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https://en.wikipedia.org/wiki/Arginine%202-monooxygenase | Arginine 2-monooxygenase () is an enzyme that catalyzes the chemical reaction
L-arginine + O2 4-guanidinobutanamide + CO2 + H2O
Thus, the two substrates of this enzyme are L-arginine and oxygen, whereas its 3 products are 4-guanidinobutanamide, carbon dioxide, and water.
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 L-arginine:oxygen 2-oxidoreductase (decarboxylating). Other names in common use include arginine monooxygenase, arginine decarboxylase, arginine oxygenase (decarboxylating), and arginine decarboxy-oxidase. This enzyme participates in urea cycle and metabolism of amino groups. It has one cofactor: the flavin FAD.
References
EC 1.13.12
Flavoproteins
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Ascorbate%202%2C3-dioxygenase | Ascorbate 2,3-dioxygenase () is an enzyme that catalyzes the chemical reaction
ascorbate + O2 + H2O oxalate + threonate
The 3 substrates of this enzyme are ascorbate, oxygen, and water, whereas its two products are oxalate and threonate.
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 ascorbate:oxygen 2,3-oxidoreductase (bond-cleaving). This enzyme is also called AAoxygenase. This enzyme participates in ascorbate and aldarate metabolism. It employs one cofactor, iron.
References
EC 1.13.11
Iron enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Biphenyl-2%2C3-diol%201%2C2-dioxygenase | Biphenyl-2,3-diol 1,2-dioxygenase () is an enzyme that catalyzes the chemical reaction
biphenyl-2,3-diol + O2 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate + H2O
Thus, the two substrates of this enzyme are biphenyl-2,3-diol and oxygen, whereas its two products are 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate and water.
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 biphenyl-2,3-diol:oxygen 1,2-oxidoreductase (decyclizing). Other names in common use include 2,3-dihydroxybiphenyl dioxygenase, and biphenyl-2,3-diol dioxygenase. This enzyme participates in gamma-hexachlorocyclohexane degradation and biphenyl degradation.
Structural studies
As of late 2007, 16 structures have been solved for this class of enzymes, with PDB accession codes , , , , , , , , , , , , , , , and .
References
EC 1.13.11
Enzymes of known structure |
https://en.wikipedia.org/wiki/Caffeate%203%2C4-dioxygenase | Caffeate 3,4-dioxygenase () is an enzyme that catalyzes the chemical reaction
3,4-dihydroxy-trans-cinnamate + O2 3-(2-carboxyethenyl)-cis,cis-muconate
Thus, the two substrates of this enzyme are 3,4-dihydroxy-trans-cinnamate (caffeic acid) and oxygen, whereas its product is 3-(2-carboxyethenyl)-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 3,4-dihydroxy-trans-cinnamate:oxygen 3,4-oxidoreductase (decyclizing). This enzyme participates in phenylpropanoid biodegradation.
References
EC 1.13.11
Enzymes of unknown structure
Hydroxycinnamic acids metabolism |
https://en.wikipedia.org/wiki/Chloridazon-catechol%20dioxygenase | Chloridazon-catechol dioxygenase () is an enzyme that catalyzes the chemical reaction
5-amino-4-chloro-2-(2,3-dihydroxyphenyl)-3(2H)-pyridazinone + O2 5-amino-4-chloro-2-(2-hydroxymuconoyl)-3(2H)-pyridazinone
Thus, the two substrates of this enzyme are 5-amino-4-chloro-2-(2,3-dihydroxyphenyl)-3(2H)-pyridazinone and oxygen, whereas its product is 5-amino-4-chloro-2-(2-hydroxymuconoyl)-3(2H)-pyridazinone.
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 5-amino-4-chloro-2-(2,3-dihydroxyphenyl)-3(2H)-pyridazinone 1,2-oxidoreductase (decyclizing). It employs one cofactor, iron.
References
EC 1.13.11
Iron enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Chloride%20peroxidase | Chloride peroxidase () is a family of enzymes that catalyzes the chlorination of organic compounds. This enzyme combines the inorganic substrates chloride and hydrogen peroxide to produce the equivalent of Cl+, which replaces a proton in hydrocarbon substrate:
R-H + Cl− + H2O2 + H+ → R-Cl + 2 H2O
In fact the source of "Cl+" is hypochlorous acid (HOCl). Many organochlorine compounds are biosynthesized in this way.
This enzyme belongs to the family of oxidoreductases, specifically those acting on a peroxide as acceptors (peroxidases). The systematic name of this enzyme class is chloride:hydrogen-peroxide oxidoreductase. This enzyme is also called chloroperoxidase. It employs one cofactor which may be either heme or vanadium.
The heme-containing chloroperoxidase (CPO) exhibits peroxidase, catalase and cytochrome P450-like activities in addition to catalyzing halogenation reactions. Despite functional similarities with other heme enzymes, the structure of CPO is unique, which folds into a tertiary structure dominated by eight helical segments. The catalytic acid base, required to cleave the peroxide O-O bond, is glutamic acid rather than histidine as in horseradish peroxidase.
Structural studies
As of late 2007, 30 structures have been solved for this class of enzymes, with PDB accession codes , , , , , , , , , , , , , , , , , , , , , , , , , , , , , and .
References
Further reading
EC 1.11.1
Heme enzymes
Enzymes of known structure |
https://en.wikipedia.org/wiki/Cyclin%20D2 | G1/S-specific cyclin-D2 is a protein that in humans is encoded by the CCND2 gene.
Function
The protein encoded by this gene belongs to the highly conserved cyclin family, whose members are characterized by a dramatic periodicity in protein abundance through the cell cycle. Cyclins function as regulators of cyclin-dependent kinases. Different cyclins exhibit distinct expression and degradation patterns which contribute to the temporal coordination of each mitotic event. This cyclin forms a complex with and functions as a regulatory subunit of CDK4 or CDK6, whose activity is required for cell cycle G1/S transition. This protein has been shown to interact with and be involved in the phosphorylation of tumor suppressor protein Rb. Knockout studies of the homologous gene in mouse suggest the essential roles of this gene in ovarian granulosa and germ cell proliferation. High level expression of this gene was observed in ovarian and testicular tumors.
Clinical significance
Mutations in CCND2 are associated to megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome.
References
Further reading
External links |
https://en.wikipedia.org/wiki/Chlorite%20dismutase | Chlorite dismutase, also known as Chlorite O2-lyase (), is an enzyme that catalyzes the chemical reaction
ClO → Cl− + O2
Reactions that generate oxygen molecules are exceedingly rare in biology and difficult to mimic synthetically. Perchlorate - respiring bacteria enzymatically detoxify chlorite, ClO, the end product of the perchlorate, ClO, respiratory pathway, by converting it to dioxygen, O2, and chloride, Cl−. Chlorite dismutase is a heme-containing protein, but it bears no structural or sequence relationships with known peroxidases or other heme proteins and is part of a large family of proteins with more than one biochemical function.
References
EC 1.13.11
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Coenzyme%20F420%20hydrogenase | In enzymology, a coenzyme F420 hydrogenase () is an enzyme that catalyzes the chemical reaction
H2 + coenzyme F420 reduced coenzyme F420
Thus, the two substrates of this enzyme are H2 and coenzyme F420, whereas its product is reduced coenzyme F420.
This enzyme belongs to the family of oxidoreductases, specifically those acting on hydrogen as donor with other, known, acceptors. The systematic name of this enzyme class is hydrogen:coenzyme F420 oxidoreductase. Other names in common use include 8-hydroxy-5-deazaflavin-reducing hydrogenase, F420-reducing hydrogenase, and coenzyme F420-dependent hydrogenase. This enzyme participates in folate biosynthesis and is a critical part of energy conservation in some methanogens such as Methanosarcina barkeri. It has 3 cofactors: iron, nickel, and deazaflavin.
References
EC 1.12.98
Iron enzymes
Nickel enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/CMA1 | Chymase is an enzyme that in humans is encoded by the CMA1 gene.
This gene product is a chymotryptic serine proteinase that belongs to the peptidase family S1. It is expressed in mast cells and thought to function in the degradation of the extracellular matrix, the regulation of submucosal gland secretion, and the generation of vasoactive peptides. In the heart and blood vessels, this protein, rather than angiotensin converting enzyme, is largely responsible for converting angiotensin I to the vasoactive peptide angiotensin II. Angiotensin II has been implicated in blood pressure control and in the pathogenesis of hypertension, cardiac hypertrophy, and heart failure. Thus, this gene product is a target for cardiovascular disease therapies. This gene maps to 14q11.2 in a cluster of genes encoding other proteases.
References
Further reading
External links |
https://en.wikipedia.org/wiki/Cypridina-luciferin%202-monooxygenase | In enzymology, a Cypridina-luciferin 2-monooxygenase () is an enzyme that catalyzes the chemical reaction
Cypridina luciferin + O2 oxidized Cypridina luciferin + CO2 + hnu
Thus, the two substrates of this enzyme are Cypridina luciferin and O2, whereas its 3 products are oxidized Cypridina luciferin, CO2, and light.
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 Cypridina-luciferin:oxygen 2-oxidoreductase (decarboxylating). Other names in common use include Cypridina-type luciferase, luciferase (Cypridina luciferin), and Cypridina luciferase.
The primary sequence was determined by cloning the cDNA.
References
EC 1.13.12
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Cysteamine%20dioxygenase | In enzymology, a cysteamine dioxygenase () is an enzyme that catalyzes the chemical reaction
2-aminoethanethiol + O2 hypotaurine
Thus, the two substrates of this enzyme are 2-aminoethanethiol and O2, whereas its product is hypotaurine.
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-aminoethanethiol:oxygen oxidoreductase. Other names in common use include persulfurase, cysteamine oxygenase, and cysteamine:oxygen oxidoreductase. This enzyme participates in taurine and hypotaurine metabolism. It employs one cofactor, iron.
References
EC 1.13.11
Iron enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Cytochrome-c3%20hydrogenase | In enzymology, a cytochrome-c3 hydrogenase () is an enzyme that catalyzes the chemical reaction
2 H2 + ferricytochrome c3 4 H+ + ferrocytochrome c3
Thus, the two substrates of this enzyme are H2 and ferricytochrome c3, whereas its two products are H+ and ferrocytochrome c3.
This enzyme belongs to the family of oxidoreductases, specifically those acting on hydrogen as donor with a cytochrome as acceptor. The systematic name of this enzyme class is hydrogen:ferricytochrome-c3 oxidoreductase. Other names in common use include H2:ferricytochrome c3 oxidoreductase, cytochrome c3 reductase, cytochrome hydrogenase, and hydrogenase [ambiguous]. It has 3 cofactors: iron, Nickel, and Iron-sulfur.
Structural studies
As of late 2007, 19 structures have been solved for this class of enzymes, with PDB accession codes , , , , , , , , , , , , , , , , , , and .
References
EC 1.12.2
Iron enzymes
Nickel enzymes
Iron-sulfur enzymes
Enzymes of known structure |
https://en.wikipedia.org/wiki/MYBL2 | Myb-related protein B is a protein that in humans is encoded by the MYBL2 gene.
Function
The protein encoded by this gene, a member of the MYB family of transcription factor genes, is a nuclear protein involved in cell cycle progression. The encoded protein is phosphorylated by cyclin A/cyclin-dependent kinase 2 during the S-phase of the cell cycle and possesses both activator and repressor activities. It has been shown to activate the cell division cycle 2, cyclin D1, and insulin-like growth factor-binding protein 5 genes. Transcript variants may exist for this gene, but their full-length natures have not been determined. MYBL2 is deregulated in various cancer types and can contribute to cancer progression.
Interactions
MYBL2 has been shown to interact with:
CDK9
CREB-binding protein
Cyclin A1
Cyclin-dependent kinase inhibitor 1C
EP300
PARP1
Retinoblastoma-like protein 1
References
Further reading
External links
Transcription factors |
https://en.wikipedia.org/wiki/Fatty-acid%20peroxidase | In enzymology, a fatty-acid peroxidase () is an enzyme that catalyzes the chemical reaction
palmitate + 2 H2O2 pentadecanal + CO2 + 3 H2O
Thus, the two substrates of this enzyme are palmitate and H2O2, whereas its 3 products are pentadecanal, CO2, and H2O.
This enzyme belongs to the family of oxidoreductases, specifically those acting on a peroxide as acceptor (peroxidases). The systematic name of this enzyme class is hexadecanoate:hydrogen-peroxide oxidoreductase. This enzyme is also called long chain fatty acid peroxidase.
References
EC 1.11.1
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Gentisate%201%2C2-dioxygenase | In enzymology, a gentisate 1,2-dioxygenase () is an enzyme that catalyzes the chemical reaction
2,5-dihydroxybenzoate + O2 maleylpyruvate
Thus, the two substrates of this enzyme are 2,5-dihydroxybenzoate and O2, whereas its product is 3-maleylpyruvate.
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 gentisate:oxygen 1,2-oxidoreductase (decyclizing). Other names in common use include gentisate oxygenase, 2,5-dihydroxybenzoate dioxygenase, gentisate dioxygenase, and gentisic acid oxidase. This enzyme participates in tyrosine metabolism. It employs one cofactor, iron.
Structural studies
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code .
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/Hydrogenase%20%28acceptor%29 | In enzymology, a hydrogenase (acceptor) () is an enzyme that catalyzes the chemical reaction
H2 + A AH2
Thus, the two substrates of this enzyme are H2 and A, whereas its product is AH2.
This enzyme belongs to the family of oxidoreductases, specifically those acting on hydrogen as donor with other acceptors. The systematic name of this enzyme class is hydrogen:acceptor oxidoreductase. Other names in common use include H2 producing hydrogenase[ambiguous], hydrogen-lyase[ambiguous], hydrogenlyase[ambiguous], uptake hydrogenase[ambiguous], and hydrogen:(acceptor) oxidoreductase.
References
EC 1.12.99
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/RAD9A | Cell cycle checkpoint control protein RAD9A is a protein that in humans is encoded by the RAD9A gene.Rad9 has been shown to induce G2 arrest in the cell cycle in response to DNA damage in yeast cells. Rad9 was originally found in budding yeast cells but a human homolog has also been found and studies have suggested that the molecular mechanisms of the S and G2 checkpoints are conserved in eukaryotes. Thus, what is found in yeast cells are likely to be similar in human cells.
Function
This gene product is highly similar to S. pombe rad9, a cell cycle checkpoint protein required for cell cycle arrest and DNA damage repair in response to DNA damage. This protein is found to possess 3' to 5' exonuclease activity, which may contribute to its role in sensing and repairing DNA damage. It forms a checkpoint protein complex with Rad1 and Hus1. This is also known as the Rad9-Rad1-Hus1 or 9-1-1 complex. This complex is recruited by checkpoint protein Rad17 to the sites of DNA damage, which is thought to be important for triggering the checkpoint-signaling cascade. Use of alternative polyA sites has been noted for this gene. This complex plays a role in DNA base excision repair. Hus1 binds and stimulates MYH DNA glycosylase which stimulates base excision repair. Rad9 binds with the strongest affinity to DNA which attaches the complex to damaged DNA. Rad1 recruits other base excision factors. Previous research has suggested that Rad9 is not necessary to repair DNA, but it does not m |
https://en.wikipedia.org/wiki/Hydrogen%20dehydrogenase | In enzymology, a hydrogen dehydrogenase () is an enzyme that catalyzes the chemical reaction
H2 + NAD+ H+ + NADH
Thus, the two substrates of this enzyme are H2 and NAD+, whereas its two products are H+ and NADH.
This enzyme belongs to the family of oxidoreductases, specifically those acting on hydrogen as donor with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is hydrogen:NAD+ oxidoreductase. Other names in common use include H2:NAD+ oxidoreductase, NAD+-linked hydrogenase, bidirectional hydrogenase, and hydrogenase. This enzyme participates in glyoxylate and dicarboxylate metabolism and methane metabolism. It has 6 cofactors: FAD, Iron, FMN, Flavin, Nickel, and Iron-sulfur.
References
EC 1.12.1
NADH-dependent enzymes
Flavoproteins
Iron enzymes
Nickel enzymes
Iron-sulfur enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Hydrogen%20dehydrogenase%20%28NADP%2B%29 | In enzymology, a hydrogen dehydrogenase (NADP+) () is an enzyme that catalyzes the chemical reaction
H2 + NADP+ H+ + NADPH
Thus, the two substrates of this enzyme are H2 and NADP+, whereas its two products are H+ and NADPH.
This enzyme belongs to the family of oxidoreductases, specifically those acting on hydrogen as donor with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is hydrogen:NADP+ oxidoreductase. Other names in common use include NADP+-linked hydrogenase, NADP+-reducing hydrogenase, hydrogen dehydrogenase (NADP+), and simply hydrogenase (which is ambiguous).
Structural studies
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code .
References
EC 1.12.1
NADPH-dependent enzymes
Enzymes of known structure |
https://en.wikipedia.org/wiki/Hydrogen%3Aquinone%20oxidoreductase | In enzymology, a hydrogen:quinone oxidoreductase () is an enzyme that catalyzes the chemical reaction
H2 + quinone quinol
Thus, the two substrates of this enzyme are H2 and quinone, whereas its product is quinol. The quinone can be menaquinone, ubiquinone, demethylmenaquinone or methionaquinone.
This enzyme belongs to the family of oxidoreductases, specifically those acting on hydrogen as donor with a quinone or similar compound as acceptor. The systematic name of this enzyme class is hydrogen:quinone oxidoreductase. Other names in common use include hydrogen-ubiquinone oxidoreductase, hydrogen:menaquinone oxidoreductase, membrane-bound hydrogenase, and quinone-reactive Ni/Fe-hydrogenase.
References
EC 1.12.5
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Hydroxyquinol%201%2C2-dioxygenase | In enzymology, a hydroxyquinol 1,2-dioxygenase () is an enzyme that catalyzes the chemical reaction
benzene-1,2,4-triol + O2 3-hydroxy-cis,cis-muconate
Thus, the two substrates of this enzyme are benzene-1,2,4-triol (hydroxyquinol) and O2, whereas its product is 3-hydroxy-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 benzene-1,2,4-triol:oxygen 1,2-oxidoreductase (decyclizing). This enzyme is also called hydroxyquinol dioxygenase. This enzyme participates in benzoate degradation via hydroxylation and 1,4-dichlorobenzene degradation. It employs one cofactor, iron.
Structural studies
, only one structure has been solved for this class of enzymes, with the PDB accession code .
References
EC 1.13.11
Iron enzymes
Enzymes of known structure
Natural phenols metabolism |
https://en.wikipedia.org/wiki/Indole%202%2C3-dioxygenase | In enzymology, an indole 2,3-dioxygenase () is an enzyme that catalyzes the chemical reaction
indole + O2 2-formylaminobenzaldehyde
Thus, the two substrates of this enzyme are indole and O2, whereas its product is 2-formylaminobenzaldehyde.
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 indole:oxygen 2,3-oxidoreductase (decyclizing). Other names in common use include indole oxidase, indoleamine 2,3-dioxygenase (ambiguous), indole:O2 oxidoreductase, indole-oxygen 2,3-oxidoreductase (decyclizing), and IDO (ambiguous). This enzyme participates in tryptophan metabolism. It has 3 cofactors: copper, Flavin, and Flavoprotein.
Indole dioxygenase is not specific to indole but rather operates on a broad range of indole derivatives, including the amino acids tryptophan and 5-hydroxytryptophan (5-HTP), and many indole-analog plant phytochemicals. IDO is a peripheral enzyme, in contrast to tryptophan oxidase, an enzyme of similar amino acid sequence, which is active only in the liver. IDO is induced (produced on demand) by activation of inflammatory processes involving cytokine expression by white blood cells.
References
EC 1.13.11
Copper enzymes
Flavoproteins
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Lactate%202-monooxygenase | In enzymology, a lactate 2-monooxygenase () is an enzyme that catalyzes the chemical reaction
(S)-lactate + O2 acetate + CO2 + H2O
Thus, the two substrates of this enzyme are (S)-lactate and O2, whereas its 3 products are acetate, CO2, and H2O.
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 (S)-lactate:oxygen 2-oxidoreductase (decarboxylating). Other names in common use include lactate oxidative decarboxylase, lactate oxidase, lactic oxygenase, lactate oxygenase, lactic oxidase, L-lactate monooxygenase, lactate monooxygenase, and L-lactate-2-monooxygenase. This enzyme participates in pyruvate metabolism. It employs one cofactor, FMN.
Structural studies
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code .
References
EC 1.13.12
Flavoproteins
Enzymes of known structure |
https://en.wikipedia.org/wiki/L-ascorbate%20oxidase | In enzymology, a L-ascorbate oxidase () is an enzyme that catalyzes the chemical reaction
2 L-ascorbate + O2 2 dehydroascorbate + 2 H2O
Thus, the two substrates of this enzyme are L-ascorbate and O2, whereas its two products are dehydroascorbate and H2O.
Function
This enzyme belongs to the family of oxidoreductases, specifically those acting on diphenols and related substances as donor with oxygen as acceptor. This enzyme participates in ascorbate metabolism. It employs one cofactor, copper.
Nomenclature
The systematic name of this enzyme class is L-ascorbate:oxygen oxidoreductase. Other names in common use include ascorbase, ascorbic acid oxidase, ascorbate oxidase, ascorbic oxidase, ascorbate dehydrogenase, L-ascorbic acid oxidase, AAO, L-ascorbate:O2 oxidoreductase, and AA oxidase.
References
Further reading
EC 1.10.3
Copper enzymes
Enzymes of known structure |
https://en.wikipedia.org/wiki/CUL1 | Cullin 1, also known as CUL1, is a human protein and gene from cullin family.
This protein plays an important role in protein degradation and protein ubiquitination.
This is an essential component of the SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complex, which mediates the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. In the SCF complex, it serves as a rigid scaffold that organizes the SKP1-F-box protein and RBX1 subunits. May contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme.
This protein is a part of a SCF complex consisting of CUL1, RBX1, SKP1 and SKP2. It also interacts with RNF7. Part of a complex with TIP120A/CAND1 and RBX1. The unneddylated form interacts with TIP120A/CAND1 and the interaction negatively regulates the association with SKP1 in the SCF complex. Interacts with COPS2.
It is expressed in lung fibroblasts.
The protein is neddylated, which enhances the ubiquitination activity of SCF. Deneddylated via its interaction with the COP9 signalosome (CSN) complex.
Further reading
External links |
https://en.wikipedia.org/wiki/Lignin%20peroxidase | In enzymology, a lignin peroxidase () is an enzyme that catalyzes the chemical reaction
1,2-bis(3,4-dimethoxyphenyl)propane-1,3-diol + H2O2 3,4-dimethoxybenzaldehyde + 1-(3,4-dimethoxyphenyl)ethane-1,2-diol + H2O
Thus, the two substrates of this enzyme are 1,2-bis(3,4-dimethoxyphenyl)propane-1,3-diol and H2O2, whereas its 3 products are 3,4-dimethoxybenzaldehyde, 1-(3,4-dimethoxyphenyl)ethane-1,2-diol, and H2O.
This enzyme belongs to the family of oxidoreductases, specifically those acting on a peroxide as acceptor (peroxidases) and can be included in the broad category of ligninases. The systematic name of this enzyme class is 1,2-bis(3,4-dimethoxyphenyl)propane-1,3-diol:hydrogen-peroxide oxidoreductase. Other names in common use include diarylpropane oxygenase, ligninase I, diarylpropane peroxidase, LiP, diarylpropane:oxygen,hydrogen-peroxide oxidoreductase (C-C-bond-cleaving). It employs one cofactor, heme.
Background
Lignin is highly resistant to biodegradation and only higher fungi and some bacteria are capable of degrading the polymer via an oxidative process. This process has been studied extensively in the past twenty years, but the mechanism has not yet been fully elucidated.
Lignin is found to be degraded by enzyme lignin peroxidases produced by some fungi like Phanerochaete chrysosporium. The mechanism by which lignin peroxidase (LiP) interacts with the lignin polymer involves veratrole alcohol, which is a secondary metabolite of white rot fungi that acts as |
https://en.wikipedia.org/wiki/Lignostilbene%20alphabeta-dioxygenase | In enzymology, a lignostilbene alphabeta-dioxygenase () is an enzyme that catalyzes the chemical reaction
1,2-bis(4-hydroxy-3-methoxyphenyl)ethylene + O2 2 vanillin
Thus, the two substrates of this enzyme are 1,2-bis(4-hydroxy-3-methoxyphenyl)ethylene and O2, whereas its product is vanillin.
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-bis(4-hydroxy-3-methoxyphenyl)ethylene:oxygen oxidoreductase (alphabeta-bond-cleaving). It employs one cofactor, iron.
References
EC 1.13.11
Iron enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Linoleate%2011-lipoxygenase | In enzymology, a linoleate 11-lipoxygenase () is an enzyme that catalyzes the chemical reaction
linoleate + O2 (9Z,12Z)-(11S)-11-hydroperoxyoctadeca-9,12-dienoate
Thus, the two substrates of this enzyme are linoleate and O2, whereas its product is (9Z,12Z)-(11S)-11-hydroperoxyoctadeca-9,12-dienoate.
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 linoleate:oxygen 11S-oxidoreductase. This enzyme is also called linoleate dioxygenase, manganese lipoxygenase. This enzyme participates in linoleic acid metabolism.
References
EC 1.13.11
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Linoleate%20diol%20synthase | In enzymology, a linoleate diol synthase () is an enzyme that catalyzes the chemical reaction
linoleate + O2 (9Z,12Z)-(7S,8S)-dihydroxyoctadeca-9,12-dienoate
Thus, the two substrates of this enzyme are linoleate and O2, whereas its product is (9Z,12Z)-(7S,8S)-dihydroxyoctadeca-9,12-dienoate.
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 linoleate:oxygen 7S,8S-oxidoreductase. This enzyme is also called linoleate (8R)-dioxygenase. This enzyme participates in linoleic acid metabolism.
References
EC 1.13.11
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Lysine%202-monooxygenase | In enzymology, a lysine 2-monooxygenase () is an enzyme that catalyzes the chemical reaction
L-lysine + O2 5-aminopentanamide + CO2 + H2O
Thus, the two substrates of this enzyme are L-lysine and O2, whereas its 3 products are 5-aminopentanamide, CO2, and H2O.
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 L-lysine:oxygen 2-oxidoreductase (decarboxylating). Other names in common use include lysine oxygenase, lysine monooxygenase, and L-lysine-2-monooxygenase. This enzyme participates in lysine degradation. It employs one cofactor, FAD.
References
EC 1.13.12
Flavoproteins
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Caspase%2010 | Caspase-10 is an enzyme that, in humans, is encoded by the CASP10 gene.
This gene encodes a protein that is a member of the cysteine-aspartic acid protease (caspase) family. Sequential activation of caspases plays a central role in the execution-phase of cell apoptosis. Caspases exist as inactive proenzymes that undergo proteolytic processing at conserved aspartic residues to produce two subunits, large and small, that dimerize to form the active enzyme.
That protein cleaves and activates caspases 3 and 7, and the protein itself is processed by caspase 8. Mutations in this gene are associated with apoptosis defects seen in type II autoimmune lymphoproliferative syndrome. Three alternatively spliced transcript variants encoding different isoforms have been described for this gene.
Interactions
Caspase 10 has been shown to interact with FADD, CFLAR, Caspase 8, Fas receptor, RYBP, TNFRSF1A and TNFRSF10B.
See also
The Proteolysis Map
References
Further reading
External links
GeneReviews/NCBI/NIH/UW entry on Autoimmune Lymphoproliferative Syndrome
The MEROPS online database for peptidases and their inhibitors: C14.011
Enzymes
Caspases |
https://en.wikipedia.org/wiki/FBLN1 | FBLN1 is the gene encoding fibulin-1, an extracellular matrix and plasma protein.
Function
Fibulin-1 is a secreted glycoprotein that is found in association with extracellular matrix structures including fibronectin-containing fibers, elastin-containing fibers and basement membranes. Fibulin-1 binds to a number of extracellular matrix constituents including fibronectin, nidogen-1, and the proteoglycan, versican. Fibulin-1 is also a blood protein capable of binding to fibrinogen.
Structure
Fibulin-1 has modular domain structure and includes a series of nine epidermal growth factor-like modules followed by a fibulin-type module, a module found in all members of the fibulin gene family.
The human fibulin-1 gene, FBLN1, encodes four splice variants designated fibulin-1A, B, C and D, which differ in their carboxy terminal regions. In mouse, chicken and the nematode, C. elegans, only two fibulin-1 variants are produced, fibulin-1C and fibulin-1D.
Interactions
FBLN1 has been shown to interact with:
NOV/CCN3,
amyloid precursor protein,
entactin,
fibrinogen, and
fibronectin.
See also
Synpolydactyly
References
Further reading |
https://en.wikipedia.org/wiki/PRMT1 | Protein arginine N-methyltransferase 1 is an enzyme that in humans is encoded by the PRMT1 gene. The HRMT1L2 gene encodes a protein arginine methyltransferase that functions as a histone methyltransferase specific for histone H4.
Function
PRMT1 gene encodes for the protein arginine methyltransferase that functions as a histone methyltransferase specific for histone H4 in eukaryotic cells. Specifically altering histone H4 in eukaryotes gives it the ability to remodel chromatin acting as a post-translational modifier.
Through regulation of gene expression, arginine methyltransferases control the cell cycle and death of eukaryotic cells.
Reaction pathway
While all PRMT enzymes catalyze the methylation of arginine residues in proteins, PRMT1 is unique in that is catalyzes the formation of asymmetric dimethylarginine as opposed to the PRMT2 that catalyzes the formation of symmetrically dimethylated arginine. Individual PRMT utilize S-adenosyl-L-methionine (SAM) as the methyl donor and catalyze methyl group transfer to the ω-nitrogen of an arginine residue.
Clinical significance
In humans, these enzymes regulate gene expression and hence are involved in pathogenesis of many human diseases. Using enzyme inhibitors for arginine methyltransferase 1, studies were able to demonstrate the enzyme's potential as an early catalyst of various cancers.
Interactions
PRMT1 has been shown to interact with:
BTG1,
BTG2,
DHX9,
FUS,
HNRNPR,
HNRPK,
IFNAR1,
ILF3,
KHDRBS1, |
https://en.wikipedia.org/wiki/Microtubule-associated%20protein%202 | Microtubule-associated protein 2 is a protein in humans that is encoded by the MAP2 gene.
Function
This gene encodes a protein that belongs to the microtubule-associated protein family. The proteins of this family were originally isolated since they copurify with tubulin in polymerization experiments: tubulin in cell extracts can be made to polymerize to produce microtubules (MT) under the influence of heat and the addition of GTP, and the MT can then be collected by centrifugation. When this is done a series of microtubule associated proteins are collected along with the MT and can be detected by SDS-PAGE and other methods. Brain extracts are rich in several of these proteins, MAP2 being one of these. The single MAP2 gene produces four major transcripts producing four proteins, MAP2A, MAP2B, MAP2C and MAP2D. MAP2A and MAP2B are very high molecular weight proteins, with apparent molecular weight on SDS-PAGE about 250kDa, while MAP2C and MAP2D are much lower molecular weight forms with apparent SDS-PAGE size about 70kDa. All forms of MAP2 share a common core sequence which includes MT binding domains, 18 amino acid sequences which are found in other MT associated proteins such as MAP Tau and MAP1B. The MAP2 isoforms are thought to be involved in MT assembly, which is an essential step in neuritogenesis. MAP2 serves to stabilize MT growth by crosslinking MT with intermediate filaments and other MTs. MAP2 isoforms are neuron-specific cytoskeletal proteins enriched in dendrit |
https://en.wikipedia.org/wiki/Manganese%20peroxidase | In enzymology, a manganese peroxidase () is an enzyme that catalyzes the chemical reaction
2 Mn(II) + 2 H+ + H2O2 2 Mn(III) + 2 H2O
The 3 substrates of this enzyme are Mn(II), H+, and H2O2, whereas its two products are Mn(III) and H2O.
This enzyme belongs to the family of oxidoreductases, to be specific those acting on a peroxide as acceptor (peroxidases). The systematic name of this enzyme class is Mn(II):hydrogen-peroxide oxidoreductase. Other names in common use include peroxidase-M2, and Mn-dependent (NADH-oxidizing) peroxidase. It employs one cofactor, heme. This enzyme needs Ca2+ for activity.
White rot fungi secrete this enzyme to aid lignin degradation.
Discovery and characterization
Manganese peroxidase (commonly referred to as MnP) was discovered in 1985 simultaneously by the research groups of Michael H. Gold and Ronald Crawford in the fungus Phanerochaete chrysosporium. The protein was genetically sequenced in P. chrysoporium in 1989. The enzyme is thought to be unique to Basidiomycota as no bacterium, yeast, or mold species has yet been found which naturally produces it.
Reaction mechanism
MnP catalysis occurs in a series of irreversible oxidation-reduction (redox) reactions which follow a ping-pong mechanism with second order kinetics. In the first step of the catalytic cycle, H2O2, or an organic peroxide, enters the active site of MnP. There the oxygen in H2O2 binds to an Fe(III) ion in the heme cofactor to form an iron peroxide complex. Two electro |
https://en.wikipedia.org/wiki/Methanosarcina-phenazine%20hydrogenase | In enzymology, a Methanosarcina-phenazine hydrogenase () is an enzyme that catalyzes the chemical reaction
H2 + 2-(2,3-dihydropentaprenyloxy)phenazine 2-dihydropentaprenyloxyphenazine
Thus, the two substrates of this enzyme are H2 and 2-(2,3-dihydropentaprenyloxy)phenazine, whereas its product is 2-dihydropentaprenyloxyphenazine.
This enzyme belongs to the family of oxidoreductases, specifically those acting on hydrogen as donor with other, known, acceptors. The systematic name of this enzyme class is hydrogen:2-(2,3-dihydropentaprenyloxy)phenazine oxidoreductase. Other names in common use include methanophenazine hydrogenase, and methylviologen-reducing hydrogenase.
References
EC 1.12.98
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Pyruvate%20dehydrogenase%20%28lipoamide%29%20alpha%201 | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial is an enzyme that in humans is encoded by the PDHA1 gene.The pyruvate dehydrogenase complex is a nuclear-encoded mitochondrial matrix multienzyme complex that provides the primary link between glycolysis and the tricarboxylic acid (TCA) cycle by catalyzing the irreversible conversion of pyruvate into acetyl-CoA. The PDH complex is composed of multiple copies of 3 enzymes: E1 (PDHA1); dihydrolipoyl transacetylase (DLAT) (E2; EC 2.3.1.12); and dihydrolipoyl dehydrogenase (DLD) (E3; EC 1.8.1.4). The E1 enzyme is a heterotetramer of 2 alpha and 2 beta subunits. The E1-alpha subunit contains the E1 active site and plays a key role in the function of the PDH complex.
Structure
The PDHA1 gene has about 17 kilobase pairs; it contains 11 exons, which range from 61 to 174 base pairs, and introns, whose sizes range from 600 base pairs to 5.7 kilobase pairs. The splice donor and acceptor sites present within the gene all conform to GT/AC rule of splicing. The DNA sequence in the transcription initiation site is very GC-rich. There is a "TATA box"-like sequence and a "CAAT present upstream from the cap site. There are also several sets of repeats, sequences resembling the Sp1 transcription factor binding site, and two cAMP receptor binding sites upstream of the cap.
The preliminary peptide encoded by this gene was 29 amino acids at the very start of the sequence that correspond to a typical mitochondrial ta |
https://en.wikipedia.org/wiki/NADH%20peroxidase | In enzymology, a NADH peroxidase () is an enzyme that catalyzes the chemical reaction
NADH + H+ + H2O2 NAD+ + 2 H2O
The presumed function of NADH peroxidase is to inactivate H2O2 generated within the cell, for example by glycerol-3-phosphate oxidase during glycerol metabolism or dismutation of superoxide, before the H2O2 causes damage to essential cellular components.
The 3 substrates of this enzyme are NADH, H+, and H2O2, whereas its two products are NAD+ and H2O. It employs one cofactor, FAD, however no discrete FADH2 intermediate has been observed.
This enzyme belongs to the family of oxidoreductases, specifically those acting on a peroxide as acceptor (peroxidases). The systematic name of this enzyme class is NADH:hydrogen-peroxide oxidoreductase. Other names in common use include DPNH peroxidase, NAD peroxidase, diphosphopyridine nucleotide peroxidase, NADH-peroxidase, nicotinamide adenine dinucleotide peroxidase, and NADH2 peroxidase.
Structure
The crystal structure of NADH peroxidase resembles glutathione reductase with respect to chain fold and location as well as conformation of the prosthetic group FAD
His10 of the NADH peroxidase is located near the N-terminus of the R1 helix within the FAD-binding site. One of the oxygen atoms of Cys42-SO3H is hydrogen-bonded both to the His10 imidazole and to Cys42 N terminus. The His10 functions in part to stabilize the unusual Cys42-SOH redox center. Arg303 also stabilizes the Cys42-SO3H. Glu-14 participates in formi |
https://en.wikipedia.org/wiki/NADPH%20peroxidase | In enzymology, a NADPH peroxidase () is an enzyme that catalyzes the chemical reaction
NADPH + H+ + H2O2 NADP+ + 2 H2O
The 3 substrates of this enzyme are NADPH, H+, and H2O2, whereas its two products are NADP+ and H2O.
This enzyme belongs to the family of oxidoreductases, specifically those acting on a peroxide as acceptor (peroxidases). The systematic name of this enzyme class is NADPH:hydrogen-peroxide oxidoreductase. Other names in common use include TPNH peroxidase, NADP peroxidase, nicotinamide adenine dinucleotide phosphate peroxidase, TPN peroxidase, triphosphopyridine nucleotide peroxidase, and NADPH2 peroxidase.
References
EC 1.11.1
NADPH-dependent enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Oplophorus-luciferin%202-monooxygenase | In enzymology, an Oplophorus-luciferin 2-monooxygenase (), also known as Oplophorus luciferase (referred in this article as OpLuc) is a luciferase, an enzyme, from the deep-sea shrimp Oplophorus gracilirostris [2], belonging to a group of coelenterazine luciferases. Unlike other luciferases, it has a broader substrate specificity [3,4,6] and can also bind to bisdeoxycoelenterazine efficiently [3,4]. It is the third example of a luciferase (Other than Aequorea and Renilla) to be purified in lab [2]. The systematic name of this enzyme class is Oplophorus-luciferin:oxygen 2-oxidoreductase (decarboxylating). This enzyme is also called Oplophorus luciferase.
Chemical reaction
The two substrates of this enzyme are the luciferin, Coelenterazine and O2 and its 3 products are the oxyluciferin, Coelenteramide, CO2, and light.
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). Although the enzyme is part of the group of enzymes that act on coelenterazine, such as Renilla and Gaussia luciferases, it does not share base pair sequences with these enzymes [3,4,5,7].
OpLuc catalyzes the ATP independent chemical reaction [3,4,5,6]:
coelenterazine (Oplophorus luciferin) + O2 coelenteramide + CO2 + hν |
https://en.wikipedia.org/wiki/Peptide-tryptophan%202%2C3-dioxygenase | In enzymology, a peptide-tryptophan 2,3-dioxygenase () is an enzyme that catalyzes the chemical reaction
peptide tryptophan + O2 peptide formylkynurenine
Thus, the two substrates of this enzyme are peptide tryptophan and O2, whereas its product is peptide formylkynurenine.
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 peptide-tryptophan:oxygen 2,3-oxidoreductase (decyclizing). Other names in common use include pyrrolooxygenase, peptidyltryptophan 2,3-dioxygenase, and tryptophan pyrrolooxygenase.
References
EC 1.13.11
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Phenylalanine%202-monooxygenase | In enzymology, a phenylalanine 2-monooxygenase () is an enzyme that catalyzes the chemical reaction
L-phenylalanine + O2 2-phenylacetamide + CO2 + H2O
Thus, the two substrates of this enzyme are L-phenylalanine and O2, whereas its 3 products are 2-phenylacetamide, CO2, and H2O.
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 L-phenylalanine:oxygen 2-oxidoreductase (decarboxylating). Other names in common use include L-phenylalanine oxidase (deaminating and decarboxylating), and phenylalanine (deaminating, decarboxylating)oxidase. This enzyme participates in phenylalanine metabolism.
References
EC 1.13.12
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Folate%20transporter%201 | Folate transporter 1 is a protein which in humans is encoded by the SLC19A1 gene.
Function
Transport of folate compounds into mammalian cells can occur via receptor-mediated (see folate receptor 1) or carrier-mediated mechanisms. A functional coordination between these 2 mechanisms has been proposed to be the method of folate uptake in certain cell types. Methotrexate (MTX) is an antifolate chemotherapeutic agent that is actively transported by the carrier-mediated uptake system. RFC1 plays a role in maintaining intracellular concentrations of folate. SLC19A1 has also been shown to transport the immune second messenger 2'3'-cGAMP.
Clinical significance
Individuals carrying a specific polymorphism of SLC19A1 (c.80GG) have lower levels of folate. Other studies have also shown that individuals carrying the c.80AA polymorphism who are treated with methotrexate have higher levels of this anti-folate chemotherapeutic agent. Personalized dosing of the drug depending on the patient's genotype may therefore be required.
Alternative names
Reduced folate carrier 1
Intestinal folate carrier 1
See also
Solute carrier family
Folate-binding protein
Reduced folate carrier family
References
Further reading
Solute carrier family |
https://en.wikipedia.org/wiki/Phospholipid-hydroperoxide%20glutathione%20peroxidase | In enzymology, a phospholipid-hydroperoxide glutathione peroxidase () is an enzyme that catalyzes the chemical reaction
2 glutathione + a lipid hydroperoxide glutathione disulfide + lipid + 2 H2O
Thus, the two substrates of this enzyme are glutathione and lipid hydroperoxide, whereas its 3 products are glutathione disulfide, lipid, and H2O.
This enzyme belongs to the family of oxidoreductases, to be specific those acting on a peroxide as acceptor (peroxidases). The systematic name of this enzyme class is glutathione:lipid-hydroperoxide oxidoreductase. Other names in common use include peroxidation-inhibiting protein, PHGPX, peroxidation-inhibiting protein: peroxidase, glutathione, (phospholipid hydroperoxide-reducing), phospholipid hydroperoxide glutathione peroxidase, hydroperoxide glutathione peroxidase, or glutathione peroxidase 4 (GPX4). This enzyme participates in glutathione metabolism.
Structural studies
As of late 2007, two structures have been solved for this class of enzymes, with PDB accession codes and .
References
EC 1.11.1
Enzymes of known structure |
https://en.wikipedia.org/wiki/SOD3 | Extracellular superoxide dismutase [Cu-Zn] is an enzyme that in humans is encoded by the SOD3 gene.
This gene encodes a member of the superoxide dismutase (SOD) protein family. SODs are antioxidant enzymes that catalyze the dismutation of two superoxide radicals into hydrogen peroxide and oxygen. The product of this gene is thought to protect the brain, lungs, and other tissues from oxidative stress. The protein is secreted into the extracellular space and forms a glycosylated homotetramer that is anchored to the extracellular matrix (ECM) and cell surfaces through an interaction with heparan sulfate proteoglycan and collagen. A fraction of the protein is cleaved near the C-terminus before secretion to generate circulating tetramers that do not interact with the ECM.
Among black garden ants (Lasius niger), the lifespan of queens is an order of magnitude greater than of workers despite no systematic nucleotide sequence difference between them. The SOD3 gene was found to be the most differentially over-expressed gene in the brains of queen vs worker ants. This finding raises the possibility that SOD3 antioxidant activity plays a key role in the striking longevity of social insect queens.
References
Further reading
Oxidoreductases
Copper enzymes
Zinc enzymes |
https://en.wikipedia.org/wiki/Protocatechuate%203%2C4-dioxygenase | In enzymology, a protocatechuate 3,4-dioxygenase () is an enzyme that catalyzes the chemical reaction
3,4-dihydroxybenzoate + O2 3-carboxy-cis,cis-muconate
Thus, the two substrates of this enzyme are 3,4-dihydroxybenzoate (protocatechuic acid) and O2, whereas its product is 3-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 systematic name of this enzyme class is protocatechuate:oxygen 3,4-oxidoreductase (decyclizing). Other names in common use include protocatechuate oxygenase, protocatechuic acid oxidase, protocatechuic 3,4-dioxygenase, and protocatechuic 3,4-oxygenase. This enzyme participates in benzoate degradation via hydroxylation and 2,4-dichlorobenzoate degradation. It employs one cofactor, iron.
This enzyme has been found effective at improving organic fluorophore-stability in single-molecule experiments. Commercial preps of the enzyme isolated from Pseudomonas spp. generally require further purification to remove strong contaminating nuclease activity.
Structural studies
As of late 2007, 37 structures have been solved for this class of enzymes, with PDB accession codes , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , and .
See also
Protocatechuic acid
References
EC 1.13.11
Iron enzymes
Enzymes of known structure
Natural phenols metabolism |
https://en.wikipedia.org/wiki/Protocatechuate%204%2C5-dioxygenase | In enzymology, a protocatechuate 4,5-dioxygenase () is an enzyme that catalyzes the chemical reaction
protocatechuate + O2 4-carboxy-2-hydroxymuconate semialdehyde
Thus, the two substrates of this enzyme are protocatechuate and O2, whereas its product is 4-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 protocatechuate:oxygen 4,5-oxidoreductase (decyclizing). Other names in common use include protocatechuate 4,5-oxygenase, protocatechuic 4,5-dioxygenase, and protocatechuic 4,5-oxygenase. This enzyme participates in benzoate degradation via hydroxylation and 2,4-dichlorobenzoate degradation. It employs one cofactor, iron.
Structural studies
As of late 2007, two 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/Pyrogallol%201%2C2-oxygenase | In enzymology, a pyrogallol 1,2-oxygenase () is an enzyme that catalyzes the chemical reaction
1,2,3-trihydroxybenzene + O2 (Z)-5-oxohex-2-enedioate
Thus, the two substrates of this enzyme are 1,2,3-trihydroxybenzene and O2, whereas its product is (Z)-5-oxohex-2-enedioate.
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 1,2,3-trihydroxybenzene:oxygen 1,2-oxidoreductase (decyclizing). This enzyme is also called pyrogallol 1,2-dioxygenase.
References
EC 1.13.11
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Quercetin%202%2C3-dioxygenase | In enzymology, a quercetin 2,3-dioxygenase () is an enzyme that catalyzes the chemical reaction
quercetin + O2 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate + CO + H+
Thus, the two substrates of this enzyme are quercetin and O2, whereas its 3 products are 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate, CO, and H+.
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 quercetin:oxygen 2,3-oxidoreductase (decyclizing). Other names in common use include quercetinase, and flavonol 2,4-oxygenase. It has 2 cofactors: iron, and Copper.
Structural studies
As of late 2007, 6 crystal structures have been solved for this class of enzymes, with PDB accession codes , , , , , and .
References
EC 1.13.11
Iron enzymes
Copper enzymes
Enzymes of known structure
Quercetin |
https://en.wikipedia.org/wiki/Renilla-luciferin%202-monooxygenase | Renilla-luciferin 2-monooxygenase, Renilla luciferase, or RLuc, is a bioluminescent enzyme found in Renilla reniformis, belonging to a group of coelenterazine luciferases. Of this group of enzymes, the luciferase from Renilla reniformis has been the most extensively studied, and due to its bioluminescence requiring only molecular oxygen, has a wide range of applications, with uses as a reporter gene probe in cell culture, in vivo imaging, and various other areas of biological research.
Recently, chimeras of RLuc have been developed and demonstrated to be the brightest luminescent proteins to date, and have proved effective in both noninvasive single-cell and whole body imaging.
Note that the EC record also includes other unrelated enzymes that catalyze the same reaction. An example is the calcium-dependent photoprotein aequorin: while Rluc is in the AB hydrolase superfamily, aequorin is an EF hand protein. The name does not specifically refer to Renilla, but instead refers to Renilla-luciferin, a chemical also known as coelenterazine.
Chemical reaction
RLuc is an oxidoreductase, specifically acting on single donors with O2 as the oxidant. However, this enzyme appears to be unrelated from most other luciferases that act on coelenterazine, such as those from copepods.
RLuc catalyzes the chemical reaction
Coelenterazine + O2 coelenteramide + CO2 + hν
In the process, coelenterazine is oxidized with a concurrent loss of CO2, and a photon of blue light is emitted.
Biological |
https://en.wikipedia.org/wiki/GGA1 | ADP-ribosylation factor-binding protein GGA1 is a protein that in humans is encoded by the GGA1 gene.
This gene encodes a member of the Golgi-localized, gamma adaptin ear-containing, ARF-binding (GGA) protein family. Members of this family are ubiquitous coat proteins that regulate the trafficking of proteins between the trans-Golgi network and the lysosome. These proteins share an amino-terminal VHS domain which mediates sorting of the mannose 6-phosphate receptors at the trans-Golgi network. They also contain a carboxy-terminal region with homology to the ear domain of gamma-adaptins. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene.
Interactions
GGA1 has been shown to interact with Sortilin 1, BACE2, RABEP1 and ARF3.
References
Further reading |
https://en.wikipedia.org/wiki/Ribosyldihydronicotinamide%20dehydrogenase%20%28quinone%29 | In enzymology, a ribosyldihydronicotinamide dehydrogenase (quinone) () is an enzyme that catalyzes the chemical reaction
1-(beta-D-ribofuranosyl)-1,4-dihydronicotinamide + a quinone 1-(beta-D-ribofuranosyl)nicotinamide + a hydroquinone
Thus, the two substrates of this enzyme are 1-(beta-D-ribofuranosyl)-1,4-dihydronicotinamide and quinone, whereas its two products are 1-(beta-D-ribofuranosyl)nicotinamide and hydroquinone.
This enzyme belongs to the family of oxidoreductases, specifically those acting on diphenols and related substances as donor with other acceptors. The systematic name of this enzyme class is 1-(beta-D-ribofuranosyl)-1,4-dihydronicotinamide:quinone oxidoreductase. Other names in common use include NRH:quinone oxidoreductase 2, NQO2, NQO2, NAD(P)H:quinone oxidoreductase-2 (misleading), QR2, quinone reductase 2, N-ribosyldihydronicotinamide dehydrogenase (quinone), and NAD(P)H:quinone oxidoreductase2 (misleading).
References
EC 1.10.99
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Rifamycin-B%20oxidase | In enzymology, a rifamycin-B oxidase () is an enzyme that catalyzes the chemical reaction
rifamycin B + O2 rifamycin O + H2O2
Thus, the two substrates of this enzyme are rifamycin B and O2, whereas its two products are rifamycin O 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 rifamycin-B:oxygen oxidoreductase. This enzyme is also called rifamycin B oxidase.
References
EC 1.10.3
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Stizolobate%20synthase | In enzymology, a stizolobate synthase () is an enzyme that catalyzes the chemical reaction
3,4-dihydroxy-L-phenylalanine + O2 4-(L-alanin-3-yl)-2-hydroxy-cis,cis-muconate 6-semialdehyde
Thus, the two substrates of this enzyme are 3,4-dihydroxy-L-phenylalanine and O2, whereas its product is 4-(L-alanin-3-yl)-2-hydroxy-cis,cis-muconate 6-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-dihydroxy-L-phenylalanine:oxygen 4,5-oxidoreductase (recyclizing). This enzyme participates in tyrosine metabolism. It employs one cofactor, zinc.
References
EC 1.13.11
Zinc enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Stizolobinate%20synthase | In enzymology, a stizolobinate synthase () is an enzyme that catalyzes the chemical reaction
3,4-dihydroxy-L-phenylalanine + O2 5-(L-alanin-3-yl)-2-hydroxy-cis,cis-muconate 6-semialdehyde
Thus, the two substrates of this enzyme are 3,4-dihydroxy-L-phenylalanine and O2, whereas its product is 5-(L-alanin-3-yl)-2-hydroxy-cis,cis-muconate 6-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-dihydroxy-L-phenylalanine:oxygen 2,3-oxidoreductase (recyclizing). This enzyme participates in tyrosine metabolism. It employs one cofactor, zinc.
References
EC 1.13.11
Zinc enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/RUNX3 | Runt-related transcription factor 3 is a protein that in humans is encoded by the RUNX3 gene.
Function
This gene encodes a member of the runt domain-containing family of transcription factors. A heterodimer of this protein and a beta subunit forms a complex that binds to the core DNA sequence 5'-YGYGGT-3' found in a number of enhancers and promoters, and can either activate or suppress transcription. It also interacts with other transcription factors. It functions as a tumor suppressor, and the gene is frequently deleted or transcriptionally silenced in cancer. Multiple transcript variants encoding different isoforms have been found for this gene.
In melanocytic cells RUNX3 gene expression may be regulated by MITF.
Knockout mouse
Runx3 null mouse gastric mucosa exhibits hyperplasia due to stimulated proliferation and suppressed apoptosis in epithelial cells, and the cells are resistant to TGF-beta stimulation.
The RUNX3 controversy
In 2011 serious doubt was cast over the tumor suppressor function of Runx3 originated from the earlier publication by Li and co-workers.
On the basis of the original study by Li and co-workers (2002), the majority of later literature citing Li and co-workers (2002) assumed that RUNX3 was expressed in the normal gut epithelium and that it is therefore likely to act as a tumor suppressor in the particular epithelial cancer investigated. Most of this literature used RUNX3 promoter methylation status in various cancers as a proxy for its expr |
https://en.wikipedia.org/wiki/Sulfur%20oxygenase/reductase | In enzymology, a sulfur oxygenase/reductase () is an enzyme that catalyzes the chemical reaction
4 sulfur + 4 H2O + O2 2 hydrogen sulfide + 2 bisulfite + 2 H+
The 3 substrates of this enzyme are sulfur, H2O, and O2, whereas its 3 products are hydrogen sulfide, bisulfite, and H+.
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 sulfur:oxygen oxidoreductase (hydrogen-sulfide- and sulfite-forming). Other names in common use include SOR, sulfur oxygenase, and sulfur oxygenase reductase.
References
EC 1.13.11
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Trans-acenaphthene-1%2C2-diol%20dehydrogenase | In enzymology, a trans-acenaphthene-1,2-diol dehydrogenase () is an enzyme that catalyzes the chemical reaction
(+/-)-trans-acenaphthene-1,2-diol + 2 NADP+ acenaphthenequinone + 2 NADPH + 2 H+
Thus, the two substrates of this enzyme are (+/-)-trans-acenaphthene-1,2-diol and NADP+, whereas its 3 products are acenaphthenequinone, NADPH, and H+.
This enzyme belongs to the family of oxidoreductases, specifically those acting on diphenols and related substances as donor with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is . This enzyme is also called .
References
EC 1.10.1
NADPH-dependent enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Tryptophan%202%2C3-dioxygenase | In enzymology, tryptophan 2,3-dioxygenase () is a heme enzyme that catalyzes the oxidation of -tryptophan (-Trp) to N-formyl--kynurenine, as the first and rate-limiting step of the kynurenine pathway.
-tryptophan + O2 N-formyl--kynurenine
Tryptophan 2,3-dioxygenase plays a central role in the physiological regulation of tryptophan flux in the human body, as part of the overall biological process of tryptophan metabolism. TDO catalyses the first and rate-limiting step of tryptophan degradation along the kynurenine pathway and thereby regulates systemic tryptophan levels. In humans, tryptophan 2,3-dioxygenase is encoded by the TDO2 gene.
Function
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). This family includes tryptophan 2,3-dioxygenase (TDO, also sometimes referred to as tryptophan oxygenase and -tryptophan pyrrolase) and the closely related indoleamine 2,3-dioxygenase enzyme (IDO). Both TDO and IDO contain one noncovalently bound heme per monomer; TDO is usually tetrameric, whereas IDO is monomeric.
Tryptophan 2,3-dioxygenase was initially discovered in the 1930s and is found in both eukaryotes and prokaryotes. Expression of tryptophan 2,3-dioxygenase in mammals is normally restricted to the liver, but it has been identified in the brain and epididymis of some species, and, in some tissues, its production can be induced in r |
https://en.wikipedia.org/wiki/DUSP1 | Dual specificity protein phosphatase 1 is an enzyme that in humans is encoded by the DUSP1 gene.
Function
The expression of DUSP1 gene is induced in human skin fibroblasts by oxidative/heat stress and growth factors. It specifies a protein with structural features similar to members of the non-receptor-type protein-tyrosine phosphatase family, and which has significant amino-acid sequence similarity to a Tyr/Ser-protein phosphatase encoded by the late gene H1 of vaccinia virus. The bacterially expressed and purified DUSP1 protein has intrinsic phosphatase activity, and specifically inactivates mitogen-activated protein (MAP) kinase in vitro by the concomitant dephosphorylation of both its phosphothreonine and phosphotyrosine residues. Furthermore, it suppresses the activation of MAP kinase by oncogenic ras in extracts of Xenopus oocytes. Thus, DUSP1 may play an important role in the human cellular response to environmental stress as well as in the negative regulation of cellular proliferation.
Interactions
DUSP1 has been shown to interact with MAPK14, MAPK1 and MAPK8.
References
Further reading
EC 3.1.3 |
https://en.wikipedia.org/wiki/Tryptophan%202%27-dioxygenase | In enzymology, a tryptophan 2'-dioxygenase () is an enzyme that catalyzes the chemical reaction
L-tryptophan + + (indol-3-yl)glycolaldehyde + +
Thus, the 3 substrates of this enzyme are L-tryptophan, and , whereas its 3 products are (indol-3-yl)glycolaldehyde, , and .
Classification
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 miscellaneous.
Nomenclature
The systematic name of this enzyme class is L-tryptophan:oxygen 2'-oxidoreductase (side-chain-cleaving). Other names in common use include indole-3-alkane alpha-hydroxylase, tryptophan side-chain alpha,beta-oxidase, tryptophan side chain oxidase II, tryptophan side-chain oxidase, TSO, indolyl-3-alkan alpha-hydroxylase, tryptophan side chain oxidase type I, TSO I, TSO II, and tryptophan side chain oxidase.
Biological role
This enzyme participates in tryptophan metabolism. It employs one cofactor, heme.
References
EC 1.13.99
Heme enzymes
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/FABP2 | Fatty acid-binding protein 2 (FABP2), also known as Intestinal-type fatty acid-binding protein (I-FABP), is a protein that in humans is encoded by the FABP2 gene.
Function
The intracellular fatty acid-binding proteins (FABPs) belong to a multigene family with nearly twenty identified members. FABPs are divided into at least three distinct types, namely the hepatic-, intestinal- and cardiac-type. They form 14-15 kDa proteins and are thought to participate in the uptake, intracellular metabolism and/or transport of long-chain fatty acids. They may also be responsible in the modulation of cell growth and proliferation. Intestinal fatty acid-binding protein 2 gene contains four exons and is an abundant cytosolic protein in small intestine epithelial cells.
Clinical significance
This gene has a polymorphism at codon 54 that identified an alanine-encoding allele and a threonine-encoding allele. Thr-54 protein is associated with increased fat oxidation and insulin resistance.
References
Further reading
Obesity |
https://en.wikipedia.org/wiki/Tryptophan%202-monooxygenase | In enzymology, a tryptophan 2-monooxygenase () is an enzyme that catalyzes the chemical reaction
L-tryptophan + O2 (indol-3-yl)acetamide + CO2 + H2O
Thus, the two substrates of this enzyme are L-tryptophan and O2, and its 3 products are (indol-3-yl)acetamide, CO2, and H2O.
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 L-tryptophan:oxygen 2-oxidoreductase (decarboxylating). This enzyme participates in tryptophan metabolism.
References
EC 1.13.12
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/Watasenia-luciferin%202-monooxygenase | In enzymology, a Watasenia-luciferin 2-monooxygenase () is an enzyme that catalyzes the chemical reaction
Watasenia luciferin + O2 oxidized Watasenia luciferin + CO2 + hnu
Thus, the two substrates of this enzyme are Watasenia luciferin and O2, whereas its 3 products are oxidized Watasenia luciferin, CO2, and hn.
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 the incorporation of one atom of oxygen (internal monooxygenases o internal mixed-function oxidases). The systematic name of this enzyme class is Watasenia-luciferin:oxygen 2-oxidoreductase (decarboxylating). This enzyme is also called Watasenia-type luciferase.
References
EC 1.13.12
Enzymes of unknown structure |
https://en.wikipedia.org/wiki/PDX1 | PDX1 (pancreatic and duodenal homeobox 1), also known as insulin promoter factor 1, is a transcription factor in the ParaHox gene cluster. In vertebrates, Pdx1 is necessary for pancreatic development, including β-cell maturation, and duodenal differentiation. In humans this protein is encoded by the PDX1 gene, which was formerly known as IPF1. The gene was originally identified in the clawed frog Xenopus laevis and is present widely across the evolutionary diversity of bilaterian animals, although it has been lost in evolution in arthropods and nematodes. Despite the gene name being Pdx1, there is no Pdx2 gene in most animals; single-copy Pdx1 orthologs have been identified in all mammals. Coelacanth and cartilaginous fish are, so far, the only vertebrates shown to have two Pdx genes, Pdx1 and Pdx2.
Function
Pancreatic development
In pancreatic development, Pdx1 is expressed by a population of cells in the posterior foregut region of the definitive endoderm, and Pdx1+ epithelial cells give rise to the developing pancreatic buds, and eventually, the whole of the pancreas—its exocrine, endocrine, and ductal cell populations. Pancreatic Pdx1+ cells first arise at mouse embryonic day 8.5-9.0 (E8.5-9.0), and Pdx1 expression continues until E12.0-E12.5. Homozygous Pdx1 knockout mice form pancreatic buds but fail to develop a pancreas, and transgenic mice in which tetracycline application results in death of Pdx1+ cells are almost completely apancreatic if doxycycline (tetrac |
https://en.wikipedia.org/wiki/IPO5 | Importin-5 is a protein that in humans is encoded by the IPO5 gene. The protein encoded by this gene is a member of the importin beta family. Structurally, the protein adopts the shape of a right hand solenoid and is composed of 24 HEAT repeats.
Function
Nuclear 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. Interactions between importin beta and the FG repeats of nucleoporins are essential in translocation through the pore complex.
IPO5 facilitates cytoplasmic polyadenylation element-binding protein (CPEB)3 translocation by binding to RRM1 motif of CPEB3 in neurons. NMDAR signaling increases RanBP1 expression and reduces the level of cytoplasmic GTP-bound Ran. These changes enhance CPEB3–IPO5 interaction, which consequently accelerates the nuclear import of CPEB3 and promotes its nuclear function |
https://en.wikipedia.org/wiki/MHC%20class%20I%20polypeptide%E2%80%93related%20sequence%20B | MHC class I polypeptide-related sequence B (MICB) is a protein that is encoded by the MICB gene located within MHC locus. MICB is related to MHC class I and has similar domain structure, which is made up of external α1α2α3 domain, transmembrane segment and C-terminal cytoplasmic tail. MICB is a stress-induced ligand for NKG2D receptor. The heat shock stress pathway is involved in the regulation of MICB expression as transcription of MICB is regulated by promoter heat shock element.
See also
MICA
References
Further reading |
https://en.wikipedia.org/wiki/PDGFA | Platelet-derived growth factor subunit A is a protein that in humans is encoded by the PDGFA gene.
The protein encoded by this gene is a member of the platelet-derived growth factor family. The four members of this family are mitogenic factors for cells of mesenchymal origin and are characterized by a motif of eight cysteines. This gene product can exist either as a homodimer or as a heterodimer with the platelet-derived growth factor beta polypeptide, where the dimers are connected by disulfide bonds. Studies using knockout mice have shown cellular defects in oligodendrocytes, alveolar smooth muscle cells, and Leydig cells in the testis; knockout mice die either as embryos or shortly after birth. Two splice variants have been identified for this gene.
References
Further reading |
https://en.wikipedia.org/wiki/RANBP2 | RAN binding protein 2 (RANBP2) is protein which in humans is encoded by the RANBP2 gene. It is also known as nucleoporin 358 (Nup358) since it is a member nucleoporin family that makes up the nuclear pore complex. RanBP2 has a mass of 358 kDa.
Function
RAN is a small GTP-binding protein of the RAS superfamily. Ran GTPase is a master regulatory switch, which among other functions, controls the shuttling of proteins between the nuclear and cytoplasm compartments of the cell. Ran GTPase controls a variety of cellular functions through its interactions with other proteins. The RanBP2 gene encodes a very large RAN-binding protein that localizes to cytoplasmic filaments emanating from the nuclear pore complex. RanBP2/Nup358 is a giant scaffold and mosaic cyclophilin-related nucleoporin implicated in controlling selective processes of the Ran-GTPase cycle. RanBP2 is composed of multiple domains. Each domain of RanBP2 selectively and directly interacts with distinct proteins such as Ran GTPase, importin-beta, exportin-1/CRM1, red opsin, subunits of the proteasome, cox11 and the kinesin-1 isoforms, KIF5B and KIF5C. Another partner of RanBP2 is the E2 enzyme UBC9. RanBP2 strongly enhances SUMO1 transfer from UBC9 to the SUMO1 target SP100. Another target for SUMOylation is RanGAP which is the GTPase activating protein for Ran. SUMO-RanGAP interacts with a domain near the carboxyl terminus of RanBP2. These findings place sumoylation at the cytoplasmic filaments of the nuclear pore c |
https://en.wikipedia.org/wiki/Syndecan-4 | Syndecan-4 is a protein that in humans is encoded by the SDC4 gene. Syndecan-4 is one of the four vertebrate syndecans and has a molecular weight of ~20 kDa. Syndecans are the best-characterized plasma membrane proteoglycans. Their intracellular domain of membrane-spanning core protein interacts with actin cytoskeleton and signaling molecules in the cell cortex. Syndecans are normally found on the cell surface of fibroblasts and epithelial cells. Syndecans interact with fibronectin on the cell surface, cytoskeletal and signaling proteins inside the cell to modulate the function of integrin in cell-matrix adhesion. Also, syndecans bind to FGFs and bring them to the FGF receptor on the same cell. As a co-receptor or regulator, mutated certain proteoglycans could cause severe developmental defects, like disordered distribution or inactivation of signaling molecules.
Syndecans have similar structural features:
Attach to heparan sulfate chains – interacting factors (e.g. Matrix molecules, growth factors, and enzymes)
Chondroitin sulfate chain
Transmembrane domain – self-association
C1 domain – actin-association cytoskeleton
Variable domain – syndecan-specific
C2 domain – attach to PDZ proteins
Syndecans normally form homodimers or multimers. Their biological function includes cell growth regulation, differentiation, and adhesion.
Syndecan-4 has more widespread distribution than other syndecans and it is the only syndecan that has been found consistently in focal adhesio |
https://en.wikipedia.org/wiki/CALCRL | Calcitonin receptor-like (CALCRL), also known as the calcitonin receptor-like receptor (CRLR), is a human protein; it is a receptor for calcitonin gene-related peptide.
Function
The protein encoded by the CALCRL gene is a G protein-coupled receptor related to the calcitonin receptor. CALCRL is linked to one of three single transmembrane domain receptor activity-modifying proteins (RAMPs) that are essential for functional activity.
The association of CALCRL with different RAMP proteins produces different receptors:
with RAMP1: produces a CGRP receptor
with RAMP2: produces an adrenomedullin (AM) receptor, designated AM1
with RAMP3: produces a dual CGRP/AM receptor designated AM2
These receptors are linked to the G protein Gs, which activates adenylate cyclase and activation results in the generation of intracellular cyclic adenosine monophosphate (cAMP).
CGRP receptors are found throughout the body, suggesting that the protein may modulate a variety of physiological functions in all major systems (e.g., respiratory, endocrine, gastrointestinal, immune, and cardiovascular).
Wounds
In wounds, CGRP receptors found in nerve cells deactivate the immune system, to prevent collateral damage in case of a clean wound (common case). In very preliminary research, nerve blockers like e.g. lidocaine or botox have been demonstrated to block CGRP cascade, thereby allowing immune system involvement and control of pathogens, resulting in complete control and recovery.
Structure
CAL |
https://en.wikipedia.org/wiki/Calpain-2%20catalytic%20subunit | Calpain-2 catalytic subunit is a protein that in humans is encoded by the CAPN2 gene.
Function
The calpains, calcium-activated neutral proteases, are nonlysosomal, intracellular cysteine proteases. The mammalian calpains include ubiquitous, stomach-specific, and muscle-specific proteins. The ubiquitous enzymes consist of heterodimers with distinct large, catalytic subunits associated with a common small, regulatory subunit. This gene encodes the large subunit of the ubiquitous enzyme, calpain 2. Multiple heterogeneous transcriptional start sites in the 5' UTR have been reported.
Interactions
CAPN2 has been shown to interact with Bcl-2.
References
Further reading
External links
The MEROPS online database for peptidases and their inhibitors: C02.002
EF-hand-containing proteins |
https://en.wikipedia.org/wiki/CD74 | HLA class II histocompatibility antigen gamma chain also known as HLA-DR antigens-associated invariant chain or CD74 (Cluster of Differentiation 74), is a protein that in humans is encoded by the CD74 gene. The invariant chain (Abbreviated Ii) is a polypeptide which plays a critical role in antigen presentation. It is involved in the formation and transport of MHC class II peptide complexes for the generation of CD4+ T cell responses. The cell surface form of the invariant chain is known as CD74. CD74 is a cell surface receptor for the cytokine macrophage migration inhibitory factor (MIF).
Function
The nascent MHC class II protein in the rough endoplasmic reticulum (RER) binds a segment of the invariant chain (Ii; a trimer) in order to shape the peptide-binding groove and prevent the formation of a closed conformation.
The invariant chain also facilitates the export of MHC class II from the RER in a vesicle. The signal for endosomal targeting resides in the cytoplasmic tail of the invariant chain. This fuses with a late endosome containing the endocytosed antigen proteins (from the exogenous pathway). Binding to Ii ensures that no antigen peptides from the endogenous pathway meant for MHC class I molecules accidentally bind to the groove of MHC class II molecules. The Ii is then cleaved by cathepsin S (cathepsin L in cortical thymic epithelial cells), leaving only a small fragment called CLIP remaining bound to the groove of MHC class II molecules. The rest of the Ii is de |
https://en.wikipedia.org/wiki/CDC25B | M-phase inducer phosphatase 2 is an enzyme that in humans is encoded by the CDC25B gene.
CDC25B is a member of the CDC25 family of phosphatases. CDC25B activates the cyclin dependent kinase CDC2 by removing two phosphate groups and it is required for entry into mitosis. CDC25B shuttles between the nucleus and the cytoplasm due to nuclear localization and nuclear export signals. The protein is nuclear in the M and G1 phases of the cell cycle and moves to the cytoplasm during S and G2. CDC25B has oncogenic properties, although its role in tumor formation has not been determined. Multiple transcript variants for this gene exist.
Interactions
CDC25B has been shown to interact with MAPK14, Casein kinase 2, alpha 1, CHEK1, MELK, Estrogen receptor alpha, YWHAB, YWHAZ, YWHAH and YWHAE.
References
Further reading
External links
Enzymes |
https://en.wikipedia.org/wiki/Corticotropin-releasing%20hormone%20receptor%201 | Corticotropin-releasing hormone receptor 1 (CRHR1) is a protein, also known as CRF1, with the latter (CRF1) now being the IUPHAR-recommended name. In humans, CRF1 is encoded by the CRHR1 gene at region 17q21.31, beside micrototubule-associated protein tau MAPT.
Structure
The human CRHR1 gene contains 14 exons over 20 kb of DNA, and its full gene product is a peptide composed of 444 amino acids. Excision of exon 6 yields in the mRNA for the primary functional CRF1, which is a peptide composed of 415 amino acids, arranged in seven hydrophobic alpha-helices.
The CRHR1 gene is alternatively spliced into a series of variants. These variants are generated through deletion of one of the 14 exons, which in some cases causes a frame-shift in the open reading frame, and encode corresponding isoforms of CRF1. Though these isoforms have not been identified in native tissues, the mutations of the splice variants of mRNA suggest the existence of alternate CRF receptors, with differences in intracellular loops or deletions in N-terminus or transmembrane domains. Such structural changes suggest that the alternate CRF1 receptors have different degrees of capacity and efficiency in binding CRF and its agonists. Though the functions of these CRF1 receptors is yet unknown, they are suspected to be biologically significant.
CRF1 is 70% homologous with the second human CRF receptor family, CRF2; the greatest divergence between the two lies at the N-terminus of the protein.
Mechanism of activ |
https://en.wikipedia.org/wiki/GABBR1 | Gamma-aminobutyric acid B receptor, 1 (GABAB1), is a G-protein coupled receptor subunit encoded by the GABBR1 gene.
Function
GABAB1 is a receptor for Gamma-aminobutyric acid. Upon binding, GABAB1 will produce a slow and prolonged inhibitory effect. GABAB1 is one part of a heterodimer, which is the GABAB receptor, consisting of it and the related GABAB2 protein. The GABA(B) receptor 1 gene is mapped to chromosome 6p21.3 within the HLA class I region close to the HLA-F gene. Susceptibility loci for multiple sclerosis, epilepsy, and schizophrenia have also been mapped in this region. Alternative splicing of this gene generates 4 transcript variants.
Interactions
GABBR1 has been shown to interact with ATF4 and GABBR2.
See also
GABAB receptor
References
Further reading
External links
G protein-coupled receptors |
https://en.wikipedia.org/wiki/HNRNPA2B1 | Heterogeneous nuclear ribonucleoproteins A2/B1 is a protein that in humans is encoded by the HNRNPA2B1 gene.
Structure
HNRNPA2B1 gene contains 12 exons, including a B1 protein specific 36-nucleotide mini-exon. The entire length of intron/exon organization of HNRNPA2B1 is identical to that of the HNRNPA1 gene which indicates a common origin by gene duplication.
Function
This gene belongs to the A/B subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are RNA binding proteins and they complex with heterogeneous nuclear RNA (hnRNA). These proteins are associated with pre-mRNAs in the nucleus and appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. While all of the hnRNPs are present in the nucleus, some seem to shuttle between the nucleus and the cytoplasm. The hnRNP proteins have distinct nucleic acid binding properties. The protein encoded by this gene has two repeats of quasi-RRM domains that bind to RNAs. This gene has been described to generate two alternatively spliced transcript variants which encode different isoforms.
HnRNPA2B1 is an autoantigen in autoimmune diseases such as rheumatoid arthritis, systemic lupus erythematosus and mixed connective tissue disease. When referred to as an autoantigen, hnRNPA2B1 is also known as RA33.
The HNRNPA2 and HNRNPB1 proteins are involved in packaging nascent mRNA, in alternative splicing, and in cytoplasmic RNA trafficking, translation, and stab |
https://en.wikipedia.org/wiki/Wee1-like%20protein%20kinase | WEE1 homolog (S. pombe), also known as WEE1, is a protein which in humans is encoded by the WEE1 gene.
Function
This gene encodes a nuclear protein, which is a tyrosine kinase belonging to the Ser/Thr family of protein kinases. This protein catalyzes the inhibitory tyrosine phosphorylation of CDC2/cyclin B kinase, and appears to coordinate the transition between DNA replication and mitosis by protecting the nucleus from cytoplasmically activated CDC2 kinase.
Interactions
Wee1-like protein kinase has been shown to interact with YWHAB and PIN1.
References
Further reading
External links
EC 2.7.11 |
https://en.wikipedia.org/wiki/ACTR3 | Actin-related protein 3 is a protein that in humans is encoded by the ACTR3 gene.
Function
The specific function of this gene has not yet been determined; however, the protein it encodes is known to be a major constituent of the ARP2/3 complex. This complex is located at the cell surface and is essential to cell shape and motility through lamellipodial actin assembly and protrusion.
Interactions
ACTR3 has been shown to interact with Cortactin.
References
Further reading
External links
Human proteins |
https://en.wikipedia.org/wiki/SH3KBP1 | SH3 domain-containing kinase-binding protein 1 (synonyms - CIN85, in rodents - Ruk) is an adaptor protein that in humans is encoded by the SH3KBP1 gene.
Function
CBL (MIM 165360) constitutively interacts with SH3 domain-containing proteins and, upon tyrosine phosphorylation, with SH2 domain-containing proteins. The SH3KBP1 gene encodes an 85-kD CBL-interacting protein that enhances tumor necrosis factor (MIM 191160)-mediated apoptotic cell death (Narita et al., 2001).[supplied by OMIM]
Interactions
SH3KBP1 has been shown to interact with B-cell linker, Grb2, SH3GLB2, SH3GL3, SH3GL2, BCAR1, Epidermal growth factor receptor, CBLB, Cbl gene, SOS1, CRK and PAK2.
References
Further reading |
https://en.wikipedia.org/wiki/HIST4H4 | Histone H4 is a protein that in humans is encoded by the HIST4H4 gene.
Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene is intronless and encodes a member of the histone H4 family. Transcripts from this gene lack polyA tails; instead, they contain a palindromic termination element.
References
Further reading |
https://en.wikipedia.org/wiki/AP2M1 | AP-2 complex subunit mu is a protein that in humans is encoded by the AP2M1 gene.
Function
This gene encodes a subunit of the heterotetrameric coat assembly protein complex 2 (AP2), which belongs to the adaptor complexes medium subunits family. The encoded protein is required for the activity of a vacuolar ATPase, which is responsible for proton pumping occurring in the acidification of endosomes and lysosomes. The encoded protein may also play an important role in regulating the intracellular trafficking and function of CTLA-4 protein. Two transcript variants encoding different isoforms have been found for this gene.
Interactions
AP2M1 has been shown to interact with CTLA-4 and Alpha-1B adrenergic receptor.
References
Further reading
External links |
https://en.wikipedia.org/wiki/Mucin%204 | Mucin-4 (MUC-4) is a mucin protein that in humans is encoded by the MUC4 gene. Like other mucins, MUC-4 is a high-molecular weight glycoprotein.
The major constituents of mucus, the viscous secretion that covers epithelial surfaces such as those in the trachea, colon, and cervix, are highly glycosylated proteins called mucins. These glycoproteins play important roles in the protection of the epithelial cells and have been implicated in epithelial renewal and differentiation. This gene encodes an integral membrane glycoprotein found on the cell surface, although secreted isoforms may exist. At least two dozen transcript variants of this gene have been found, although for many of them the full-length transcript has not been determined or they are found only in tumor tissues.
MUC-4 has been found to play various roles in the progression of cancer, particularly due to its signaling and anti-adhesive properties which contribute to tumor development and metastasis. It is also found to play roles in other diseases such as endometriosis and inflammatory bowel disease. MUC-4 belongs to the human mucin family that is membrane-anchored and can range in molecular weight from 550 to 930 kDa for the actual protein, and up to 4,650 kDa with glycosylation.
Structure
MUC4 is an O-glycoprotein that can reach up to 2 micrometers outside the cell. MUC4 mucin consists of a large extracellular alpha subunit that is heavily glycosylated and a beta subunit that is anchored in the cell membrane |
https://en.wikipedia.org/wiki/Neutrophil%20cytosolic%20factor%202 | Neutrophil cytosol factor 2 is a protein that in humans is encoded by the NCF2 gene.
Function
This gene encodes neutrophil cytosolic factor 2, the 67-kilodalton cytosolic subunit of the multi-protein complex known as NADPH oxidase found in neutrophils. This oxidase produces a burst of superoxide which is delivered to the lumen of the neutrophil phagosome. Mutations in this gene, as well as in other NADPH oxidase subunits, can result in chronic granulomatous disease.
References
Further reading
External links |
https://en.wikipedia.org/wiki/PAX2 | Paired box gene 2, also known as Pax-2, is a protein which in humans is encoded by the PAX2 gene.
Function
The Pax Genes, or Paired-Box Containing Genes, play important roles in the development and proliferation of multiple cell lines, development of organs, and development and organization of the central nervous system. The transcription factor gene PAX2 is important in the regionalized embryological development of the central nervous system. In mammals, the brain is developed in three regions: the forebrain, midbrain, and the hindbrain. Concentration gradients of fibroblast growth factor 8 (FGF8) and Wingless-Type MMTV Integration Site Family, Member 1 (Wnt1) control expression of Pax-2 during development of the Mesencephalon, or midbrain. Similar patterning during embryological development can be observed in “basal chordates or ascidians,” in which organization of the central nervous system in ascidian larvae are also controlled by fibroblast growth factor genes. PAX2 encodes for the transcription factor which appears to be essential in the organization of the midbrain and hindbrain regions, and at the earliest can be detected on either side of the sulcus limitans, which separates motor and sensory nerve nuclei.
PAX2 encodes paired box gene 2, one of many human homologues of the Drosophila melanogaster gene prd. The central feature of this transcription factor gene family is the conserved DNA-binding paired box domain. PAX2 is believed to be a target of transcription |
https://en.wikipedia.org/wiki/PMS2 | Mismatch repair endonuclease PMS2 is an enzyme that in humans is encoded by the PMS2 gene.
Function
This gene is one of the PMS2 gene family members which are found in clusters on chromosome 7. Human PMS2 related genes are located at bands 7p12, 7p13, 7q11, and 7q22. Exons 1 through 5 of these homologues share high degree of identity to human PMS2 The product of this gene is involved in DNA mismatch repair. The protein forms a heterodimer with MLH1 and this complex interacts with MSH2 bound to mismatched bases. Defects in this gene are associated with hereditary nonpolyposis colorectal cancer, with Turcot syndrome, and are a cause of supratentorial primitive neuroectodermal tumors. Alternatively spliced transcript variants have been observed.
Mismatch repair and endonuclease activity
PMS2 is involved in mismatch repair and is known to have latent endonuclease activity that depends on the integrity of the meta-binding motif in MutL homologs. As an endonuclease, PMS2 introduces nicks into a discontinuous DNA strand.
Interactions
PMS2 has been shown to interact with MLH1 by forming the heterodimer MutLα. There is competition between MLH3, PMS1, and PMS2 for the interacting domain on MLH1, which is located in residues 492-742.
The interacting domains in PMS2 have heptad repeats that are characteristic of leucine zipper proteins. MLH1 interacts with PMS2 at residues 506-756.
The MutS heterodimers, MutSα and MutSβ, associate with MutLα upon mismatch binding. MutLα is be |
https://en.wikipedia.org/wiki/CYB5R3 | NADH-cytochrome b5 reductase 3 is an enzyme that in humans is encoded by the CYB5R3 gene.
Structure
The CYB5R3 gene is located on the 22nd chromosome, with its specific location being 22q13.2. The gene contains 12 exons. CYB5R3 encodes a 34.2 kDa protein that is composed of 301 amino acids; 63 peptides have been observed through mass spectrometry data.
The entire gene is about 31 kb in length. Exon 2 contains the junction of the membrane-binding domain and the catalytic domain of b5R, which shows that there are two forms of b5R: a soluble form and a membrane-bound form. The 5' portion of this gene does not have typical regulatory transcriptional elements, but has the sequence G-G-G-C-G-G a total of five times. The GC content of this 5' portion of the gene is 86%, much higher than the average GC of the entire gene, which is 55%. There is also an atypical polyadenylation signal in the 3'-untranslated region of the gene.
The protein encoded by the CYB5R3 gene is cytochrome b5 reductase, a flavoprotein that is produced as two different isoforms with different localizations. There is an amphipathic microsomal isoform that is found in all cell types but red blood cells; this isoform has one hydrophobic membrane-anchoring domain and one catalytic domain that is hydrophilic. The other isoform, a soluble cytochrome b5 reductase isoform, is found in human erythrocytes. This protein is truncated, and encoded by an alternative transcript that produces only the larger, hydrophilic dom |
https://en.wikipedia.org/wiki/DMBT1 | Deleted in malignant brain tumors 1 protein is a protein that in humans is encoded by the DMBT1 gene.
Function
Loss of sequences from human chromosome 10q has been associated with the progression of human cancers. The gene DMBT1 was originally isolated based on its deletion in a medulloblastoma cell line. DMBT1 is expressed with transcripts of 6.0, 7.5, and 8.0 kb in fetal lung and with one transcript of 8.0 kb in adult lung, although the 7.5 kb transcript has not been characterized. The DMBT1 protein is a glycoprotein containing multiple scavenger receptor cysteine-rich (SRCR) domains separated by SRCR-interspersed domains (SID). Transcript variant 2 (8.0 kb) has been shown to bind surfactant protein D independently of carbohydrate recognition. This indicates that DMBT1 may not be a classical tumor suppressor gene, but rather play a role in the interaction of tumor cells and the immune system.
Pattern recognition and potential use of DMBT1 in nanomedicine
At epithelial barriers molecular pattern recognition mechanisms act as minesweepers against harmful environmental factors and thereby play a crucial role in the defense against invading bacterial and viral pathogens. However, it became evident that some of the proteins participating in these host defense processes may simultaneously function as regulators of tissue regeneration when in the extracellular matrix, thus coupling defense functions with regulation of stem cells. Although molecular pattern recognition ha |
https://en.wikipedia.org/wiki/DOK1 | Docking protein 1 is a protein that in humans is encoded by the DOK1 gene.
Function
Docking protein 1 is constitutively tyrosine phosphorylated in hematopoietic progenitors isolated from chronic myelogenous leukemia (CML) patients in the chronic phase. It may be a critical substrate for p210(bcr/abl), a chimeric protein whose presence is associated with CML. Docking protein 1 contains a putative pleckstrin homology domain at the amino terminus and ten PXXP SH3 recognition motifs. Docking protein 2 binds p120 (RasGAP) from CML cells. It has been postulated to play a role in mitogenic signaling.
Interactions
DOK1 has been shown to interact with:
ABL1 and
CD117,
INPP5D,
LYN,
RASA1,
RET,
SH2D1A,
SHC1, and
TEC.
References
Further reading |
https://en.wikipedia.org/wiki/HOXA9 | Homeobox protein Hox-A9 is a protein that in humans is encoded by the HOXA9 gene.
In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation. This gene is highly similar to the abdominal-B (Abd-B) gene of Drosophila fly. A specific translocation event which causes a fusion between this gene and the NUP98 gene has been associated with myeloid leukemogenesis.
As HOXA9 dysfunction has been implicated in acute myeloid leukemia, and expression of the gene has been shown to differ markedly between erythrocyte lineages of different stages of development, the gene is of particular interest from a hematopoietic perspective.
Function
Role in hematopoiesis
As HOXA9 is part of the homeobox family, involved in setting the body plans of animals, it is likely that HOXA9 would display increased expression in cells with higher differentiation potentials. Indeed in the hematopoietic lineage, it has been found that HOXA9 is preferentially expressed in hematopoietic stem cells (HSCs), and is down-regulated as the cell differentiates and matures further.
HOXA9 knockout mice have been shown to develop a reduction in the numbe |
https://en.wikipedia.org/wiki/ICAM3 | Intercellular adhesion molecule 3 (ICAM3) also known as CD50 (Cluster of Differentiation 50), is a protein that in humans is encoded by the ICAM3 gene. The protein is constitutively expressed on the surface of leukocytes, which are also called white blood cells and are part of the immune system. ICAM3 mediates adhesion between cells by binding to specific integrin receptors. It plays an important role in the immune cell response through its facilitation of interactions between T cells and dendritic cells, which allows for T cell activation. ICAM3 also mediates the clearance of cells undergoing apoptosis by attracting and binding macrophages, a type of cell that breaks down infected or dying cells through a process known as phagocytosis, to apoptotic cells.
Protein Structure
ICAM3 is a 110-160 kDa protein that belongs to the intercellular adhesion molecule (ICAM) family. Like the other proteins in this family, ICAM3 is a type I transmembrane glycoprotein and consists in part of a hydrophobic transmembrane domain and a short domain that extends into the cytoplasm. ICAM3 also contains 5 extracellular immunoglobulin domains.
Function
ICAM3 is found on the surface of leukocytes, and the ICAM3 gene is constitutively expressed in these cells. Interactions between ICAM3 and specific integrin receptors facilitate adhesion between cells.
Dendritic and T Cell Binding
ICAM3 has an important function in the immune cell response, as it helps facilitate initial interactions between T |
https://en.wikipedia.org/wiki/PEPCK-Cmus%20mouse | {{DISPLAYTITLE:PEPCK-Cmus mouse}}
PEPCK-Cmus mice are genetically modified mice (Mus musculus) which as a result of their modification have up to 100 times the concentration of the PEPCK-C enzyme in their muscles, compared to ordinary mice.
They were created by a team of American scientists led by Richard Hanson, professor of biochemistry at Case Western Reserve University at Cleveland, Ohio, to gain a greater understanding of the PEPCK-C enzyme, which is present mainly in the liver and kidneys.
Professor Hanson noted that PEPCK-Cmus mice, dubbed "the mighty mice", "are metabolically similar to Lance Armstrong biking up the Pyrenees. They utilize mainly fatty acids for energy and produce very little lactic acid. Without eating or drinking, they can run for four or five hours. They are 10 times more active than ordinary mice in their home cage. They also live longer – up to three years of age – and are reproductively active for almost three years. In short, they are remarkable animals." However, "they eat twice as much as control mice, but they are half the weight, and are very aggressive. Why this is the case, we are not really sure."
See also
Oncomouse
Knockout mice
Transhumanism
References
Genetically modified organisms
Laboratory mouse strains |
https://en.wikipedia.org/wiki/JUNB | Transcription factor jun-B is a protein that in humans is encoded by the JUNB gene. Transcription factor jun-B is a transcription factor involved in regulating gene activity following the primary growth factor response. It binds to the DNA sequence 5'-TGA[CG]TCA-3'.
Interactions
JUNB has been shown to interact with
BRCA1, and
SMAD3.
See also
AP-1 (transcription factor)
References
Further reading
External links
Transcription factors |
https://en.wikipedia.org/wiki/Lipocalin-2 | Lipocalin-2 (LCN2), also known as oncogene 24p3 or neutrophil gelatinase-associated lipocalin (NGAL), is a protein that in humans is encoded by the LCN2 gene. NGAL is involved in innate immunity by sequestering iron and preventing its use by bacteria, thus limiting their growth. It is expressed in neutrophils and in low levels in the kidney, prostate, and epithelia of the respiratory and alimentary tracts. NGAL is used as a biomarker of kidney injury.
Function
The binding of NGAL to bacterial siderophores is important in the innate immune response to bacterial infection. Upon encountering invading bacteria, the toll-like receptors on immune cells stimulate the synthesis and secretion of NGAL. Secreted NGAL then limits bacterial growth by sequestering iron-containing siderophores. Lipocalin-2 binds, next to bacterial siderophores, also to the mammalian siderophore 2,5-dihydroxybenzoic acid (2,5-DHBA). This complex ensures that excess free iron does not accumulate in the cytoplasm. Mammalian cells lacking 2,5-DHBA accumulate abnormal intracellular levels of iron leading to high levels of reactive oxygen species. Lipocalin-2 also functions as a growth factor and participates in synaptic plasticity.
Clinical significance
In the case of acute kidney injury (AKI), NGAL is secreted in high levels into the blood and urine within 2 hours of injury. Because NGAL is protease resistant and small, the protein is easily excreted and detected in the urine. NGAL levels in patients wi |
https://en.wikipedia.org/wiki/MCM3 | DNA replication licensing factor MCM3 is a protein that in humans is encoded by the MCM3 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 is a subunit of the protein complex that consists of MCM2-7. It has been shown to interact directly with MCM5/CDC46. This protein also interacts with, and thus is acetylated by MCM3AP, a chromatin-associated acetyltransferase. The acetylation of this protein inhibits the initiation of DNA replication and cell cycle progression.
Interactions
MCM3 has been shown to interact with:
CDC45-related protein,
CDC6,
DBF4,
MCM2
MCM3AP,
MCM5,
MCM7,
ORC4L, and
ORC5L.
See also
Mini Chromosome Maintenance
References
Further reading |
https://en.wikipedia.org/wiki/MNAT1 | CDK-activating kinase assembly factor MAT1 is an enzyme that in humans is encoded by the MNAT1 gene.
Function
Cyclin-dependent kinases (CDKs), which play an essential role in cell cycle control of eukaryotic cells, are phosphorylated and thus activated by the CDK-activating kinase (CAK). CAK is a multisubunit protein that includes CDK7 (MIM 601955), cyclin H (CCNH; MIM 601953), and MAT1. MAT1 (for 'ménage à trois-1') is involved in the assembly of the CAK complex.[supplied by OMIM]
Interactions
MNAT1 has been shown to interact with:
Cyclin H,
Cyclin-dependent kinase 7,
Estrogen receptor alpha,
MCM7,
MTA1,
P53, and
POU2F1.
References
Further reading
External links |
https://en.wikipedia.org/wiki/NEDD8 | NEDD8 is a protein that in humans is encoded by the NEDD8 gene. (in saccharomyces cerevisiae this protein is known as Rub1) This ubiquitin-like (UBL) protein becomes covalently conjugated to a limited number of cellular proteins, in a process called NEDDylation similar to ubiquitination. Human NEDD8 shares 60% amino acid sequence identity to ubiquitin. The primary known substrates of NEDD8 modification are the cullin subunits of cullin-based E3 ubiquitin ligases, which are active only when NEDDylated. Their NEDDylation is critical for the recruitment of E2 to the ligase complex, thus facilitating ubiquitin conjugation. NEDD8 modification has therefore been implicated in cell cycle progression and cytoskeletal regulation.
Activation and conjugation
As with ubiquitin and SUMO, NEDD8 is conjugated to cellular proteins after its C-terminal tail is processed. The NEDD8 activating E1 enzyme is a heterodimer composed of APPBP1 and UBA3 subunits. The APPBP1/UBA3 enzyme has homology to the N- and C-terminal halves of the ubiquitin E1 enzyme, respectively. The UBA3 subunit contains the catalytic center and activates NEDD8 in an ATP-dependent reaction by forming a high-energy thiolester intermediate. The activated NEDD8 is subsequently transferred to the UbcH12 E2 enzyme, and is then conjugated to specific substrates in the presence of the appropriate E3 ligases.
Substrates for NEDD8
As reviewed by Brown et al., the best-characterized activated-NEDD8 substrates are the cullins (CUL1 |
https://en.wikipedia.org/wiki/Notch%204 | Neurogenic locus notch homolog 4 (Notch 4) is a protein that in humans is encoded by the NOTCH4 gene located on chromosome 6.
Gene
An alternative splice variant of the NOTCH4 gene has been described, but its biological significance has not been determined.
Structure
The neurogenic locus notch homolog 4 protein is a member of the Notch family. Members of this type 1 transmembrane protein family share structural characteristics. These include an extracellular domain consisting of multiple epidermal growth factor-like (EGF) repeats, and an intracellular domain that consists of multiple, but different, domain types.
Function
Notch protein family members play a role in a variety of developmental processes by controlling cell fate decisions. The Notch signaling pathway is an evolutionarily conserved intercellular signaling pathway that regulates interactions between physically adjacent cells
In Drosophila, notch interacts with its cell-bound ligands (delta and serrate), and establishes an intercellular signaling pathway that then plays a key role in development. Homologues of the notch-ligands have also been identified in humans, but precise interactions between these ligands and the human notch homologues remain to be determined. The notch protein is cleaved in the trans-Golgi network, and then presented on the cell surface as a heterodimer. The protein functions as a receptor for membrane bound ligands, and may play a role in vascular, renal, and hepatic development.
Clin |
https://en.wikipedia.org/wiki/PIK3R2 | Phosphatidylinositol 3-kinase regulatory subunit beta is an enzyme that in humans is encoded by the PIK3R2 gene.
A recent study on gene expression indicated that the PIK3R2 gene might have a key role in pan-cancer prognosis.
Interactions
PIK3R2 has been shown to interact with:
CRKL
Cbl gene,
Epidermal growth factor,
FYN,
HER2/neu,
Macrophage colony-stimulating factor, and
PIK3CD.
Clinical relevance
PIK3R2 mutations were recently shown to be associated with polymicrogyria.
References
Further reading |
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