol desaturase (also known as lathosterol oxidase) oxidizes lathosterol, while its ortholog ERG3 in the yeast "Saccharomyces cerevisiae" oxidizes episterol.
Mechanism.
C-5 sterol desaturase couples sterol oxidation to the oxidation of NAD(P)H and the reduction of molecular oxygen. Either NADH or NADPH can be used; in the model plant species "Arabidopsis thaliana" C-5 sterol desaturase catalyzes the reaction twice as fast with NADH while in "S. cerevisiae" the enzyme has little preference. The precise details of the reaction have been thought to vary between mammals and yeast. However, the enzymes do share a conserved cluster of histidine residues, which when mutated (in "A. thaliana") dramatically reduce or eliminate enzyme activity, suggesting the involvement of a coordinated iron cation in the mechanism. Mutagenesis studies suggest that in "A. thaliana" threonine 114 (which is a serine in humans, mice, and yeast) may help to stabilize the enzyme-substrate complex. Rahier has proposed a reaction mechanism in which an iron-coordinated oxygen abstracts a hydrogen from the substrate leading to a radical intermediate.
Biological role.
C-5 sterol desaturase catalyzes an intermediate step in the synthesis of major sterols. The particular biosynthetic pathway varies across eukaryotes. In animals C5SD catalyzes the dehydration of lathosterol to 7-dehydrocholesterol, a step in the synthesis of cholesterol. Cholesterol serves multiple roles in the cell including modulating membrane fluidity serving as a precursor to steroid hormones. In fungi C5SD catalyzes the dehydration of episterol as a step in the synthesis of ergosterol, a sterol that regulates cell membrane fluidity and permeability. In plants such as "Arabidopsis thaliana", C-5 sterol desaturase catalyzes the dehydrogenation of episterol and avenasterol in a pathway thought to lead to a variety of membrane components as well as a class of hormones called brassinosteroids.
Subcellular localization.
Based on its amino acid profile C-5 sterol desaturase appears to have four to five membrane-spanning regions, suggesting that it is a transmembrane protein. C5SD activity has been demonstrated in microsomes from rat tissue, implying that rat enzyme localizes to the endoplasmic reticulum Fluorescence microscopy experiments have shown that in the ciliate "Tetrahymena thermophila" C5SD localizes to the endoplasmic reticulum and that in "S. cerevisiae" C5SD localizes to both the endoplasmic reticulum and vesicles. In "Arabidopsis thaliana" C5SD is located in both the endoplasmic reticulum and lipid particles.
Clinical Relevance.
Antifungal Resistance.
The common class of antifungal drugs known as azoles disrupts the fungal sterol biosynthesis pathway, upstream of C-5 sterol desaturase leading to the accumulation of nontoxic 14α-methylated sterols. C5SD then converts these intermediates into a toxic product. Consequently, in both the pathogenic fungus "Candida albicans" and model organism "S. cerevisiae" mutations in the gene encoding C-5 sterol desaturase (ERG3) allow the cell to avoid synthesizing the toxic sterol products and have been shown to confer azole resistance. In at least the case of fluconazole, antifungal resistance due to C5SD inactivation is dependent on the activity of the chaperone protein Hsp90 and the phosphatase calcineurin. However, the clinical relevance of this azole resistance mechanism is controversial because while the deletion of ERG3 alone confers fluconazole resistance to "C. albicans in vitro", it is insufficient to confer fluconazole resistance in a live mouse model.
Lathosterolosis.
In at least one patient, a deficiency in C-5 sterol desaturase activity (termed lathosterolosis) was associated with multiple malformations, metal retardation, and liver disease. This patient was also found to have low levels of blood cholesterol and high levels of lathosterol in cell membranes when compared to those of healthy control subjects. These symptoms resemble those of other defects in cholesterol synthesis such as Smith–Lemli–Opitz syndrome.
Potential applications.
Scientists have found that tomato plants engineered with the C-5 sterol desaturase from the mushroom "Flammulina velutipes" show improved drought tolerance and fungal pathogen resistance as well as increased iron and polyunsaturated fat content. The authors of the study suggest that the fungal enzyme may be a useful tool for plant biotechnology as improving multiple aspects of a crop is typically time- and labor-intensive.


Mercury transporter

The mercury transporter superfamily (TC# 1.A.72) is a family of transmembrane bacterial transporters of mercury ions. The common origin of all Mer superfamily members has been established. The common elements between family members are included in TMSs 1-2. A representative list of the subfamilies and proteins that belong to those subfamilies is available in the Transporter Classification Database.
Transport Reaction.
The transport reaction catalyzed by Mer Superfamily members is:
Hg2+ or methyl-Hg2+ (out) → Hg2+ or methyl-Hg2+ (in)
MerF.
The MerF protein encoded on plasmid pMER327/419 is an 81 residue polypeptide with two putative TMSs. It catalyzes uptake of Hg2+ in preparation for reduction by mercuric reductase. The MerF gene is found on mercury resistant plasmids from many gram-negative bacteria, but the sequence of the protein from these plasmids is the same. Limited sequence similarity is shown with the first two TMSs of MerT (TC# 1.A.72.3) and MerC (TC# 1.A.72.4). MerF has two vicinal pairs of cysteine residues which are involved in the transport of Hg(II) across the membrane and are exposed to the cytoplasm. Some members of the MerF family have been designated MerH.
MerTP.
The MerTP permeases catalyze uptake into bacterial cells of Hg2+ in preparation for its reduction by the MerA mercuric reductase. The Hgo produced by MerA is volatile and passively diffuses out of the cell. The "merT" and "merP" genes are found on mercury resistance plasmids and transposons of gram-negative and gram-positive bacteria but are also chromosomally encoded in some bacteria. MerT consists of about 130 amino acids and has 3 transmembrane helical segments. Operon analyses have been reported.
MerP.
MerP is a periplasmic Hg2+-binding receptor of about 70-80 amino acyl residues, synthesized with a cleavable N-terminal leader. It is homologous to the N-terminal heavy metal binding domains of the copper-and cadmium-transporting P-type ATPases. The 3-D structure of MerP from "Ralstonia metallidurans" has been solved to 2 Å resolution (). It is 91 amino acyl residues (aas) long with its leader sequence, is monomeric, and binds a single Hg2+ ion. Hg2+ is bound to a sequence GMTCXXC found in metallochaperones as well as metal-transporting ATPases. The fold is βαββαβ, called the "ferridoxin-like fold".
MerT.
MerT homologues have been identified in which the 3 TMS MerT is fused to a MerP "heavy metal associated" (HMA) domain, possibly via a linker region that includes a fourth TMS (see 1.A.72.3.3). HMA domains of ~30 aas are found in MerP, copper chaperone proteins, mercuric reductase, and at the N-termini of both copper and heavy metal P-type ATPases, sometimes in multiple copies.
MerC.
The MerC protein encoded on the IncJ plasmid pMERPH of the "Shewanella putrefaciens" mercuric resistance operon is 137 amino acids in length and possesses four putative transmembrane α-helical spanners (TMSs). It has been shown to bind and take up Hg2+ ions. "merC" genes are encoded on several plasmids of gram-negative bacteria and may also be chromosomally encoded. MerC proteins are homologous to other bacterial Hg2+ bacterial transporters.
MerE.
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Carbonyl reductase II


Bacteriocin IId

Bacteriocin AS-48 is a cyclic peptide antibiotic produced by the eubacteria "Enterococcus faecalis" (Streptococcus faecalis) that shows a broad antimicrobial spectrum against both Gram-positive and Gram-negative bacteria. Bacteriocin AS-48 is encoded by the pheromone-responsive plasmid pMB2, and acts on the plasma membrane in which it opens pores leading to ion leakage and cell death. The globular structure of bacteriocin AS-48 is composed of five alpha helices enclosing a hydrophobic core. The mammalian NK-lysin effector protein of T and natural killer cells has a similar structure, though it lacks sequence homology with bacteriocins AS-48.
Bacteriocin uses components of the mannose phosphotransferase system (man-PTS) of susceptible cells as target/receptor. The immunity protein LciA forms a strong complex with the receptor proteins and the bacteriocin, thereby preventing cells from being killed. The complex between LciA and the man-PTS components (IIAB, IIC, and IID) appears to involve an on–off type mechanism that allows complex formation only in the presence of bacteriocin; otherwise no complexes were observed between LciA and the receptor proteins.


Transport protein

A transport protein (variously referred to as a transmembrane pump, transporter, escort protein, acid transport protein, cation transport protein, or anion transport protein) is a protein that serves the function of moving other materials within an organism. Transport proteins are vital to the growth and life of all living things. There are several different kinds of transport proteins.
Carrier proteins are proteins involved in the movement of ions, small molecules, or macromolecules, such as another protein, across a biological membrane. Carrier proteins are integral membrane proteins; that is, they exist within and span the membrane across which they transport substances. The proteins may assist in the movement of substances by facilitated diffusion (i.e., passive transport) or active transport. These mechanisms of movement are known as carrier-mediated transport. Each carrier protein is designed to recognize only one substance or one group of very similar substances. Research has correlated defects in specific carrier proteins with specific diseases. A membrane transport protein (or simply "transporter") is a membrane protein that acts as such a carrier.
A vesicular transport protein is a transmembrane or membrane associated protein. It regulates or facilitates the movement by vesicles of the contents of the cell.


Gamma-aminobutyrate transaminase

Gamma-aminobutyrate transaminase may refer to:


Demethylspheroidene O-methyltransferase

Demethylspheroidene O-methyltransferase (, "1-hydroxycarotenoid O-methylase", "1-hydroxycarotenoid methylase", "1-HO-carotenoid methylase", "CrtF") is an enzyme with systematic name "S-adenosyl-L-methionine:demethylspheroidene O-methyltransferase". This enzyme catalyses the following chemical reaction
In "Rhodopseudomonas capsulata" and "Rubrivivax gelatinosus" the enzyme is involved in biosynthesis of spheroidene.