source stringlengths 32 209 | text stringlengths 18 1.5k |
|---|---|
https://en.wikipedia.org/wiki/MAPKAPK2 | MAP kinase-activated protein kinase 2 is an enzyme that in humans is encoded by the MAPKAPK2 gene.
Function
This gene encodes a member of the Ser/Thr protein kinase family. This kinase is regulated through direct phosphorylation by p38 MAP kinase. In conjunction with p38 MAP kinase, this kinase is known to be involved in many cellular processes including stress and inflammatory responses, nuclear export, gene expression regulation and cell proliferation. Heat shock protein HSP27 was shown to be its major direct substrate in vivo. Two transcript variants encoding two different isoforms have been found for this gene.
Vascular barrier
MK2 pathway has been demonstrated to have a key role in maintaining and repairing the integrity of endothelial barrier in the lung via actin and vimentin remodeling. Activation of MK2 via its phosphorylation by p38 has been shown to restore the vascular barrier and repair vascular leak, associated with over 60 medical conditions, including Acute Respiratory Distress Syndrome (ARDS), a major cause of death around the world.
SASP initiation
MAPKAPK2 mediates the initiation of the senescence-associated secretory phenotype (SASP) by mTOR (mechanistic target of rapamycin). Interleukin 1 alpha (IL1A) is found on the surface of senescent cells, where it contributes to the production of SASP factors due to a positive feedback loop with NF-κB. Translation of mRNA for IL1A is highly dependent upon mTOR activity. mTOR activity increases levels of I |
https://en.wikipedia.org/wiki/GRB2-associated-binding%20protein%201 | GRB2-associated-binding protein 1 is a protein that in humans is encoded by the GAB1 gene.
Function
The protein encoded by this gene is a member of the IRS1-like multisubstrate docking protein family. The encoded protein is an important mediator of branching tubulogenesis and plays a central role in cellular growth response, transformation and apoptosis. Two transcript variants encoding different isoforms have been found for this gene.
Interactions
GAB1 has been shown to interact with:
CRKL,
Grb2,
MAP3K3,
PIK3R1,
PLCG1 and
PTPN11.
References
Further reading |
https://en.wikipedia.org/wiki/GATA4 | Transcription factor GATA-4 is a protein that in humans is encoded by the GATA4 gene.
Function
This gene encodes a member of the GATA family of zinc finger transcription factors. Members of this family recognize the GATA motif which is present in the promoters of many genes. This protein is thought to regulate genes involved in embryogenesis and in myocardial differentiation and function. Mutations in this gene have been associated with cardiac septal defects as well as reproductive defects.
GATA4 is a critical transcription factor for proper mammalian cardiac development and essential for survival of the embryo. GATA4 works in combination with other essential cardiac transcription factors as well, such as Nkx2-5 and Tbx5. GATA4 is expressed in both embryo and adult cardiomyocytes where it functions as a transcriptional regulator for many cardiac genes, and also regulates hypertrophic growth of the heart. GATA4 promotes cardiac morphogenesis, cardiomyocytes survival, and maintains cardiac function in the adult heart.
Mutations or defects in the GATA4 gene can lead to a variety of cardiac problems including congenital heart disease, abnormal ventral folding, and defects in the cardiac septum separating the atria and ventricles, and hypoplasia of the ventricular myocardium. As seen from the abnormalities from deletion of GATA4, it is essential for cardiac formation and the survival of the embryo during fetal development.
GATA4 is not only important for cardiac development, |
https://en.wikipedia.org/wiki/GPX1 | Glutathione peroxidase 1, also known as GPx1, is an enzyme that in humans is encoded by the GPX1 gene on chromosome 3. This gene encodes a member of the glutathione peroxidase family. Glutathione peroxidase functions in the detoxification of hydrogen peroxide, and is one of the most important antioxidant enzymes in humans.
Structure
This gene encodes a member of the glutathione peroxidase family, consisting of eight known glutathione peroxidases (GPx1-8) in humans. Mammalian Gpx1 (this gene), Gpx2, Gpx3, and Gpx4 have been shown to be selenium-containing enzymes, whereas Gpx6 is a selenoprotein in humans with cysteine-containing homologues in rodents. In selenoproteins, the 21st amino acid selenocysteine is inserted in the nascent polypeptide chain during the process of translational recoding of the UGA stop codon. In addition to the UGA-codon, a cis-acting element in the mRNA, called SECIS, binds SBP2 to recruit other proteins, such as eukaryotic elongation factor selenocysteine-tRNA specific, to form the complex responsible for the recoding process.
The protein encoded by this gene forms a homotetramer structure. As with other glutathione peroxidases, GPx1 has a conserved catalytic tetrad composed of Sec or Cys, Gln, Trp, and Asn, where the Sec is surrounded by four arginines (R 57, 103, 184, 185; bovine numbering) and a lysine of an adjacent subunit (K 91'). These 5 residues bind glutathione (GSH) and are only present in GPx1.
Two alternatively spliced transcript varia |
https://en.wikipedia.org/wiki/ID2 | DNA-binding protein inhibitor ID-2 is a protein that in humans is encoded by the ID2 gene.
Function
The protein encoded by this gene belongs to the inhibitor of DNA binding (ID) family, members of which are transcriptional regulators that contain a helix-loop-helix (HLH) domain but not a basic domain. Members of the ID family inhibit the functions of basic helix-loop-helix transcription factors in a dominant-negative manner by suppressing their heterodimerization partners through the HLH domains. This protein may play a role in negatively regulating cell differentiation. A pseudogene has been identified for this gene.
A research published by "Nature" in 01/2016, authored by Italian researchers Antonio Iavarone and Anna Lasorella, from Columbia University, states that ID2 protein has a relevant role in the development and resistance to therapies of glioblastoma, the most aggressive of brain cancers.
Interactions
ID2 has been shown to interact with MyoD and NEDD9.
See also
Inhibitor of DNA-binding protein
References
Further reading
External links
Transcription factors |
https://en.wikipedia.org/wiki/Tadao%20Kasami | was a noted Japanese information theorist who made significant contributions to error correcting codes. He was the earliest to publish the key ideas for the CYK algorithm, separately discovered by Daniel Younger (1967) and John Cocke (1970).
Kasami was born in Kobe, Japan, and studied electrical engineering at Osaka University, where he received his B.E. degree in 1958, M.E. in 1960, and Ph.D. in 1963. He then joined the faculty, teaching until 1994, and was dean 1990–1992. He was subsequently professor in the Graduate School of Information Science at the Nara Institute of Science and Technology 1992–1998, and professor of information science at Hiroshima City University 1998–2004.
Kasami was an IEEE Fellow, and received the 1987 Achievement Award from the Institute of Electronics, Information, and Communications Engineers of Japan and the 1999 IEEE Claude E. Shannon Award.
See also
CYK algorithm
Kasami code
References
1930 births
2007 deaths
Fellow Members of the IEEE
Japanese computer scientists
Japanese information theorists
Osaka University alumni
People from Kobe
Academic staff of Nara Institute of Science and Technology |
https://en.wikipedia.org/wiki/Sterol%20regulatory%20element-binding%20protein%202 | Sterol regulatory element-binding protein 2 (SREBP-2) also known as sterol regulatory element binding transcription factor 2 (SREBF2) is a protein that in humans is encoded by the SREBF2 gene.
Function
This gene encodes a ubiquitously expressed transcription factor that controls cholesterol homeostasis by stimulating transcription of sterol-regulated genes. The encoded protein contains a basic helix-loop-helix leucine zipper (bHLH-Zip) domain.
Various single nucleotide polymorphisms (SNPs) of the SREBF2 have been identified and some of them are found to be associated with higher risk of knee osteoarthritis.
Interactions
SREBF2 has been shown to interact with INSIG1 and CREB-binding protein.
See also
Sterol regulatory element-binding protein
References
Further reading
External links
Transcription factors |
https://en.wikipedia.org/wiki/CAPN10 | Calpain-10 is a protein that in humans is encoded by the CAPN10 gene.
Calpains are ubiquitous, well-conserved family of calcium-dependent, cysteine proteases. The typical calpain proteins are heterodimers consisting of an invariant small subunit and variable large subunits. The large catalytic subunit has four domains: domain I, the N-terminal regulatory domain that is processed upon calpain activation; domain II, the protease domain; domain III, a linker domain of unknown function; and domain IV, the calmodulin-like calcium-binding domain. The heterodimer interface is predominantly found between domain IV and the small subunit, which is also a calmodulin-like calcium-binding domain. This gene encodes a large subunit. It is an atypical calpain in that it lacks the calmodulin-like calcium-binding domain and instead has a divergent C-terminal domain. It therefore cannot heterodimerize with the small subunit. It is similar in organization to calpains 5 and 6. This gene is associated with type 2 or non-insulin-dependent diabetes mellitus (NIDDM) and located within the NIDDM1 region. Multiple alternative transcript variants encoding different isoforms have been described for this gene.
References
Further reading
External links
The MEROPS online database for peptidases and their inhibitors: C02.018 |
https://en.wikipedia.org/wiki/CALM3 | Calmodulin 3 is a protein that in humans is encoded by the CALM3 gene.
CALM-3 is best known for contracting the heart muscles, and depending on whether this activity is consistent or not, other diseases could emerge as a downside. It is able to maintain or regulate in different types of biological systems, such as cytokinesis or the centrosome cycle.
Calmodulin-3 is able to perform different types of activities and roles, such as binding of calcium and significant activity in regulating an enzyme. The gene CALM-3 is likely to contribute to illnesses that may lead to death, such as Ventricular tachycardia which is associated with the ventricular tachycardia functioning in 2 directions and long QT syndrome which is associated with the QT interval in the electrocardiogram that is significantly longer than normal. In its structure, there are 2 helices that are observed in each of its helix-loop-helix and are then shaped into a perpendicular pattern due to the surface of the protein changing over time. Through transcription, the gene CALM-3 is able to perform the activity of a regulator for its own gene expression and has 6 exons, indicating that each exon has a specific function that takes place in the initiation stage. If there are potentially variants that could impact the calmodulin protein, it could affect the concentration of the Ca mediators that are a part of the protein.
Context
The CALM-3 gene, along with the protein of calmodulin, has been included in different type |
https://en.wikipedia.org/wiki/EZH2 | Enhancer of zeste homolog 2 (EZH2) is a histone-lysine N-methyltransferase enzyme (EC 2.1.1.43) encoded by gene, that participates in histone methylation and, ultimately, transcriptional repression. EZH2 catalyzes the addition of methyl groups to histone H3 at lysine 27, by using the cofactor S-adenosyl-L-methionine. Methylation activity of EZH2 facilitates heterochromatin formation thereby silences gene function. Remodeling of chromosomal heterochromatin by EZH2 is also required during cell mitosis.
EZH2 is the functional enzymatic component of the Polycomb Repressive Complex 2 (PRC2), which is responsible for healthy embryonic development through the epigenetic maintenance of genes responsible for regulating development and differentiation. EZH2 is responsible for the methylation activity of PRC2, and the complex also contains proteins required for optimal function (EED, SUZ12, JARID2, AEBP2, RbAp46/48, and PCL).
Mutation or over-expression of EZH2 has been linked to many forms of cancer. EZH2 inhibits genes responsible for suppressing tumor development, and blocking EZH2 activity may slow tumor growth. EZH2 has been targeted for inhibition because it is upregulated in multiple cancers including, but not limited to, breast, prostate, melanoma, and bladder cancer. Mutations in the EZH2 gene are also associated with Weaver syndrome, a rare congenital disorder, and EZH2 is involved in causing neurodegenerative symptoms in the nervous system disorder, ataxia telangiectasia.
|
https://en.wikipedia.org/wiki/IL12A | Interleukin-12 subunit alpha (IL-12 p35) is a protein that in humans is encoded by the IL12A gene.
Function
This gene encodes a subunit of the cytokine Interleukin 12 (IL-12) that acts on T and natural killer cells, and has a broad array of biological activities. The cytokine is a disulfide-linked heterodimer composed of the 35-kD subunit encoded by this gene, and a 40-kD subunit that is a member of the cytokine receptor family. This cytokine is required for the T-cell-dependent induction of interferon gamma (IFN-γ), and is important for the differentiation of both Th1 and Th2 cells. The responses of lymphocytes to this cytokine are mediated by the activator of transcription protein STAT4. Nitric oxide synthase 2A (NOS2A/NOS2) is found to be required for the signaling process of this cytokine in innate immunity.
References
Further reading |
https://en.wikipedia.org/wiki/Liver%20X%20receptor%20alpha | Liver X receptor alpha (LXR-alpha) is a nuclear receptor protein that in humans is encoded by the NR1H3 gene (nuclear receptor subfamily 1, group H, member 3).
Expression
miRNA hsa-miR-613 autoregulates the human LXRα gene by targeting the endogenous LXRα through its specific miRNA response element (613MRE) within the LXRα 3′-untranslated region. LXRα autoregulates its own suppression via induction of SREBP1c which upregulates miRNA has-miR-613.
Function
The liver X receptors, LXRα (this protein) and LXRβ, form a subfamily of the nuclear receptor superfamily and are key regulators of macrophage function, controlling transcriptional programs involved in lipid homeostasis and inflammation. Additionally, they play an important role in the local activation of thyroid hormones via deiodinases. The inducible LXRα is highly expressed in liver, adrenal gland, intestine, adipose tissue, macrophages, lung, and kidney, whereas LXRβ is ubiquitously expressed. Ligand-activated LXRs form obligate heterodimers with retinoid X receptors (RXRs) and regulate expression of target genes containing LXR response elements. Restoration of LXR-alpha expression/function within a psoriatic lesion may help to switch the transition from psoriatic to symptomless skin.
Interactions
Liver X receptor alpha has been shown to interact with EDF1 and Small heterodimer partner. LXRα activates the transcription factor SREBP-1c, resulting in lipogenesis.
Link to multiple sclerosis
In 2016, a study found |
https://en.wikipedia.org/wiki/ADH1B | Alcohol dehydrogenase 1B is an enzyme that in humans is encoded by the ADH1B gene.
The protein encoded by this gene is a member of the alcohol dehydrogenase family. Members of this enzyme family metabolize a wide variety of substrates, including ethanol (beverage alcohol), retinol, other aliphatic alcohols, hydroxysteroids, and lipid peroxidation products. The encoded protein, known as ADH1B or beta-ADH, can form homodimers and heterodimers with ADH1A and ADH1C subunits, exhibits high activity for ethanol oxidation and plays a major role in ethanol catabolism (oxidizing ethanol into acetaldehyde). The acetaldehyde is further metabolized to acetate by aldehyde dehydrogenase genes. Three genes encoding the closely related alpha, beta and gamma subunits are tandemly organized in a genomic segment as a gene cluster.
The human gene is located on chromosome 4 in 4q22.
Previously ADH1B was called ADH2. There are more genes in the family of alcohol dehydrogenase. These genes are now referred to as ADH1A, ADH1C, and ADH4, ADH5, ADH6 and ADH7.
Variants
A single nucleotide polymorphism (SNP) in ADH1B is rs1229984, that changes arginine to histidine at residue 47 of the mature protein; standard nomenclature now includes the initiating methionine, so the position is officially 48. The 'typical' variant of this has been referred to as ADH2(1) or ADH2*1 while the 'atypical' has been referred to as, e.g., ADH2(2), ADH2*2, ADH1B*48His. This SNP is associated with the risk for alcohol dep |
https://en.wikipedia.org/wiki/H3F3A | Histone H3.3 is a protein that in humans is encoded by the H3F3A and H3F3B genes. It plays an essential role in maintaining genome integrity during mammalian development.
Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene contains introns and its mRNA is polyadenylated, unlike most histone genes. The protein encoded is a replication-independent member of the histone H3 family.
Mutation of H3F3A are also linked to certain cancers. p.Lys27Met were discovered in Diffuse Intrinsic Pontine Glioma (DIPG), where they are present 65-75% of tumors and confer a worse prognosis. p.Lys27Met alterations in HIST1H3B and HIST1H3C, which code for histone H3.1 have also been reported in ~10% of DIPG. H3F3A is also mutated in a smaller portion of pediatric and young adult high grade astrocytomas but more frequently as p.Gly34Arg/Val. Mutations in H3F3A and H3F3B are also found in chondroblastoma and giant cell tumor of bone.
References
Further reading |
https://en.wikipedia.org/wiki/MCM7 | DNA replication licensing factor MCM7 is a protein that in humans is encoded by the MCM7 gene.
Function
The protein encoded by this gene is one of the highly conserved mini-chromosome maintenance proteins (MCM) that are essential for the initiation of eukaryotic genome replication. The hexameric protein complex formed by the MCM proteins is a key component of the pre-replication complex (pre-RC) and may be involved in the formation of replication forks and in the recruitment of other DNA replication related proteins. The MCM complex consisting of this protein and MCM2, 4 and 6 proteins possesses DNA helicase activity, and may act as a DNA unwinding enzyme. Cyclin D1-dependent kinase, CDK4, is found to associate with this protein, and may regulate the binding of this protein with the tumor suppressor protein RB1/RB. Alternatively spliced transcript variants encoding distinct isoforms have been reported.
Interactions
MCM7 has been shown to interact with:
CDC45-related protein
CDC6,
Cell division cycle 7-related protein kinase,
DBF4,
MCM2,
MCM3,
MCM4,
MCM5,
MCM6,
MNAT1,
ORC1L,
ORC2L,
ORC3L,
ORC5L,
Replication protein A1,
Retinoblastoma protein, and
UBE3A.
See also
Mini Chromosome Maintenance
References
Further reading |
https://en.wikipedia.org/wiki/NEDD4 | E3 ubiquitin-protein ligase NEDD4, also known as neural precursor cell expressed developmentally down-regulated protein 4 (whence "NEDD4") is an enzyme that is, in humans, encoded by the NEDD4 gene.
NEDD4 is an E3 ubiquitin ligase enzyme, that targets proteins for ubiquitination. NEDD4 is, in eukaryotes, a highly conserved gene, and the founding member of the NEDD4 family of E3 HECT ubiquitin ligases, which in humans consists of 9 members:
NEDD4 (the core topic of this article)
NEDD4-2 (or NEDD4L)
ITCH
SMURF1
SMURF2
WWP1
WWP2
NEDL1 (HECW1)
NEDDL2 (HECW2)].
NEDD4 regulates a large number of membrane proteins, such as ion channels and membrane receptors, via ubiquitination and endocytosis; its eponymous protein is widely expressed, and a large number of proteins have been predicted or demonstrated to bind in vitro.
In vivo, it is involved in the regulation of a diverse range of processes,
including
insulin-like growth factor signalling,
neuronal architecture, and
viral budding.
NEDD4 also is an essential protein in animals, both for development and for survival.
Structure
The NEDD4 protein has a modular structure that is shared among the NEDD4 family, consisting of an amino-terminal C2 calcium-dependent phospholipid binding domain, 3-4 WW protein-protein interaction domains, and a carboxyl-terminal catalytic HECT ubiquitin ligase domain. The C2 domain targets proteins to the phospholipid membrane, and can also be involved in targeting substrates. The |
https://en.wikipedia.org/wiki/Phospholipid%20transfer%20protein | Phospholipid transfer protein is a protein that in humans is encoded by the PLTP gene.
Function
The protein encoded by this gene is one of at least two lipid transfer proteins found in human plasma. The encoded protein transfers phospholipids from triglyceride-rich lipoproteins to high density lipoprotein (HDL). In addition to regulating the size of HDL particles, this protein may be involved in cholesterol metabolism. At least two transcript variants encoding different isoforms have been found for this gene.
Interactions
PLTP has been shown to interact with Apolipoprotein A1 and APOA2.
Interactive pathway map
References
Further reading |
https://en.wikipedia.org/wiki/RAB5A | Ras-related protein Rab-5A is a protein that in humans is encoded by the RAB5A gene.
Function
RAB5A localizes to early endosomes where it is involved in the recruitment of RAB7A and the maturation of these compartments to late endosomes. It drives the maturation of endosomes by transporting vacuolar (H+)-ATPases (V-ATPases) from trans-Golgi network to endocytic vesicles.
Interactions
RAB5A has been shown to interact with:
CHML,
RABEP1,
SDCBP, and
ZFYVE20
References
Further reading |
https://en.wikipedia.org/wiki/Glutathione%20S-transferase%20A1 | Glutathione S-transferase A1 is an enzyme that in humans is encoded by the GSTA1 gene.
Cytosolic and membrane-bound forms of glutathione S-transferase are encoded by two distinct supergene families. These enzymes function in the detoxification of electrophilic compounds, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress, by conjugation with glutathione. The genes encoding these enzymes are known to be highly polymorphic. These genetic variations can change an individual's susceptibility to carcinogens and toxins as well as affect the toxicity and efficacy of some drugs. At present, eight distinct classes of the soluble cytoplasmic mammalian glutathione S-transferases have been identified: alpha, kappa, mu, omega, pi, sigma, theta and zeta. This gene encodes a glutathione S-transferase belonging to the alpha class. The alpha class genes, located in a cluster mapped to chromosome 6, are the most abundantly expressed glutathione S-transferases in liver (hepatocytes) and kidney (proximal tubules). In addition to metabolizing bilirubin and certain anti-cancer drugs in the liver, the alpha class of these enzymes exhibit glutathione peroxidase activity, thereby protecting the cells from reactive oxygen species and the products of peroxidation.
Release of GST-A1 as an indication of cellular necrosis
Increases in serum and urinary GST-A1 have been found in association with hepatocyte and renal proximal tubular necrosis respectively, and |
https://en.wikipedia.org/wiki/LRP2 | Low density lipoprotein receptor-related protein 2 also known as LRP-2 or megalin is a protein which in humans is encoded by the LRP2 gene.
Function
LRP2 was identified as the antigen of rat experimental membranous nephropathy (Heyman nephritis) and originally named gp330 and subsequently megalin and later LRP2. LRP2/megalin is a multiligand binding receptor found in the plasma membrane of many absorptive epithelial cells. LRP2 is an approximately 600kDa (4665 amino acids) transmembrane glycoprotein with structural similarities to the low density lipoprotein receptor (LDLR). LRP2 has a NPXY motif that is the binding site for Dab2 to initiate clathrin-mediated endocytosis. LRP2 forms a homodimer that changes conformation in response to pH. At pH 7.5 (extracellular pH), LRP2 is considered active, with the leucine loops in an open conformation to allow ligands to bind. At acidic endosomal pHs, the leucine loops collapse to prevent ligands binding.
LRP2 is expressed in epithelial cells of the thyroid (thyrocytes), where it can serve as a receptor for the protein thyroglobulin (Tg). LRP2 is also expressed on the apical surface of epithelial cells in the proximal tubule of the kidney. It is highly expressed in the first segment (S1) of the proximal tubule, with decreasing expression in the second (S2) and third segment (S3) of the proximal tubule. LRP2 is also expressed in podocytes, and antigenic response to LRP2 in podocytes is the primary cause of Heymann nephritis in rats. |
https://en.wikipedia.org/wiki/HSP90B1 | Heat shock protein 90kDa beta member 1 (HSP90B1), known also as endoplasmin, gp96, grp94, or ERp99, is a chaperone protein that in humans is encoded by the HSP90B1 gene.
HSP90B1 is an HSP90 paralogue that is found in the endoplasmic reticulum. It plays critical roles in folding proteins in the secretory pathway such as Toll-like receptors and integrins. It has been implicated as an essential immune chaperone to regulate both innate and adaptive immunity. Tumor-derived HSP90B1 (vitespen) has entered clinical trials for cancer immunotherapy.
grp94 has been shown to be a target for treatment of a plethora of diseases such as glaucoma, multiple myeloma, and metastatic cancer. grp94 includes 5 distinct amino acids in its primary sequence which creates 2 unique sub-pockets, S1 and S2. These sub-pockets have been utilized in current research in order to inhibit the chaperone since its client proteins seem to be up-regulated in cancer cells.
References
Further reading
Molecular chaperones
Endoplasmic reticulum resident proteins |
https://en.wikipedia.org/wiki/U2AF2 | Splicing factor U2AF 65 kDa subunit is a protein that in humans is encoded by the U2AF2 gene.
Function
In eukaryotes, the introns in the transcribed pre-mRNA first have to be removed by spliceosome in order to form a mature mRNA. A spliceosome is assembled from small nuclear ribonucleoproteins(snRNP) and small nuclear RNAs(snRNA). And the splicing factor can be divided into snRNP and non snRNP proteins.U2 auxiliary factor (U2AF), composed of a large and a small subunit, is a non-snRNP protein required for the binding of U2 snRNP to the pre-mRNA branch site. This gene encodes the U2AF large subunit, which contains a sequence-specific RNA-binding region with 3 RNA recognition motifs and an Arg/Ser-rich domain necessary for splicing. The large subunit binds to the polypyrimidine tract of introns early during spliceosome assembly. Multiple alternatively spliced transcript variants have been detected for this gene, but the full-length natures of only two have been determined to date.
In humans and other tetrapods, it has been shown that without U2AF2, the splicing process is inhibited. However, in zebrafish and other teleosts the RNA splicing process can still occur on certain genes in the absence of U2AF2. This may be because 10% of genes have alternating TG and AC base pairs at the 3' splice site (3'ss) and 5' splice site (5'ss) respectively on each intron, which alters the secondary structure of the RNA and influences splicing.
The splicing factor U2AF65 can specifically r |
https://en.wikipedia.org/wiki/Importin%20subunit%20alpha-7 | Importin subunit alpha-7 is a protein that in humans is encoded by the KPNA6 gene.
Nucleocytoplasmic transport, a signal- and energy-dependent process, takes place through nuclear pore complexes embedded in the nuclear envelope. The import of proteins containing a nuclear localization signal (NLS) requires the NLS import receptor, a heterodimer of importin alpha and beta subunits also known as karyopherins. Importin alpha binds the NLS-containing cargo in the cytoplasm and importin beta docks the complex at the cytoplasmic side of the nuclear pore complex. In the presence of nucleoside triphosphates and the small GTP binding protein Ran, the complex moves into the nuclear pore complex and the importin subunits dissociate. Importin alpha enters the nucleoplasm with its passenger protein and importin beta remains at the pore. The protein encoded by this gene is a member of the importin alpha family.
References
Further reading
External links
Armadillo-repeat-containing proteins |
https://en.wikipedia.org/wiki/BMI1 | Polycomb complex protein BMI-1 also known as polycomb group RING finger protein 4 (PCGF4) or RING finger protein 51 (RNF51) is a protein that in humans is encoded by the BMI1 gene (B cell-specific Moloney murine leukemia virus integration site 1). BMI1 is a polycomb ring finger oncogene.
Function
BMI1 (B lymphoma Mo-MLV insertion region 1 homolog) has been reported as an oncogene by regulating p16 and p19, which are cell cycle inhibitor genes. Bmi1 knockout in mice results in defects in hematopoiesis, skeletal patterning, neurological functions, and development of the cerebellum. Recently it has been reported that BMI1 is rapidly recruited to sites of DNA damage, where it sustains for over 8h. Loss of BMI1 leads to radiation sensitive and impaired repair of DNA double-strand breaks by homologous recombination.
Bmi1 is necessary for efficient self-renewing cell divisions of adult hematopoietic stem cells as well as adult peripheral and central nervous system neural stem cells. However, it is less important for the generation of differentiated progeny. Given that phenotypic changes in Bmi1 knockout mice are numerous and that Bmi1 has very broad tissue distribution, it is possible that it regulates the self-renewal of other types of somatic stem cells.
Bmi1 is also thought to inhibit ageing in neurons through the suppression of p53.
The Bmi-1 protein interacts with several signaling pathways containing Wnt, Akt, Notch, Hedgehog and receptor tyrosine kinases (RTK). In Ewi |
https://en.wikipedia.org/wiki/EPS15 | Epidermal growth factor receptor substrate 15 is a protein that in humans is encoded by the EPS15 gene.
Function
This gene encodes a protein that is part of the EGFR pathway. The protein is present at clathrin-coated pits and is involved in receptor-mediated endocytosis of EGF. Notably, this gene is rearranged with the HRX/ALL/MLL gene in acute myelogeneous leukemias. Alternate transcriptional splice variants of this gene have been observed but have not been thoroughly characterized.
Model organisms
Model organisms have been used in the study of EPS15 function. A conditional knockout mouse line, called Eps15tm1a(KOMP)Wtsi was generated as part of the International Knockout Mouse Consortium program—a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists—at the Wellcome Trust Sanger Institute.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty six tests were carried out on mutant mice and one significant abnormality was observed: homozygous mutant animals had a decreased mean corpuscular hemoglobin concentration.
Interactions
EPS15 has been shown to interact with:
CRK
EPN1,
HGS,
HRB, and
REPS2.
References
Further reading
Genes mutated in mice
EH-domain-containing proteins |
https://en.wikipedia.org/wiki/Importin%20subunit%20alpha-3 | Importin subunit alpha-3, also known as karyopherin subunit alpha-4, is a protein that in humans is encoded by the KPNA4 gene.
Function
The nuclear import of karyophilic proteins is directed by short amino acid sequences termed nuclear localization signals (NLSs). Karyopherins, or importins, are cytoplasmic proteins that recognize NLSs and dock NLS-containing proteins to the nuclear pore complex. The protein encoded by this gene shares the sequence similarity with Xenopus importin-alpha and Saccharomyces cerevisiae Srp1. This protein is found to interact with the NLSs of DNA helicase Q1 and SV40 T antigen.
Interactions
KPNA4 has been shown to interact with RECQL and STAT3.
References
Further reading
Armadillo-repeat-containing proteins |
https://en.wikipedia.org/wiki/MAPK7 | Mitogen-activated protein kinase 7 also known as MAP kinase 7 is an enzyme that in humans is encoded by the MAPK7 gene.
Function
MAPK7 is a member of the MAP kinase family. MAP kinases act as an integration point for multiple biochemical signals, and are involved in a wide variety of cellular processes such as proliferation, differentiation, transcription regulation and development. This kinase is specifically activated by mitogen-activated protein kinase kinase 5 (MAP2K5/MEK5). It is involved in the downstream signaling processes of various receptor molecules including receptor tyrosine kinases, and G protein-coupled receptors. In response to extracellular signals, this kinase translocates to the cell nucleus, where it regulates gene expression by phosphorylating, and activating different transcription factors. Four alternatively spliced transcript variants of this gene encoding two distinct isoforms have been reported.
MAPK7 is also critical for cardiovascular development and is essential for endothelial cell function.
Interactions
MAPK7 has been shown to interact with:
C-Raf,
Gap junction protein, alpha 1
MAP2K5,
MEF2C,
MEF2D,
PTPRR,
SGK, and
YWHAB.
ERK5 (= MAPK7) Inhibitors
XMD8-92 was one of the first described ERK5 inhibitors and was used in several pharmacological studies as tool compound. However, XMD8-92 hits BRD4 as an off-target leading to false or inconclusive results. Consequently, ERK5 inhibitors with improved selectivity (void of the BR |
https://en.wikipedia.org/wiki/PSMA3 | Proteasome subunit alpha type-3 also known as macropain subunit C8 and proteasome component C8 is a protein that in humans is encoded by the PSMA3 gene. This protein is one of the 17 essential subunits (alpha subunits 1–7, constitutive beta subunits 1–7, and inducible subunits including beta1i, beta2i, beta5i) that contributes to the complete assembly of 20S proteasome complex.
Function
The eukaryotic proteasome recognized degradable proteins, including damaged proteins for protein quality control purpose or key regulatory protein components for dynamic biological processes. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. As a component of alpha ring, proteasome subunit alpha type-3 contributes to the formation of heptameric alpha rings and substrate entrance gate.
Structure
The human protein proteasome subunit alpha type-3 is 28.4 kDa in size and composed of 254 amino acids. The calculated theoretical pI of this protein is 5.08.
Complex assembly
The proteasome is a multicatalytic proteinase complex with a highly ordered 20S core structure. This barrel-shaped core structure is composed of 4 axially stacked rings of 28 non-identical subunits: the two end rings are each formed by 7 alpha subunits, and the two central rings are each formed by 7 beta subunits. Three beta subunits (beta1, beta2, and beta5) each contains a proteolytic active site and has distinct substrate preferences. Proteasomes are distri |
https://en.wikipedia.org/wiki/SIAH1 | E3 ubiquitin-protein ligase SIAH1 is an enzyme that in humans is encoded by the SIAH1 gene.
Function
This gene encodes for a polypeptide structure that is a member of the seven in absentia homolog (SIAH) family. The protein is an E3 ligase and is involved in ubiquitination and proteasome-mediated degradation of specific proteins. The activity of this ubiquitin ligase has been implicated in the development of certain forms of Parkinson's disease, the regulation of the cellular response to hypoxia and induction of apoptosis. Alternative splicing results in several additional transcript variants, some encoding different isoforms and others that have not been fully characterized.
Interactions
SIAH1 has been shown to interact with:
APC,
BAG1,
CACYBP,
KHDRBS3,
KIF22,
NUMB,
PEG10,
PEG3
POU2AF1,
RBBP8, and
TRIB3.
References
Further reading |
https://en.wikipedia.org/wiki/Telomeric%20repeat-binding%20factor%202 | Telomeric repeat-binding factor 2 is a protein that is present at telomeres throughout the cell cycle. It is also known as TERF2, TRF2, and TRBF2, and is encoded in humans by the TERF2 gene. It is a component of the shelterin nucleoprotein complex and a second negative regulator of telomere length, playing a key role in the protective activity of telomeres. It was first reported in 1997 in the lab of Titia de Lange, where a DNA sequence similar, but not identical, to TERF1 was discovered, with respect to the Myb-domain. De Lange isolated the new Myb-containing protein sequence and called it TERF2.
Structure and domains
TERF2 has a similar structure to that of TERF1. Both proteins carry a C-terminus Myb motif and large TERF1-related dimerization domains near their N-terminus. However, both proteins exist exclusively as homodimers and do not heterodimerize with each other, as proven by co-immunoprecipitation assay analysis. Also, TERF2 has a basic N-terminus, differing from TERF1’s acidic N-terminus, and was found to be much more conserved, suggesting that the two proteins have distinct functions.
There are 4 domain categories on the TERF2 protein that allow it to bind to both other proteins in the shelterin protein complex, and to specific types of DNA.
TERF homology domain
The TERF Homology Domain (TRFH; ) is an area that helps to promote homodimerization of TERF2 with itself. This results in the formation of a quaternary structure that is characteristic of this protein |
https://en.wikipedia.org/wiki/Photo-reactive%20amino%20acid%20analog | Photo-reactive amino acid analogs are artificial analogs of natural amino acids that can be used for crosslinking of protein complexes. Photo-reactive amino acid analogs may be incorporated into proteins and peptides in vivo or in vitro. Photo-reactive amino acid analogs in common use are photoreactive diazirine analogs to leucine and methionine, and para-benzoylphenylalanine. Upon exposure to ultraviolet light, they are activated and covalently bind to interacting proteins that are within a few angstroms of the photo-reactive amino acid analog.
L-Photo-leucine and L-photo-methionine are analogs of the naturally occurring L-leucine and L-methionine amino acids that are endogenously incorporated into the primary sequence of proteins during synthesis using the normal translation machinery. They are then ultraviolet light (UV)-activated to covalently crosslink proteins within protein–protein interaction domains in their native in-vivo environment. The method enables the determination and characterization of both stable and transient protein interactions in cells without the addition of chemical crosslinkers and associated solvents that can adversely affect the cell biology being studied in the experiment.
When used in combination with limiting media that is devoid of leucine and methionine, the photo-activatable derivatives are treated like naturally occurring amino acids by the cellular protein synthesis machinery. As a result, they can be substituted for leucine or methionin |
https://en.wikipedia.org/wiki/F%C3%A5hr%C3%A6us%E2%80%93Lindqvist%20effect | The Fåhraeus–Lindqvist effect describes how the viscosity of a fluid, in this case blood, changes with the diameter of the tube it travels through. In particular there is a 'decrease in viscosity as the tube's diameter decreases' (although only with a tube diameter of between 10 and 300 micrometers). This is because erythrocytes move over to the centre of the vessel, leaving only plasma near the wall of the vessel.
History
The effect was first documented by a German group in 1930. Shortly after, in 1931, it was reported independently by the Swedish scientists Robin Fåhræus and Torsten Lindqvist, after whom the effect is commonly named. Robert (Robin) Sanno Fåhræus was a Swedish pathologist and hematologist, born on October 15, 1888, in Stockholm. He died on September 18, 1968, in Uppsala, Sweden. Johan Torsten Lindqvist was a Swedish physician, who was born in 1906 and died in 2007. Fåhræus and Lindqvist published their article in the American Journal of Physiology in 1931 describing the effect. Their study represented an important advance in the understanding of hemodynamics which had widespread implications for the study of human physiology.
They forced blood through fine glass capillary tubes connecting two reservoirs. Capillary diameters were less than 250 μm, and experiments were conducted at sufficiently high shear rates (≥100 1/s) so that a similar flow in a large tube would be effectively Newtonian. After correcting for entrance effects, they presented their data |
https://en.wikipedia.org/wiki/ALOX12 | ALOX12 (), also known as arachidonate 12-lipoxygenase, 12-lipoxygenase, 12S-Lipoxygenase, 12-LOX, and 12S-LOX is a lipoxygenase-type enzyme that in humans is encoded by the ALOX12 gene which is located along with other lipoyxgenases on chromosome 17p13.3. ALOX12 is 75 kilodalton protein composed of 663 amino acids.
Nomenclature
Other systematic names for ALOX12 include 12S-Lipoxygenase, platelet-type 12-lipoxygenase, arachidonate:oxygen 12-oxidoreductase, Delta12-lipoxygenase, 12Delta-lipoxygenase, and C-12 lipoxygenase. ALOX12, often termed plate platelet-type 12-lipoxygenase, is distinguished from leukocyte-type 12-lipoxygenase which is found in mice, rats, cows, and pigs but not humans. Leukocyte-type 12-lipoxygenase in these animal species shares 73-86% amino acid identity with human ALOX15 but only 57-66% identity with human platelet-type 12-lipoxygenase and, like ALOX15, metabolizes arachidonic acid primarily to 15(S)-hydroperoxy-5Z,8Z,11Z,13E-eicosatetraenoic acid (i.e. 15(S)-HpETE; see 15-Hydroxyeicosatetraenoic acid). Accordingly, rodent leukocyte 12-lipoxygenase is deemed an ortholog of ALOX15 and is designated as Alox15.
Human ALOX12 and ALOX15 along with rodent leukocyte-type Alox12 and Alox15 are commonly termed 12/15-lipoxygenases based on their ability to metabolize arachidonic acid to both 12(S)-HpETE and 15(S)-HpETE and to conduct this same metabolism on arachidonic acid that is esterified to membrane phospholipids; human ALOX15B makes 15(S)-HpETE but not |
https://en.wikipedia.org/wiki/CDC20 | The cell division cycle protein 20 homolog is an essential regulator of cell division that is encoded by the CDC20 gene in humans. To the best of current knowledge its most important function is to activate the anaphase promoting complex (APC/C), a large 11-13 subunit complex that initiates chromatid separation and entrance into anaphase. The APC/CCdc20 protein complex has two main downstream targets. Firstly, it targets securin for destruction, enabling the eventual destruction of cohesin and thus sister chromatid separation. It also targets S and M-phase (S/M) cyclins for destruction, which inactivates S/M cyclin-dependent kinases (Cdks) and allows the cell to exit from mitosis. A closely related protein, Cdc20homologue-1 (Cdh1) plays a complementary role in the cell cycle.
CDC20 appears to act as a regulatory protein interacting with many other proteins at multiple points in the cell cycle. It is required for two microtubule-dependent processes: nuclear movement prior to anaphase, and chromosome separation.
Discovery
CDC20, along with a handful of other Cdc proteins, was discovered in the early 1970s when Hartwell and colleagues made cell-division cycle mutants that failed to complete major events in the cell cycle in the yeast strain S. cerevisiae. Hartwell found mutants that did not enter anaphase and thus could not complete mitosis; this phenotype could be traced back to the CDC20 gene. However, even after the biochemistry of the protein was eventually elucidated, |
https://en.wikipedia.org/wiki/IGFBP4 | Insulin-like growth factor-binding protein 4 is a protein that in humans is encoded by the IGFBP4 gene.
Function
This gene is a member of the insulin-like growth factor binding protein (IGFBP) family and encodes a protein with an IGFBP domain and a thyroglobulin type-I domain. The protein binds both insulin-like growth factors (IGFs) I and II and circulates in the plasma in both glycosylated and non-glycosylated forms. Binding of this protein prolongs the half-life of the IGFs and alters their interaction with cell surface receptors.
IGFBP-4 is a unique protein and it consistently inhibits several cancer cells in vivo and in vitro. Its inhibitory action has been shown in vivo in prostate and colon. It is secreted by all colon cancer cells.
Clinical significance
The protein itself does not prevent the formation of cancer. However it may reduce the growth of cancer and act as an apoptotic factor.
Interactions
IGFBP4 has been shown to interact with Insulin-like growth factor 1 and 2.
References
Further reading |
https://en.wikipedia.org/wiki/JunD | Transcription factor JunD is a protein that in humans is encoded by the JUND gene.
Function
The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms.
ΔJunD
The dominant negative mutant variant of JunD, known as ΔJunD or Delta JunD, is a potent antagonist of the ΔFosB transcript, as well as other forms of AP-1-mediated transcriptional activity. In the nucleus accumbens, ΔJunD directly opposes many of the neurological changes that occur in addiction (i.e., those induced by ΔFosB). ΔFosB inhibitors (drugs that oppose its action) may be an effective treatment for addiction and addictive disorders. Being an unnatural genetic variant, deltaJunD has not been observed in humans.
Interactions
JunD has been shown to interact with ATF3, MEN1, DNA damage-inducible transcript 3 and BRCA1.
See also
AP-1 (transcription factor)
References
Further reading
External links
PDBe-KB provides an overview of all the structure information available in the PDB for Human Transcription factor jun-D
Transcription factors |
https://en.wikipedia.org/wiki/KLK1 | Kallikrein-1 is a protein that in humans is encoded by the KLK1 gene. KLK1 is a member of the peptidase S1 family.
Kallikreins are a subgroup of serine proteases having diverse physiological functions. Growing evidence suggests that many kallikreins are implicated in carcinogenesis and some have potential as novel cancer and other disease biomarkers. This gene is one of the fifteen kallikrein subfamily members located in a cluster on chromosome 19. This protein is functionally conserved in its capacity to release the vasoactive peptide, Lys-bradykinin, from low molecular weight kininogen.
See also
Kinin–kallikrein system
Kininogen 1
References
Further reading
External links
The MEROPS online database for peptidases and their inhibitors: S01.160
Proteases
EC 3.1.21 |
https://en.wikipedia.org/wiki/MCM2 | DNA replication licensing factor MCM2 is a protein that in humans is encoded by the MCM2 gene.
Function
The protein encoded by this gene is one of the highly conserved mini-chromosome maintenance proteins (MCM) that are involved in the initiation of eukaryotic genome replication. The hexameric protein complex formed by MCM proteins is a key component of the pre-replication complex (pre-RC) and may be involved in the formation of replication forks and in the recruitment of other DNA replication-related proteins. This protein forms a complex with MCM4, 6, and 7, and has been shown to regulate the helicase activity of the complex. This protein is phosphorylated, and thus regulated by, protein kinases CDC2 and CDC7.
Interactions
MCM2 has been shown to interact with:
AKAP8,
Cell division cycle 7-related protein kinase,
MCM3,
MCM4,
MCM5,
MCM6,
MCM7,
ORC1L,
ORC2L,
ORC4L,
ORC5L, and
Replication protein A1.
See also
Mini Chromosome Maintenance
References
Further reading |
https://en.wikipedia.org/wiki/MT-ATP8 | MT-ATP8 (or ATP8) is a mitochondrial gene with the full name 'mitochondrially encoded ATP synthase membrane subunit 8' that encodes a subunit of mitochondrial ATP synthase, ATP synthase Fo subunit 8 (or subunit A6L). This subunit belongs to the Fo complex of the large, transmembrane F-type ATP synthase. This enzyme, which is also known as complex V, is responsible for the final step of oxidative phosphorylation in the electron transport chain. Specifically, one segment of ATP synthase allows positively charged ions, called protons, to flow across a specialized membrane inside mitochondria. Another segment of the enzyme uses the energy created by this proton flow to convert a molecule called adenosine diphosphate (ADP) to ATP. Subunit 8 differs in sequence between Metazoa, plants and Fungi.
Structure
The ATP synthase protein 8 of human and other mammals is encoded in the mitochondrial genome by the MT-ATP8 gene. When the complete human mitochondrial genome was first published, the MT-ATP8 gene was described as the unidentified reading frame URF A6L. An unusual feature of the MT-ATP8 gene is its 46-nucleotide overlap with the MT-ATP6 gene. With respect to the reading frame (+1) of MT-ATP8, the MT-ATP6 gene starts on the +3 reading frame.
The MT-ATP8 protein weighs 8 kDa and is composed of 68 amino acids. The protein is a subunit of the F1Fo ATPase, also known as Complex V, which consists of 14 nuclear- and 2 mitochondrial-encoded subunits. F-type ATPases consist of two struc |
https://en.wikipedia.org/wiki/PSMC3 | 26S protease regulatory subunit 6A, also known as 26S proteasome AAA-ATPase subunit Rpt5, is an enzyme that in humans is encoded by the PSMC3 gene. This protein is one of the 19 essential subunits of a complete assembled 19S proteasome complex Six 26S proteasome AAA-ATPase subunits (Rpt1, Rpt2, Rpt3, Rpt4, Rpt5 (this protein), and Rpt6) together with four non-ATPase subunits (Rpn1, Rpn2, Rpn10, and Rpn13) form the base sub complex of 19S regulatory particle for proteasome complex.
Gene
The gene PSMC3 encodes one of the ATPase subunits, a member of the triple-A family of ATPases that have chaperone-like activity. This subunit may compete with PSMC2 for binding to the HIV tat protein to regulate the interaction between the viral protein and the transcription complex. A pseudogene has been identified on chromosome 9. The human PSMC3 gene has 12 exons and locates at chromosome band 11p11.2.
Protein
The human protein 26S protease regulatory subunit 6A is 49kDa in size and composed of 439 amino acids. The calculated theoretical pI of this protein is 5.68.
Complex assembly
26S proteasome complex is usually consisted of a 20S core particle (CP, or 20S proteasome) and one or two 19S regulatory particles (RP, or 19S proteasome) on either one side or both side of the barrel-shaped 20S. The CP and RPs pertain distinct structural characteristics and biological functions. In brief, 20S sub complex presents three types proteolytic activities, including caspase-like, trypsin-like, |
https://en.wikipedia.org/wiki/TOP2B | DNA topoisomerase 2-beta is an enzyme that in humans is encoded by the TOP2B gene.
Function
This gene encodes a DNA topoisomerase, an enzyme that controls and alters the topologic states of DNA during transcription. This nuclear enzyme is involved in processes such as chromosome condensation, chromatid separation, and the relief of torsional stress that occurs during DNA transcription and replication. It catalyzes the transient breaking and rejoining of two strands of duplex DNA which allows the strands to pass through one another, thus altering the topology of DNA. Two forms of this enzyme exist as likely products of a gene duplication event. The gene encoding this form, beta, is localized to chromosome 3 and the alpha form is localized to chromosome 17. The gene encoding this enzyme functions as the target for several anticancer agents, for example mitoxantrone, and a variety of mutations in this gene have been associated with the development of drug resistance. Reduced activity of this enzyme may also play a role in ataxia-telangiectasia. Alternative splicing of this gene results in two transcript variants; however, the second variant has not yet been fully described.
Neuronal activity
During a new learning experience, a set of genes is rapidly expressed in the brain. This induced gene expression is considered to be essential for processing the information being learned. Such genes are referred to as immediate early genes (IEGs). TOP2B activity is essential for the ex |
https://en.wikipedia.org/wiki/RAB7A | Ras-related protein Rab-7a is a protein that in humans is encoded by the RAB7A gene.
Ras-related protein Rab-7a is involved in endocytosis, which is a process that brings substances into a cell. The process of endocytosis works by folding the cell membrane around a substance outside of the cell (for example a protein) and then forms a vesicle. The vesicle is then brought into the cell and cleaved from the cell membrane. RAB7A plays an important role in the movement of vesicles into the cell as well as with vesicle trafficking.
Various mutations of RAB7A are associated with Hereditary sensory neuropathy type 1C (HSN IC), also known as Charcot-Marie-Tooth syndrome type 2B (CMT2B).
Function
Members of the RAB family of RAS-related GTP-binding proteins are important regulators of vesicular transport and are located in specific intracellular compartments. RAB7 has been localized to late endosomes and shown to be important in the late endocytic pathway. In addition, it has been shown to have a fundamental role in the cellular vacuolation induced by the cytotoxin VacA of Helicobacter pylori.
RAB7A functions as a key regulator in endo-lysosomal trafficking, governs early-to-late endosomal maturation, microtubule minus-end as well as plus-end directed endosomal migration and positions, and endosome-lysosome transport through different protein-protein interaction cascades.
RAB7A is also involved in regulation of some specialized endosomal membrane trafficking, such as maturation |
https://en.wikipedia.org/wiki/TFPI2 | Tissue factor pathway inhibitor 2 is a protein that in humans is encoded by the TFPI2 gene.
References
Further reading |
https://en.wikipedia.org/wiki/Glencairn%20whisky%20glass | The Glencairn whisky glass is a style of glass intended for drinking whisky, developed and produced by Glencairn Crystal Ltd, in East Kilbride, a town near Glasgow, Scotland since 1981; originally designed by Raymond Davidson, managing director of the company. The shape of the glass is derived from the traditional nosing copitas used in whisky labs around Scotland. The glass design was concluded with the aid of master blenders from five of the largest whisky companies in Scotland. The glass first came into production in 2001. Since then, additional mini-Glencairns and Canadian Glencairns were introduced.
The original Glencairn glass is approximately in height and has been available in three variations: 24% lead crystal, lead-free crystal, and soda-lime glass. The vast majority of glasses in circulation are of the lead-free crystal variety. The soda-lime variation was discontinued in 2008. Mini Glencairns look the same as regular Glencairns but are smaller and used at distilleries for serving samples. Canadian Glencairns are the largest of the three, and were made for Canadian whiskey that is usually served on the rocks (with ice). Therefore, the Canadian Glencairn has a wider bowl and has a capacity.
The capacity of a typical Glencairn whisky glass is approximately , and it is intended to hold approximately of liquid.
In 2006 the glass won the Queen's Award for innovation.
The Glencairn glass is not the only glass on the market that is designed specifically for drinkin |
https://en.wikipedia.org/wiki/Blue%20Sea%20Lake | Blue Sea Lake (in French: Lac Blue Sea) is a lake in the municipalities of Blue Sea and Messines, Quebec, Canada, about north of Gatineau. It is known for its crystal clear water and is surrounded by cottages on its shores.
The blue waters of Blue Sea Lake, together with its dimensions and the absence of significant relief around, create the illusion of a sea. It feeds the Blue Sea River which empties into the Picanoc River, in turn a tributary of the Gatineau River. Its name first appeared on a map of Hull County in 1928.
Just over to the west, in Cayamant, is another, somewhat smaller lake called Lac de la Mer Bleue, which also means "Blue Sea Lake". To distinguish between these two lakes, the English name is used for the larger one, even in French.
Geography
The town of Blue Sea is in the centre of what is known as the Upper Gatineau region and is surrounded by a number of other lakes, rivers, ponds, and wetlands — and true wilderness areas. Like so many other areas of Quebec, Blue Sea grew and prospered because of the forest industry, which in turn was dependent on the abundant waterways of the region, especially the Gatineau.
Local folklore
According to legend, a monstrous snake-like animal with a horse head used to live in this lake. Presumably seen by several people between 1913 and 1930, this exceptionally long, large, and fast seahorse has no longer given any signs of life since, except around 1980 in the Baskatong Reservoir, located much further north. His "a |
https://en.wikipedia.org/wiki/ABS%20methods | ABS methods, where the acronym contains the initials of Jozsef Abaffy, Charles G. Broyden and Emilio Spedicato, have been developed since 1981 to generate a large class of algorithms for the following applications:
solution of general linear algebraic systems, determined or underdetermined,
full or deficient rank;
solution of linear Diophantine systems, i.e. equation systems where the coefficient matrix and the right hand side are integer valued and an integer solution is sought; this is a special but important case of Hilbert's tenth problem, the only one in practice soluble;
solution of nonlinear algebraic equations;
solution of continuous unconstrained or constrained optimization.
At the beginning of 2007 ABS literature consisted of over 400 papers and reports and two monographs, one due to Abaffy and Spedicato and published in 1989, one due to Xia and Zhang and published, in Chinese, in 1998. Moreover, three conferences had been organized in China.
Research on ABS methods has been the outcome of an international collaboration coordinated by Spedicato of university of Bergamo, Italy. It has involved over forty mathematicians from Hungary, UK, China, Iran and other countries.
The central element in such methods is the use of a special matrix transformation due essentially to the Hungarian mathematician Jenő Egerváry, who investigated its main properties in some papers that went unnoticed.
For the basic problem of solving a linear system of m equations in n va |
https://en.wikipedia.org/wiki/GZMB | Granzyme B is a serine protease that in humans is encoded by the GZMB gene. Granzyme B is expressed by cytotoxic T lymphocytes (CTL) and natural killer (NK) cells.
CTL and NK cells share the remarkable ability to recognize specific infected target cells. They are thought to protect their host by inducing apoptosis of cells that bear on their surface 'nonself' antigens, usually peptides or proteins resulting from infection by intracellular pathogens. The protein encoded by this gene is crucial for the rapid induction of target cell apoptosis by CTL in cell-mediated immune response.
See also
The Proteolysis Map
Granzyme
References
Further reading
External links
The MEROPS online database for peptidases and their inhibitors: S01.010 |
https://en.wikipedia.org/wiki/Cottlesville | Cottlesville is a rural community just outside Summerford on New World Island, Newfoundland and Labrador.
Demographics
In the 2021 Census of Population conducted by Statistics Canada, Cottlesville had a population of living in of its total private dwellings, a change of from its 2016 population of . With a land area of , it had a population density of in 2021.
References
Populated coastal places in Canada
Towns in Newfoundland and Labrador |
https://en.wikipedia.org/wiki/Epithelial%20cell%20rests%20of%20Malassez | In dentistry, the epithelial cell rests of Malassez (ERM) or epithelial rests of Malassez (pax epithelialis pediodontii) are part of the periodontal ligament cells around a tooth. They are discrete clusters of residual cells from Hertwig's epithelial root sheath (HERS) that didn't completely disappear. It is considered that these cell rests proliferate to form epithelial lining of various odontogenic cysts such as radicular cyst under the influence of various stimuli. They are named after Louis-Charles Malassez (1842–1909) who described them. Some rests become calcified in the periodontal ligament (cementicles).
ERM plays a role in cementum repair and regeneration. The stem cells in ERM can undergo an epithelial–mesenchymal transition and differentiate into diverse types of cells of mesodermal and ectodermal origin like bone, fat, cartilage and neuron-like cells.
References
Tooth development
Epithelial cells |
https://en.wikipedia.org/wiki/Arsenate%20reductase%20%28azurin%29 | Arsenate reductase (azurin) () is an enzyme that catalyzes the chemical reaction
arsenite + H2O + 2 azurinox arsenate + 2 azurinred + 2 H+
The 3 substrates of this enzyme are arsenite, water, and oxidised azurin, whereas its 3 products are arsenate, reduced azurin, and hydrogen ion.
Classification
This enzyme belongs to the family of oxidoreductases, specifically those acting on phosphorus or arsenic in donor with a copper protein as acceptor.
Nomenclature
The systematic name of this enzyme class is arsenite:azurin oxidoreductase. This enzyme is also called arsenite oxidase.
Structure and function
The enzyme contains a molybdopterin centre comprising two molybdopterin guanosine dinucleotide cofactors bound to molybdenum, a [3Fe-4S] cluster and a Rieske-type [2Fe-2S] cluster. Also uses a c-type cytochrome or as acceptors.
References
EC 1.20.9
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Arsenate%20reductase%20%28donor%29 | Arsenate reductase (donor) () is an enzyme that catalyzes the chemical reaction
arsenite + acceptor arsenate + reduced acceptor
Thus, the two substrates of this enzyme are arsenite and an acceptor, whereas its two products are arsenate and a reduced acceptor.
This enzyme belongs to the family of oxidoreductases, specifically those acting on phosphorus or arsenic in donor with other acceptors. The systematic name of this enzyme class is arsenate:acceptor oxidoreductase. This enzyme is also called arsenate:(acceptor) oxidoreductase.
References
EC 1.20.99
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Arsenate%20reductase%20%28glutaredoxin%29 | Arsenate reductase (glutaredoxin) () is an enzyme that catalyzes the chemical reaction
arsenate + glutaredoxin arsenite + glutaredoxin disulfide + H2O
Thus, the two substrates of this enzyme are arsenate and glutaredoxin, whereas its 3 products are arsenite, glutaredoxin disulfide, and water.
This enzyme belongs to the family of oxidoreductases, specifically those acting on phosphorus or arsenic in donor with disulfide as acceptor. The systematic name of this enzyme class is glutaredoxin:arsenate oxidoreductase.
Structural studies
As of late 2007, 12 structures have been solved for this class of enzymes, with PDB accession codes , , , , , , , , , , , and .
References
EC 1.20.4
Enzymes of known structure |
https://en.wikipedia.org/wiki/Methylarsonate%20reductase | In enzymology, a methylarsonate reductase () is an enzyme that catalyzes the chemical reaction
methylarsonate + 2 glutathione methylarsonite + glutathione disulfide + H2O
Thus, the two substrates of this enzyme are methylarsonate and glutathione, whereas its 3 products are methylarsonite, glutathione disulfide, and H2O.
This enzyme belongs to the family of oxidoreductases, specifically those acting on phosphorus or arsenic in donor with disulfide as acceptor. The systematic name of this enzyme class is gluthathione:methylarsonate oxidoreductase. This enzyme is also called MMA(V) reductase.
References
EC 1.20.4
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Phosphonate%20dehydrogenase | In enzymology, a phosphonate dehydrogenase () is an enzyme that catalyzes the chemical reaction
phosphonate + NAD+ + H2O phosphate + NADH + H+
The 3 substrates of this enzyme are phosphonate, NAD+, and H2O, whereas its 3 products are phosphate, NADH, and H+.
This enzyme belongs to the family of oxidoreductases, specifically those acting on phosphorus or arsenic in donor with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is phosphonate:NAD+ oxidoreductase. Other names in common use include NAD:phosphite oxidoreductase, and phosphite dehydrogenase.
References
EC 1.20.1
NADH-dependent enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/3alpha%2C7alpha%2C12alpha-trihydroxy-5beta-cholestanoyl-CoA%2024-hydroxylase | In enzymology, a 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase () is an enzyme that catalyzes the chemical reaction
(25R)-3alpha,7alpha,12alpha-trihydroxy-5beta-cholestan-26-oyl-CoA + H2O + acceptor (24R,25R)-3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestan-26- oyl-CoA + reduced acceptor
The 3 substrates of this enzyme are (25R)-3alpha,7alpha,12alpha-trihydroxy-5beta-cholestan-26-oyl-CoA, H2O, and acceptor, whereas its two products are (24R,25R)-3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestan-26-oyl-CoA, and reduced acceptor.
This enzyme belongs to the family of oxidoreductases, specifically those acting on CH or CH2 groups with other acceptors. The systematic name of this enzyme class is (25R)-3alpha,7alpha,12alpha-trihydroxy-5beta-cholestan-26-oyl-CoA:ac ceptor 24-oxidoreductase (24R-hydroxylating). Other names in common use include trihydroxycoprostanoyl-CoA oxidase, THC-CoA oxidase, THCA-CoA oxidase, 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA oxidase, 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestan-26-oate 24-hydroxylase. This enzyme participates in the ppar signaling pathway.
References
EC 1.17.99
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/4-Cresol%20dehydrogenase%20%28hydroxylating%29 | In enzymology, a 4-cresol dehydrogenase (hydroxylating) () is an enzyme that catalyzes the chemical reaction
4-cresol + acceptor + H2O 4-hydroxybenzaldehyde + reduced acceptor
The 3 substrates of this enzyme are 4-cresol, acceptor, and H2O, whereas its two products are 4-hydroxybenzaldehyde and reduced acceptor.
This enzyme belongs to the family of oxidoreductases, specifically those acting on CH or CH2 groups with other acceptors. The systematic name of this enzyme class is 4-cresol:acceptor oxidoreductase (methyl-hydroxylating). Other names in common use include p-cresol–(acceptor) oxidoreductase (hydroxylating), and ''p''-cresol methylhydroxylase. This enzyme participates in toluene and xylene degradation. It has 2 cofactors: FAD, and Cytochrome c.
Structural studies
As of late 2007, 4 structures have been solved for this class of enzymes, with PDB accession codes , , , and .
References
EC 1.17.99
Flavoproteins
Enzymes of known structure |
https://en.wikipedia.org/wiki/4-hydroxy-3-methylbut-2-en-1-yl%20diphosphate%20synthase | In enzymology, a 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (HMB-PP synthase, IspG, ) is an enzyme that catalyzes the chemical reaction
2-C-methyl-D-erythritol 2,4-cyclodiphosphate + protein-dithiol (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + H2O + protein-disulfide
The substrate of this enzyme is 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEcPP) and the product is (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMB-PP). Electrons are donated by two reduced ferredoxin proteins per reaction.
This enzyme participates in the MEP pathway (non-mevalonate pathway) of Isoprenoid precursor biosynthesis.
Nomenclature
This enzyme belongs to the family of oxidoreductases, specifically those acting on CH or CH2 groups with a disulfide as acceptor. The systematic name of this enzyme class is (E)-4-hydroxy-3-methylbut-2-en-1-yl-diphosphate:protein-disulfide oxidoreductase (hydrating).
References
Further reading
EC 1.17.7
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/6-hydroxynicotinate%20dehydrogenase | In enzymology, a 6-hydroxynicotinate dehydrogenase () is an enzyme that catalyzes the chemical reaction
6-hydroxynicotinate + H2O + O2 2,6-dihydroxynicotinate + H2O2
The 3 substrates of this enzyme are 6-hydroxynicotinate, H2O, and O2, whereas its two products are 2,6-dihydroxynicotinate and H2O2.
This enzyme belongs to the family of oxidoreductases, specifically those acting on CH or CH2 groups with oxygen as acceptor. The systematic name of this enzyme class is 6-hydroxynicotinate:O2 oxidoreductase. Other names in common use include 6-hydroxynicotinic acid hydroxylase, 6-hydroxynicotinic acid dehydrogenase, and 6-hydroxynicotinate hydroxylase.
References
EC 1.17.3
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/CDP-4-dehydro-6-deoxyglucose%20reductase | CDP-4-dehydro-6-deoxyglucose reductase () is an enzyme that catalyzes the chemical reaction
CDP-4-dehydro-3,6-dideoxy-D-glucose + NAD(P)+ + H2O CDP-4-dehydro-6-deoxy-D-glucose + NAD(P)H + H+
The 4 substrates of this enzyme are CDP-4-dehydro-3,6-dideoxy-D-glucose, nicotinamide adenine dinucleotide ion, nicotinamide adenine dinucleotide phosphate ion, and water, whereas its 4 products are CDP-4-dehydro-6-deoxy-D-glucose, nicotinamide adenine dinucleotide, nicotinamide adenine dinucleotide phosphate, and hydrogen ion.
This enzyme belongs to the family of oxidoreductases, specifically those acting on CH or CH2 groups with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is CDP-4-dehydro-3,6-dideoxy-D-glucose:NAD(P)+ 3-oxidoreductase. Other names in common use include CDP-4-keto-6-deoxyglucose reductase, cytidine diphospho-4-keto-6-deoxy-D-glucose reductase, cytidine diphosphate 4-keto-6-deoxy-D-glucose-3-dehydrogenase, CDP-4-keto-deoxy-glucose reductase, CDP-4-keto-6-deoxy-D-glucose-3-dehydrogenase system, and NAD(P)H:CDP-4-keto-6-deoxy-D-glucose oxidoreductase. This enzyme participates in starch and sucrose metabolism.
References
EC 1.17.1
NADPH-dependent enzymes
NADH-dependent enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Cob%28II%29alamin%20reductase | In enzymology, a cob(II)alamin reductase () is an enzyme that catalyzes the chemical reaction
2 cob(I)alamin + NAD+ 2 cob(II)alamin + NADH + H+
Thus, the two substrates of this enzyme are cob(I)alamin and NAD+, whereas its 3 products are cob(II)alamin, NADH, and H+.
This enzyme belongs to the family of oxidoreductases, specifically those oxidizing metal ion with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is cob(I)alamin:NAD+ oxidoreductase. Other names in common use include vitamin B12r reductase, B12r reductase, and NADH2:cob(II)alamin oxidoreductase. This enzyme participates in porphyrin and chlorophyll metabolism. It employs one cofactor, FAD.
References
EC 1.16.1
NADH-dependent enzymes
Flavoproteins
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Cob%28II%29yrinic%20acid%20a%2Cc-diamide%20reductase | In enzymology, a cob(II)yrinic acid a,c-diamide reductase () is an enzyme that catalyzes the chemical reaction
2 cob(I)yrinic acid a,c-diamide + FMN + 3 H+ 2 cob(II)yrinic acid a,c-diamide + FMNH2
The three substrates of this enzyme are cob(I)yrinic acid a,c-diamide, flavin mononucleotide, and H+; its two products are cob(II)yrinic acid a,c-diamide and FMNH2.
Classification
This enzyme belongs to the family of oxidoreductases, specifically those oxidizing metal ion with a flavin as acceptor.
Nomenclature
The systematic name of this enzyme class is cob(I)yrinic acid-a,c-diamide:FMN oxidoreductase. This enzyme is also called CobR and cob(II)yrinic acid-a,c-diamide:FMN oxidoreductase (incorrect).
Biological role
This enzyme is part of the biosynthetic pathway to cobalamin (vitamin B12) in bacteria.
See also
Cobalamin biosynthesis
References
EC 1.16.8
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Cyanocobalamin%20reductase%20%28cyanide-eliminating%29 | In enzymology, a cyanocobalamin reductase (cyanide-eliminating) () is an enzyme that catalyzes the chemical reaction
cob(I)alamin + cyanide + NADP+ cyanocob(III)alamin + NADPH + H+
The 3 substrates of this enzyme are cob(I)alamin, cyanide, and NADP+, whereas its 3 products are cyanocob(III)alamin, NADPH, and H+.
This enzyme belongs to the family of oxidoreductases, specifically those that oxidize metal ions and use NAD+ or NADP+ as an electron acceptor (for that oxidization reaction). The systematic name of this enzyme class is cob(I)alamin, cyanide:NADP+ oxidoreductase. Other names in common use include cyanocobalamin reductase, cyanocobalamin reductase (NADPH, cyanide-eliminating), cyanocobalamin reductase (NADPH, CN-eliminating), and NADPH:cyanocob(III)alamin oxidoreductase (cyanide-eliminating). This enzyme participates in porphyrin and chlorophyll metabolism. It uses one cofactor, FAD.
References
EC 1.16.1
NADPH-dependent enzymes
Flavoproteins
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Diferric-transferrin%20reductase | In enzymology, a diferric-transferrin reductase () is an enzyme that catalyzes the chemical reaction
transferrin[Fe(II)]2 + NAD+ + H+ transferrin[Fe(III)]2 + NADH
The 3 substrates of this enzyme are [[transferrin[Fe(II)]2]], NAD+, and H+, whereas its two products are [[transferrin[Fe(III)]2]] and NADH.
This enzyme belongs to the family of oxidoreductases, specifically those oxidizing metal ion with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is transferrin[Fe(II)]2:NAD+ oxidoreductase. Other names in common use include diferric transferrin reductase, NADH diferric transferrin reductase, and transferrin reductase. This enzyme participates in porphyrin and chlorophyll metabolism.
Structural studies
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code .
References
EC 1.16.1
NADH-dependent enzymes
Enzymes of known structure
Transferrins |
https://en.wikipedia.org/wiki/Ethylbenzene%20hydroxylase | In enzymology, an ethylbenzene hydroxylase () is an enzyme that catalyzes the chemical reaction
ethylbenzene + H2O + acceptor (S)-1-phenylethanol + reduced acceptor
The 3 substrates of this enzyme are ethylbenzene, H2O, and acceptor, whereas its two products are (S)-1-phenylethanol and reduced acceptor.
This enzyme belongs to the family of oxidoreductases, specifically those acting on CH or CH2 groups with other acceptors. The systematic name of this enzyme class is ethylbenzene:acceptor oxidoreductase. Other names in common use include ethylbenzene dehydrogenase, and ethylbenzene:(acceptor) oxidoreductase. This enzyme participates in ethylbenzene degradation by Aromatoleum aromaticum, a denitrifying bacterium related to the genera Azoarcus and Thauera. It is a molybdenum enzyme belonging to the DMSO reductase family. Molybdenum enzymes are distinguished by the presence of a unique active site containing molybdenum atom, one or two molybdopterins and additional ligands (i.e. aminoacid residue of Ser, Cys, SeCys or Asp and very often oxygen Mo=O ligand). EBDH is synthesized exclusively in cells grown anaerobically on ethylbenzene and has been identified as a soluble periplasmic protein.
Structural studies
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code . EBDH consists of three subunits of 96, 43, and 23 kDa, and contains a molybdenum cofactor and a heme b559 cofactor linked by a linear row of five iron-sulfur clu |
https://en.wikipedia.org/wiki/Ferredoxin%E2%80%94NADP%28%2B%29%20reductase | In enzymology, a ferredoxin-NADP reductase () abbreviated FNR, is an enzyme that catalyzes the chemical reaction
2 reduced ferredoxin + NADP + H 2 oxidized ferredoxin + NADPH
The 3 substrates of this enzyme are reduced ferredoxin, NADP, and H, whereas its two products are oxidized ferredoxin and NADPH. It has a flavin cofactor, FAD.
This enzyme belongs to the family of oxidoreductases, that use iron-sulfur proteins as electron donors and NAD or NADP as electron acceptors.
This enzyme participates in photosynthesis. FNR provides a major source of NADPH for photosynthetic organisms.
Nomenclature
The systematic name of this enzyme class is ferredoxin:NADP oxidoreductase. Other names in common use include:
adrenodoxin reductase,
ferredoxin-NADP reductase,
ferredoxin-NADP oxidoreductase,
ferredoxin-nicotinamide adenine dinucleotide phosphate reductase,
ferredoxin-nicotinamide-adenine dinucleotide phosphate (oxidized), reductase
ferredoxin-TPN reductase,
NADP:ferredoxin oxidoreductase,
NADPH:ferredoxin oxidoreductase,
reduced nicotinamide adenine dinucleotide phosphate-adrenodoxin, reductase, and
TPNH-ferredoxin reductase
Mechanism
During photosynthesis, electrons are removed from water and transferred to the single electron carrier ferredoxin. Ferredoxin: NADP reductase then transfers an electron from each of two ferredoxin molecules to a single molecule of the two electron carrier NADPH. FNR utilizes FAD, which can exist in an oxidized state, single electron |
https://en.wikipedia.org/wiki/Ferredoxin%E2%80%94NAD%28%2B%29%20reductase | In enzymology, a ferredoxin–NAD+ reductase () is an enzyme that catalyzes the chemical reaction:
reduced ferredoxin + NAD+ oxidized ferredoxin + NADH + H+
Thus, the two substrates of this enzyme are reduced ferredoxin and NAD+, whereas its 3 products are oxidized ferredoxin, NADH, and H+. This enzyme participates in fatty acid metabolism.
This enzyme belongs to the family of oxidoreductases, specifically those acting on iron-sulfur proteins as donor with NAD+ or NADP+ as acceptor.
The systematic name of this enzyme is ferredoxin:NAD+ oxidoreductase. There are a variety of names in common use:
ferredoxin–nicotinamide adenine dinucleotide reductase
ferredoxin reductase
NAD+-ferredoxin reductase
ferredoxin–NAD+ reductase
ferredoxin–linked NAD+ reductase
ferredoxin–NAD reductase
When NAD molecule is in its reduced form, the enzyme is referred to as:
NADH-ferredoxin oxidoreductase
reduced nicotinamide adenine dinucleotide-ferredoxin
NADH-ferredoxin reductase
NADH flavodoxin oxidoreductase
NADH2-ferredoxin oxidoreductase
Other enzymes in the family include:
NADH-ferredoxin NAP reductase (component of naphthalene dioxygenase multicomponent enzyme system)
NADH-ferredoxin TOL reductase (component of toluene dioxygenase)
Structural studies
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code .
References
EC 1.18.1
NADH-dependent enzymes
Enzymes of known structure |
https://en.wikipedia.org/wiki/Ferric-chelate%20reductase | In enzymology, a ferric-chelate reductase () is an enzyme that catalyzes the chemical reaction
2 Fe(II) + NAD+ 2 Fe(III) + NADH + H+
Thus, the two substrates of this enzyme are Fe(II) and NAD+, whereas its 3 products are Fe(III), NADH, and H+.
Nomenclature
This enzyme belongs to the family of oxidoreductases, specifically those oxidizing metal ion with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is Fe(II):NAD+ oxidoreductase. Other names in common use include:
ferric chelate reductase
iron chelate reductase
NADH:Fe3+-EDTA reductase
NADH2:Fe3+ oxidoreductase
Prokaryotes
Most studied ferric reductases in bacteria are either specific for a ferric iron complex or non-specific flavin ferric reductases, with the latter being more common in bacteria. Both reductase forms are suitable complimentary soluble pathways for the efficient extraction of iron via siderophores.
Bacterial soluble flavin reductase in E. coli
Non-specific bacterial flavin reductase has been well researched within E. coli, which is the NAD(P)H: flavin oxidoreductase (Fre). In E. coli, NAD(P)H is reduced to either free FAD or riboflavin, which is known to reduce ferric iron to ferrous iron intracellularly. Fre is also structurally similar to ferredoxin-NADP+ reductase (Fpr), and bids flavin cofactor to reduce ferredoxin and siderophore bound ferric iron. Despite these hypothesized structural commonalities, not much is known regarding this enzymatic structure overall.
Bacteri |
https://en.wikipedia.org/wiki/Leucoanthocyanidin%20reductase | In enzymology, a leucoanthocyanidin reductase () (LAR, aka leucocyanidin reductase or LCR) is an enzyme that catalyzes the chemical reaction
(2R,3S)-catechin + NADP+ + H2O 2,3-trans-3,4-cis-leucocyanidin + NADPH + H+
The 3 substrates of this enzyme are (2R,3S)-catechin, NADP+, and H2O, whereas its 3 products are 2,3-trans-3,4-cis-leucocyanidin, NADPH, and H+.
This enzyme belongs to the family of oxidoreductases, specifically those acting on CH or CH2 groups with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is (2R,3S)-catechin:NADP+ 4-oxidoreductase. This enzyme is also called leucocyanidin reductase. This enzyme participates in flavonoid biosynthesis.
The enzyme can be found in the plant Hedysarum sulphurescens and in Vitis vinifera (grape).
References
Further reading
EC 1.17.1
NADPH-dependent enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/%28Methionine%20synthase%29%20reductase | [Methionine synthase] reductase, or Methionine synthase reductase, encoded by the gene MTRR, is an enzyme that is responsible for the reduction of methionine synthase inside human body. This enzyme is crucial for maintaining the one carbon metabolism, specifically the folate cycle. The enzyme employs one coenzyme, flavoprotein.
Mechanism
MTRR works by catalyzing the following chemical reaction:
2 [methionine synthase]-methylcob(I)alamin + 2 S-adenosylhomocysteine + NADP 2 [methionine synthase]-cob(II)alamin + NADPH + H + 2 S-adenosyl-L-methionine
The 3 products of this enzyme are methionine synthase-methylcob(I)alamin, S-adenosylhomocysteine, and NADP, whereas its 4 substrates are methionine synthase-cob(II)alamin, NADPH, H, and S-adenosyl-L-methionine.
Physiologically speaking, one crucial enzyme participated in the folate cycle is methionine synthase, which incorporated a coenzyme, cobalamin, also known as Vitamin B12. The coenzyme utilizes its cofactor, cobalt to catalyze the transferring function, in which the cobalt will switch between having 1 or 3 valence electrons, dubbed cob(I)alamin, and cob(III)alamin.
Over time, the cob(I)alamin cofactor of methionine synthase becomes oxidized to cob(II)alamin, rendering the enzyme inactive. Therefore, regeneration of the enzyme is necessary. Regeneration requires reductive methylation via a reaction catalyzed by (methionine synthase) reductase in which S-adenosylmethionine is utilized as a methyl donor, reducing cob(II)ala |
https://en.wikipedia.org/wiki/Nicotinate%20dehydrogenase | In enzymology, a nicotinate dehydrogenase () is an enzyme that catalyzes the chemical reaction
nicotinate + H2O + NADP+ 6-hydroxynicotinate + NADPH + H+
The 3 substrates of this enzyme are nicotinate, H2O, and NADP+, whereas its 3 products are 6-hydroxynicotinate, NADPH, and H+.
Classification
This enzyme belongs to the family of oxidoreductases, specifically those acting on CH or CH2 groups with NAD+ or NADP+ as acceptor.
Nomenclature
The systematic name of this enzyme class is nicotinate:NADP+ 6-oxidoreductase (hydroxylating). Other names in common use include nicotinic acid hydroxylase, and nicotinate hydroxylase.
Biological role
This enzyme participates in nicotinate and nicotinamide metabolism. It has 2 cofactors: FAD, and Iron.
References
EC 1.17.1
NADPH-dependent enzymes
Flavoproteins
Iron enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Nitrogenase%20%28flavodoxin%29 | Nitrogenase (flavodoxin) () is an enzyme with systematic name reduced flavodoxin:dinitrogen oxidoreductase (ATP-hydrolysing). This enzyme catalyses the following chemical reaction
6 reduced flavodoxin + 6 H+ + N2 + n ATP 6 oxidized flavodoxin + 2 NH3 + n ADP + n phosphate
The enzyme is a complex of two proteins containing iron-sulfur centres and molybdenum.
See also
Nitrogenase
References
External links
EC 1.19.6 |
https://en.wikipedia.org/wiki/Phenylacetyl-CoA%20dehydrogenase | In enzymology, a phenylacetyl-CoA dehydrogenase () is an enzyme that catalyzes the chemical reaction
phenylacetyl-CoA + H2O + 2 quinone phenylglyoxylyl-CoA + 2 quinol
The 3 substrates of this enzyme are phenylacetyl-CoA, H2O, and quinone, whereas its two products are phenylglyoxylyl-CoA and quinol.
This enzyme belongs to the family of oxidoreductases, specifically those acting on CH or CH2 groups with a quinone or similar compound as acceptor. The systematic name of this enzyme class is phenylacetyl-CoA:quinone oxidoreductase. This enzyme is also called phenylacetyl-CoA:acceptor oxidoreductase.
References
EC 1.17.5
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Pteridine%20oxidase | In enzymology, a pteridine oxidase () is an enzyme that catalyzes the chemical reaction
2-amino-4-hydroxypteridine + O2 2-amino-4,7-dihydroxypteridine + (?)
Thus, the two substrates of this enzyme are 2-amino-4-hydroxypteridine and O2, whereas its product is 2-amino-4,7-dihydroxypteridine.
This enzyme belongs to the family of oxidoreductases, specifically those acting on CH or CH2 groups with oxygen as acceptor. The systematic name of this enzyme class is 2-amino-4-hydroxypteridine:oxygen oxidoreductase (7-hydroxylating).
References
EC 1.17.3
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Rubredoxin%E2%80%94NAD%28P%29%28%2B%29%20reductase | In enzymology, a rubredoxin—NAD(P)+ reductase () is an enzyme that catalyzes the chemical reaction
reduced rubredoxin + NAD(P)+ oxidized rubredoxin + NAD(P)H + H+
The 3 substrates of this enzyme are reduced rubredoxin, NAD+, and NADP+, whereas its 4 products are oxidized rubredoxin, NADH, NADPH, and H+.
This enzyme belongs to the family of oxidoreductases, specifically those acting on iron-sulfur proteins as donor with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is rubredoxin:NAD(P)+ oxidoreductase. Other names in common use include rubredoxin-nicotinamide adenine dinucleotide (phosphate) reductase, rubredoxin-nicotinamide adenine, dinucleotide phosphate reductase, NAD(P)+-rubredoxin oxidoreductase, and NAD(P)H-rubredoxin oxidoreductase. This enzyme participates in fatty acid metabolism.
References
External links
EC 1.18.1
NADPH-dependent enzymes
NADH-dependent enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Rubredoxin%E2%80%94NAD%28%2B%29%20reductase | In enzymology, a rubredoxin-NAD+ reductase () is an enzyme that catalyzes the chemical reaction.
2 reduced rubredoxin + NAD+ + H+ 2 oxidized rubredoxin + NADH
The 3 substrates of this enzyme are reduced rubredoxin, NAD+, and H+, whereas its two products are oxidized rubredoxin and NADH.
This enzyme belongs to the family of oxidoreductases, specifically those acting on iron-sulfur proteins as donor with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is rubredoxin:NAD+ oxidoreductase. Other names in common use include rubredoxin reductase, rubredoxin-nicotinamide adenine dinucleotide reductase, dihydronicotinamide adenine dinucleotide-rubredoxin reductase, reduced nicotinamide adenine dinucleotide-rubredoxin reductase, NADH-rubredoxin reductase, rubredoxin-NAD reductase, NADH: rubredoxin oxidoreductase, DPNH-rubredoxin reductase, and NADH-rubredoxin oxidoreductase. This enzyme participates in fatty acid metabolism. It has 2 cofactors: FAD and Iron.
Structural studies
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code .
References
EC 1.18.1
NADH-dependent enzymes
Flavoproteins
Iron enzymes
Enzymes of known structure |
https://en.wikipedia.org/wiki/Superoxide%20reductase | Superoxide reductase is an enzyme that catalyzes the conversion of highly reactive and toxic superoxide (O2−) into less toxic hydrogen peroxide (H2O2):
reduced rubredoxin + O2− + 2 H+ rubredoxin + H2O2
Fe2+ + O2− + 2 H+ Fe3++ H2O2
Hydrogen peroxide in turn is reduced to water by rubrerythrin. The 3 substrates of this enzyme are reduced rubredoxin, superoxide, and H+, whereas its two products are rubredoxin and H2O2.
This enzyme belongs to the family of oxidoreductases, specifically those acting on superoxide as acceptor (only sub-subclass identified to date). The systematic name of this enzyme class is rubredoxin:superoxide oxidoreductase. Other names in common use include neelaredoxin, and desulfoferrodoxin.
Structural studies
, 9 structures have been solved for this class of enzymes, with PDB accession codes , , , , , , , , and .
References
Further reading
EC 1.15.1
Enzymes of known structure |
https://en.wikipedia.org/wiki/Automotive%20Fuel%20Cell%20Cooperation | Automotive Fuel Cell Cooperation (AFCC) was a Vancouver, British Columbia, Canada, based automotive fuel cell technology company. The company was formed on February 1, 2008 as a spin-off from its predecessor, Ballard Power Systems to allow for further expansion of fuel cell technology. After the split, Ballard continued as a publicly traded company focusing on non-automotive applications (including buses), while AFCC became a privately held company of 150 employees, developing hydrogen fuel cell stacks for automobiles. AFCC's initial ownership split was Daimler (50.1%), Ford Motor Company (30.0%), and Ballard itself (19.9%).
Ford Motor Company purchased the portion of AFCC owned by Ballard Power Systems in 2009 for $44.5M in gross proceeds, leaving it with 49.9% ownership, and Daimler AG (at present the Mercedes-Benz Group) as the major stakeholder with 50.1%.
An AFCC stack was used in the Mercedes-Benz F-Cell vehicle in 2010.
In 2013, AFCC's owners signed a three-way agreement with Nissan Motor Company to develop next-generation fuel cell technology that they hope will lead to the world's first affordable, mass-market fuel cell electric vehicles as early as 2017. The collaboration was to be jointly led by all three automakers with engineering work taking place at various locations around the world. AFCC was responsible for the research and product development of automotive fuel cell stacks for the collaboration.
The company's first CEO was Dr. Andreas Truckenbrodt forme |
https://en.wikipedia.org/wiki/1-hydroxy-2-naphthoate%201%2C2-dioxygenase | In enzymology, a 1-hydroxy-2-naphthoate 1,2-dioxygenase () is an enzyme that catalyzes the chemical reaction
1-hydroxy-2-naphthoate + O2 (3Z)-4-(2-carboxyphenyl)-2-oxobut-3-enoate
Thus, the two substrates of this enzyme are 1-hydroxy-2-naphthoate and O2, whereas its product is (3Z)-4-(2-carboxyphenyl)-2-oxobut-3-enoate.
This enzyme participates in naphthalene and anthracene degradation. It employs one cofactor, iron.
Nomenclature
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 1-hydroxy-2-naphthoate:oxygen 1,2-oxidoreductase (decyclizing). Other names in common use include 1-hydroxy-2-naphthoate dioxygenase, 1-hydroxy-2-naphthoate-degrading enzyme, and 1-hydroxy-2-naphthoic acid dioxygenase.
References
EC 1.13.11
Iron enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/2%2C3-dihydroxybenzoate%202%2C3-dioxygenase | In enzymology, a 2,3-dihydroxybenzoate 2,3-dioxygenase () is an enzyme that catalyzes the chemical reaction
2,3-dihydroxybenzoate + O2 2-carboxy-cis,cis-muconate
Thus, the two substrates of this enzyme are 2,3-dihydroxybenzoate and O2, whereas its product is 2-carboxy-cis,cis-muconate.
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 2,3-dihydroxybenzoate:oxygen 2,3-oxidoreductase (decyclizing). This enzyme is also called 2,3-dihydroxybenzoate 2,3-oxygenase.
References
EC 1.13.11
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/2%2C3-dihydroxybenzoate%203%2C4-dioxygenase | In enzymology, a 2,3-dihydroxybenzoate 3,4-dioxygenase () is an enzyme that catalyzes the chemical reaction
2,3-dihydroxybenzoate + O2 3-carboxy-2-hydroxymuconate semialdehyde
Thus, the two substrates of this enzyme are 2,3-dihydroxybenzoate and O2, whereas its product is 3-carboxy-2-hydroxymuconate semialdehyde.
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 2,3-dihydroxybenzoate:oxygen 3,4-oxidoreductase (decyclizing). Other names in common use include o-pyrocatechuate oxygenase, 2,3-dihydroxybenzoate 1,2-dioxygenase, 2,3-dihydroxybenzoic oxygenase, and 2,3-dihydroxybenzoate oxygenase. This enzyme participates in benzoate degradation via hydroxylation.
References
EC 1.13.11
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/PTPN1 | Tyrosine-protein phosphatase non-receptor type 1 also known as protein-tyrosine phosphatase 1B (PTP1B) is an enzyme that is the founding member of the protein tyrosine phosphatase (PTP) family. In humans it is encoded by the PTPN1 gene. PTP1B is a negative regulator of the insulin signaling pathway and is considered a promising potential therapeutic target, in particular for treatment of type 2 diabetes. It has also been implicated in the development of breast cancer and has been explored as a potential therapeutic target in that avenue as well.
Structure and function
PTP1B was first isolated from a human placental protein extract, but it is expressed in many tissues. PTP1B is localized to the cytoplasmic face of the endoplasmic reticulum. PTP1B can dephosphorylate the phosphotyrosine residues of the activated insulin receptor kinase. In mice, genetic ablation of PTPN1 results in enhanced insulin sensitivity. Several other tyrosine kinases, including epidermal growth factor receptor, insulin-like growth factor 1 receptor, colony stimulating factor 1 receptor, c-Src, Janus kinase 2, TYK2, and focal adhesion kinase as well as other tyrosine-phosphorylated proteins, including BCAR1, DOK1, beta-catenin and cortactin have also been described as PTP1B substrates.
The first crystal structure of the PTP1B catalytic domain revealed that the catalytic site exists within a deep cleft of the protein formed by three loops including the WPD loop with the Asp181 residue, a pTyr loop wi |
https://en.wikipedia.org/wiki/2%2C3-dihydroxyindole%202%2C3-dioxygenase | In enzymology, a 2,3-dihydroxyindole 2,3-dioxygenase () is an enzyme that catalyzes the chemical reaction
2,3-dihydroxyindole + O2 anthranilate + CO2
Thus, the two substrates of this enzyme are 2,3-dihydroxyindole and O2, whereas its two products are anthranilate and CO2.
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 2,3-dihydroxyindole:oxygen 2,3-oxidoreductase (decyclizing). This enzyme participates in tryptophan metabolism.
References
EC 1.13.11
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/2%2C4%27-dihydroxyacetophenone%20dioxygenase | In enzymology, a 2,4'-dihydroxyacetophenone dioxygenase () is an enzyme that catalyzes the chemical reaction
2,4'-dihydroxyacetophenone + O2 4-hydroxybenzoate + formate
Thus, the two substrates of this enzyme are 2,4'-dihydroxyacetophenone and O2, whereas its two products are 4-hydroxybenzoate and formate.
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 2,4'-dihydroxyacetophenone oxidoreductase (C-C-bond-cleaving). This enzyme is also called (4-hydroxybenzoyl)methanol oxygenase. This enzyme participates in bisphenol a degradation.
References
EC 1.13.11
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/2%2C5-dihydroxypyridine%205%2C6-dioxygenase | In enzymology, a 2,5-dihydroxypyridine 5,6-dioxygenase () is an enzyme that catalyzes the chemical reaction
2,5-dihydroxypyridine + O2 N-formylmaleamic acid
The 2 substrates of this enzyme are 2,5-dihydroxypyridine and O2, whereas its product is N-formylmaleamic acid.
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. It employs one cofactor, iron.
This enzyme participates in nicotinate and nicotinamide metabolism.
Nomenclature
The systematic name of this enzyme class is 2,5-dihydroxypyridine:oxygen 5,6-oxidoreductase. Other names in common use include 2,5-dihydroxypyridine oxygenase, and pyridine-2,5-diol dioxygenase.
References
Further reading
EC 1.13.11
Iron enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/2-nitropropane%20dioxygenase | In enzymology, a 2-nitropropane dioxygenase () is an enzyme that catalyzes the chemical reaction
2 2-nitropropane + O2 2 acetone + 2 nitrite
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 .
References
EC 1.13.11
Flavoproteins
Iron enzymes
Enzymes of known structure |
https://en.wikipedia.org/wiki/3%2C4-dihydroxy-9%2C10-secoandrosta-1%2C3%2C5%2810%29-triene-9%2C17-dione%204%2C5-dioxygenase | In enzymology, a 3,4-dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione 4,5-dioxygenase () is an enzyme that catalyzes the chemical reaction
3,4-dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione + O2 3-hydroxy-5,9,17-trioxo-4,5:9,10-disecoandrosta-1(10),2-dien-4-oate
Thus, the two substrates of this enzyme are 3,4-dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione and O2, whereas its product is 3-hydroxy-5,9,17-trioxo-4,5:9,10-disecoandrosta-1(10),2-dien-4-oate.
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 3,4-dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione:oxygen 4,5-oxidoreductase (decyclizing). Other names in common use include steroid 4,5-dioxygenase, and 3-alkylcatechol 2,3-dioxygenase. It employs one cofactor, iron.
References
EC 1.13.11
Iron enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/3%2C4-dihydroxyphenylacetate%202%2C3-dioxygenase | In enzymology, a 3,4-dihydroxyphenylacetate 2,3-dioxygenase () is an enzyme that catalyzes the chemical reaction
3,4-dihydroxyphenylacetate + O2 2-hydroxy-5-carboxymethylmuconate semialdehyde
Thus, the two substrates of this enzyme are 3,4-dihydroxyphenylacetate and O2, whereas its product is 2-hydroxy-5-carboxymethylmuconate semialdehyde.
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 3,4-dihydroxyphenylacetate:oxygen 2,3-oxidoreductase (decyclizing). Other names in common use include 3,4-dihydroxyphenylacetic acid 2,3-dioxygenase, HPC dioxygenase, and homoprotocatechuate 2,3-dioxygenase. This enzyme participates in tyrosine metabolism. It employs one cofactor, iron.
Structural studies
As of late 2007, eight structures have been solved for this class of enzymes, with PDB accession codes , , , , , , , and .
References
EC 1.13.11
Iron enzymes
Enzymes of known structure |
https://en.wikipedia.org/wiki/3-carboxyethylcatechol%202%2C3-dioxygenase | In enzymology, a 3-carboxyethylcatechol 2,3-dioxygenase () is an enzyme that catalyzes the chemical reaction
3-(2,3-dihydroxyphenyl)propanoate + O2 2-hydroxy-6-oxonona-2,4-diene-1,9-dioate
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.
References
EC 1.13.11
Iron enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/3-hydroxy-2-methylquinolin-4-one%202%2C4-dioxygenase | In enzymology, a 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase () is an enzyme that catalyzes the chemical reaction
3-hydroxy-2-methyl-1H-quinolin-4-one + O2 N-acetylanthranilate + CO
Thus, the two substrates of this enzyme are 3-hydroxy-2-methyl-1H-quinolin-4-one and O2, whereas its two products are N-acetylanthranilate and CO.
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-hydroxy-2-methyl-1H-quinolin-4-one 2,4-dioxygenase (CO-forming). This enzyme is also called (1H)-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase.
References
EC 1.13.11
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/3-hydroxy-4-oxoquinoline%202%2C4-dioxygenase | In enzymology, a 3-hydroxy-4-oxoquinoline 2,4-dioxygenase () is an enzyme that catalyzes the chemical reaction
3-hydroxy-1H-quinolin-4-one + O2 N-formylanthranilate + CO
Thus, the two substrates of this enzyme are 3-hydroxy-1H-quinolin-4-one and O2, whereas its two products are N-formylanthranilate and CO.
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-hydroxy-1H-quinolin-4-one 2,4-dioxygenase (CO-forming). Other names in common use include (1H)-3-hydroxy-4-oxoquinoline 2,4-dioxygenase, 3-hydroxy-4-oxo-1,4-dihydroquinoline 2,4-dioxygenase, 3-hydroxy-4(1H)-one, 2,4-dioxygenase, and quinoline-3,4-diol 2,4-dioxygenase.
References
EC 1.13.11
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/HAAO | 3-hydroxyanthranilate 3,4-dioxygenase () is an enzyme encoded by the HAAO gene that catalyzes the chemical reaction
3-hydroxyanthranilate + O2 2-amino-3-carboxymuconate semialdehyde
Thus, the two substrates of this enzyme are 3-hydroxyanthranilate and O2, whereas its product is 2-amino-3-carboxymuconate semialdehyde.
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-hydroxyanthranilate:oxygen 3,4-oxidoreductase (decyclizing). Other names in common use include 3-hydroxyanthranilate oxygenase, 3-hydroxyanthranilic acid oxygenase, 3-hydroxyanthranilic oxygenase, 3-hydroxyanthranilic acid oxidase and 3HAO. This enzyme participates in tryptophan metabolism. It employs one cofactor, iron.
Structural studies
As of late 2007, 6 structures have been solved for this class of enzymes, with PDB accession codes , , , , , and .h
References
Boyer, P.D., Lardy, H. and Myrback, K. (Eds.), The Enzymes, 2nd ed., vol. 8, Academic Press, New York, 1963, p. 353-371.
EC 1.13.11
Iron enzymes
Enzymes of known structure |
https://en.wikipedia.org/wiki/3-hydroxyanthranilate%20oxidase | In enzymology, a 3-hydroxyanthranilate oxidase () (also called 3-HAO) is an enzyme that catalyzes the chemical reaction:
3-hydroxyanthranilate + O2 6-imino-5-oxocyclohexa-1,3-dienecarboxylate + H2O2
Thus, the two substrates of this enzyme are 3-hydroxyanthranilate and O2, whereas its two products are 6-imino-5-oxocyclohexa-1,3-dienecarboxylate and H2O2.
This enzyme belongs to the family of oxidoreductases, specifically those acting on diphenols and related substances as donor with oxygen as acceptor. The systematic name of this enzyme class is 3-hydroxyanthranilate:oxygen oxidoreductase. This enzyme is also called 3-hydroxyanthranilic acid oxidase.
References
EC 1.10.3
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/4-hydroxymandelate%20synthase | In enzymology, a 4-hydroxymandelate synthase () is an enzyme that catalyzes the chemical reaction
4-hydroxyphenylpyruvate + O2 4-hydroxymandelate + CO2
Thus, the two substrates of this enzyme are 4-hydroxyphenylpyruvate and oxygen, whereas its two products are 4-hydroxymandelate and carbon dioxide.
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 4-hydroxyphenylpyruvate:oxygen oxidoreductase (decarboxylating). This enzyme is also called 4-hydroxyphenylpyruvate dioxygenase II.
References
EC 1.13.11
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/5%2C10-Methenyltetrahydromethanopterin%20hydrogenase | The 5,10-methenyltetrahydromethanopterin hydrogenase (or Hmd), the so-called iron-sulfur cluster-free hydrogenase, is an enzyme found in methanogenic archea such as Methanothermobacter marburgensis. It was discovered and first characterized by the Thauer group at the Max Planck Institute in Marburg. Hydrogenases are enzymes that either reduce protons or oxidize molecular dihydrogen.
Enzyme function
Methanogens rely on such enzymes to catalyze the reduction of CO2 to methane. One step in methanogenesis entails conversion of a methenyl group (formic acid oxidation state) to a methylene group (formaldehyde oxidation state).
Among the hydrogenase family of enzymes, Hmd is unique in that it does not directly reduce CO2 to CH4. The natural substrate of the enzyme is the organic compound methenyltetrahydromethanopterin. The organic compound includes a methenyl group bound to two tertiary amides. The methenyl group originated as CO2 before being incorporated into the substrate, which is catalytically reduced by H2 to methylenetetrahydromethanopterin as shown. Eventually the methylene group is further reduced and released as a molecule of methane.
The hydride transfer has also been shown to be stereospecific. Given that the substrate is planar the hydride originating from H2 is always added to the pro-R face. In the reverse reaction stereospecificity is maintained and the highlighted hydride is removed.
Chemical and physical properties
Hmd holoenzyme
The Hmd holoenzyme include |
https://en.wikipedia.org/wiki/7%2C8-dihydroxykynurenate%208%2C8a-dioxygenase | In enzymology, a 7,8-dihydroxykynurenate 8,8a-dioxygenase () is an enzyme that catalyzes the chemical reaction
7,8-dihydroxykynurenate + O2 5-(3-carboxy-3-oxopropenyl)-4,6-dihydroxypyridine-2-carboxylate
Thus, the two substrates of this enzyme are 7,8-dihydroxykynurenate and O2, whereas its product is 5-(3-carboxy-3-oxopropenyl)-4,6-dihydroxypyridine-2-carboxylate.
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 7,8-dihydroxykynurenate:oxygen 8,8a-oxidoreductase (decyclizing). Other names in common use include 7,8-dihydroxykynurenate oxygenase, and 7,8-dihydroxykynurenate 8,8alpha-dioxygenase. This enzyme participates in tryptophan metabolism. It employs one cofactor, iron.
References
EC 1.13.11
Iron enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Acetylacetone-cleaving%20enzyme | In enzymology, an acetylacetone-cleaving enzyme () is an enzyme that catalyzes the chemical reaction
pentane-2,4-dione + O2 acetate + 2-oxopropanal
Thus, the two substrates of this enzyme are pentane-2,4-dione and O2, whereas its two products are acetate and 2-oxopropanal.
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 acetylacetone:oxygen oxidoreductase. Other names in common use include Dke1, acetylacetone dioxygenase, diketone cleaving dioxygenase, and diketone cleaving enzyme.
References
EC 1.13.11
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Acireductone%20dioxygenase%20%28iron%28II%29-requiring%29 | Acireductone dioxygenase [iron(II)-requiring] () is an enzyme that catalyzes the chemical reaction
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2 4-(methylthio)-2-oxobutanoate + formate
Thus, the two substrates of this enzyme are 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one and oxygen, whereas its two products are 4-methylthio-2-oxobutanoate and formate.
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 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one:oxygen oxidoreductase (formate-forming). Other names in common use include ARD', 2-hydroxy-3-keto-5-thiomethylpent-1-ene dioxygenase (ambiguous), acireductone dioxygenase (ambiguous), E-2', and E-3 dioxygenase. This enzyme participates in methionine metabolism.
Structural studies
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code .
References
EC 1.13.11
Enzymes of known structure |
https://en.wikipedia.org/wiki/Acireductone%20dioxygenase%20%28Ni2%2B-requiring%29 | Acireductone dioxygenase (Ni2+-requiring) () is an enzyme that catalyzes the chemical reaction
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2 3-(methylthio)propanoate + formate + CO
Thus, the two substrates of this enzyme are 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one and oxygen, whereas its 3 products are 3-(methylthio)propanoate, formate, and carbon monoxide.
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 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one:oxygen oxidoreductase (formate- and CO-forming). Other names in common use include ARD, 2-hydroxy-3-keto-5-thiomethylpent-1-ene dioxygenase (ambiguous), acireductone dioxygenase (ambiguous), and E-2. This enzyme participates in methionine metabolism.
References
EC 1.13.11
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Apo-beta-carotenoid-14%27%2C13%27-dioxygenase | Apo-beta-carotenoid-14',13'-dioxygenase ( is an enzyme that catalyzes the chemical reaction
8'-apo-beta-carotenol + O2 14'-apo-beta-carotenal + uncharacterized product
Thus, the two substrates of this enzyme are 8'-apo-beta-carotenol and oxygen, whereas its two products are 14'-apo-beta-carotenal and an uncharacterized product that may be (3E,5E)-7-hydroxy-6-methylhepta-3,5-dien-2-one.
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 O with incorporation of one atom of oxygen (internal monooxygenases o internal mixed-function oxidases). The systematic name of this enzyme class is 8'-apo-beta-carotenol:O2 oxidoreductase.
References
EC 1.13.12
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Arachidonate%208-lipoxygenase | Arachidonate 8-lipoxygenase () is an enzyme that catalyzes the chemical reaction
arachidonate + O2 (5Z,9E,11Z,14Z)-(8R)-8-hydroperoxyicosa-5,9,11,14-tetraenoate
Thus, the two substrates of this enzyme are arachidonate and oxygen, whereas its product is (5Z,9E,11Z,14Z)-(8R)-8-hydroperoxyicosa-5,9,11,14-tetraenoate.
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 arachidonate:oxygen 8-oxidoreductase. Other names in common use include 8-lipoxygenase, and 8(R)-lipoxygenase. This enzyme participates in arachidonic acid metabolism.
Structural studies
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code .
References
EC 1.13.11
Enzymes of known structure |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.