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14678648
|
Hydroxyethylthiazole kinase
|
In enzymology, a hydroxyethylthiazole kinase (EC 2.7.1.50) is an enzyme that catalyzes the chemical reaction
ATP + 4-methyl-5-(2-hydroxyethyl)thiazole formula_0 ADP + 4-methyl-5-(2-phosphonooxyethyl)thiazole
Thus, the two substrates of this enzyme are ATP and 4-methyl-5-(2-hydroxyethyl)thiazole, whereas its two products are ADP and 4-methyl-5-(2-phosphonooxyethyl)thiazole.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:4-methyl-5-(2-hydroxyethyl)thiazole 2-phosphotransferase. Other names in common use include hydroxyethylthiazole kinase (phosphorylating), and 4-methyl-5-(beta-hydroxyethyl)thiazole kinase. This enzyme participates in thiamine metabolism. Thiamine pyrophosphate (TPP), a required cofactor for many enzymes in the cell, is synthesised "de novo" in "Salmonella typhimurium".
In "Saccharomyces cerevisiae", hydroxyethylthiazole kinase expression is regulated at the mRNA level by intracellular thiamin pyrophosphate.
Structural studies.
As of late 2007, 6 structures have been solved for this class of enzymes, with PDB accession codes 1C3Q, 1EKK, 1EKQ, 1ESJ, 1ESQ, and 1V8A.
References.
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[
{
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"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14678648
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14678658
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Hydroxylysine kinase
|
In enzymology, a hydroxylysine kinase (EC 2.7.1.81) is an enzyme that catalyzes the chemical reaction
GTP + 5-hydroxy-L-lysine formula_0 GDP + 5-phosphonooxy-L-lysine
Thus, the two substrates of this enzyme are GTP and 5-hydroxy-L-lysine, whereas its two products are GDP and 5-phosphonooxy-L-lysine.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is GTP:5-hydroxy-L-lysine O-phosphotransferase. Other names in common use include hydroxylysine kinase (phosphorylating), and guanosine triphosphate:5-hydroxy-L-lysine O-phosphotransferase. This enzyme participates in lysine degradation.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14678658
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14678690
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Hydroxymethylpyrimidine kinase
|
In enzymology, a hydroxymethylpyrimidine kinase (EC 2.7.1.49) is an enzyme that catalyzes the chemical reaction
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine formula_0 ADP + 4-amino-5-phosphonooxymethyl-2-methylpyrimidine
Thus, the two substrates of this enzyme are ATP and 4-amino-5-hydroxymethyl-2-methylpyrimidine, whereas its two products are ADP and 4-amino-5-phosphonooxymethyl-2-methylpyrimidine.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:4-amino-5-hydroxymethyl-2-methylpyrimidine 5-phosphotransferase. This enzyme is also called hydroxymethylpyrimidine kinase (phosphorylating). This enzyme participates in thiamine metabolism.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14678690
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14678717
|
Hygromycin-B kinase
|
In enzymology, a hygromycin-B kinase (EC 2.7.1.119) is an enzyme that catalyzes the chemical reaction
ATP + hygromycin B formula_0 ADP + 7"-O-phosphohygromycin
Thus, the two substrates of this enzyme are ATP and hygromycin B, whereas its two products are ADP and 7"-O-phosphohygromycin.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:hygromycin-B 7"-O-phosphotransferase. This enzyme is also called hygromycin B phosphotransferase.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14678717
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14678754
|
Hypotaurocyamine kinase
|
In enzymology, a hypotaurocyamine kinase (EC 2.7.3.6) is an enzyme that catalyzes the chemical reaction
ATP + hypotaurocyamine formula_0 ADP + Nomega-phosphohypotaurocyamine
Thus, the two substrates of this enzyme are ATP and hypotaurocyamine, whereas its two products are ADP and Nomega-phosphohypotaurocyamine.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with a nitrogenous group as acceptor. The systematic name of this enzyme class is ATP:hypotaurocyamine N-phosphotransferase.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14678754
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14678811
|
Inosine kinase
|
Class of enzymes
In enzymology, an inosine kinase (EC 2.7.1.73) is an enzyme that catalyzes the chemical reaction
ATP + inosine formula_0 ADP + IMP
Thus, the two substrates of this enzyme are ATP and inosine, whereas its two products are ADP and IMP.
Inosine kinase belongs to the phosphofructokinase B (PfkB) family of sugar kinases. Other members of this family (also known as the Ribokinase family) include ribokinase (RK) adenosine kinase (AK), fructokinase, and 1-phosphofructokinase. The members of the PfkB/RK family are identified by the presence of three conserved sequence motifs. The structures of several PfK family of proteins have been determined from a number of organisms and the enzymatic activity of this family of this family of protein shows a dependence on the presence of pentavalent ions. Despite low sequence similarity between inosine kinase and other PfkB family of proteins, these proteins are quite similar at structural levels. Other names in common use include inosine-guanosine kinase, and inosine kinase (phosphorylating). This enzyme participates in purine metabolism.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14678811
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14678843
|
Inositol 3-kinase
|
In enzymology, an inositol 3-kinase (EC 2.7.1.64) is an enzyme that catalyzes the chemical reaction
ATP + myo-inositol formula_0 ADP + 1D-myo-inositol 3-phosphate
Thus, the two substrates of this enzyme are ATP and myo-inositol, whereas its two products are ADP and 1D-myo-inositol 3-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:myo-inositol 1-phosphotransferase. Other names in common use include inositol-1-kinase (phosphorylating), myoinositol kinase, and myo-inositol 1-kinase. This enzyme participates in inositol phosphate metabolism.
References.
<templatestyles src="Reflist/styles.css" />
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14678843
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14678877
|
Inositol-pentakisphosphate 2-kinase
|
In enzymology, an inositol-pentakisphosphate 2-kinase (EC 2.7.1.158) is an enzyme that catalyzes the chemical reaction
ATP + 1D-myo-inositol 1,3,4,5,6-pentakisphosphate formula_0 ADP + 1D-myo-inositol hexakisphosphate
Thus, the two substrates of this enzyme are ATP and 1D-myo-inositol 1,3,4,5,6-pentakisphosphate, whereas its two products are ADP and 1D-myo-inositol hexakisphosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:1D-myo-inositol 1,3,4,5,6-pentakisphosphate 2-phosphotransferase. Other names in common use include IP5 2-kinase, Gsl1p, Ipk1p, inositol polyphosphate kinase, inositol 1,3,4,5,6-pentakisphosphate 2-kinase, and Ins(1,3,4,5,6)P5 2-kinase.
References.
<templatestyles src="Reflist/styles.css" />
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14678877
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14678926
|
Inositol-tetrakisphosphate 1-kinase
|
Enzyme
In enzymology, an inositol-tetrakisphosphate 1-kinase (EC 2.7.1.134) is an enzyme that catalyzes the chemical reaction
ATP + 1D-myo-inositol 3,4,5,6-tetrakisphosphate formula_0 ADP + 1D-myo-inositol 1,3,4,5,6-pentakisphosphate
Thus, the two substrates of this enzyme are ATP and 1D-myo-inositol 3,4,5,6-tetrakisphosphate, whereas its two products are ADP and 1D-myo-inositol 1,3,4,5,6-pentakisphosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:1D-myo-inositol-3,4,5,6-tetrakisphosphate 1-phosphotransferase. Other names in common use include 1D-myo-inositol-tetrakisphosphate 1-kinase, inositol-trisphosphate 6-kinase, 1D-myo-inositol-trisphosphate 6-kinase, ATP:1D-myo-inositol-1,3,4-trisphosphate 6-phosphotransferase, inositol-trisphosphate 5-kinase, 1D-myo-inositol-trisphosphate 5-kinase, and ATP:1D-myo-inositol-1,3,4-trisphosphate 5-phosphotransferase. This enzyme participates in inositol phosphate metabolism and phosphatidylinositol signaling system.
Structural studies.
As of late 2007, 3 structures have been solved for this class of enzymes, with PDB accession codes 2ODT, 2Q7D, and 2QB5.
References.
<templatestyles src="Reflist/styles.css" />
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14678926
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14678957
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Inositol-tetrakisphosphate 5-kinase
|
In enzymology, an inositol-tetrakisphosphate 5-kinase (EC 2.7.1.140) is an enzyme that catalyzes the chemical reaction
ATP + 1D-myo-inositol 1,3,4,6-tetrakisphosphate formula_0 ADP + 1D-myo-inositol 1,3,4,5,6-pentakisphosphate
Thus, the two substrates of this enzyme are ATP and 1D-myo-inositol 1,3,4,6-tetrakisphosphate, whereas its two products are ADP and 1D-myo-inositol 1,3,4,5,6-pentakisphosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:1D-myo-inositol-1,3,4,6-tetrakisphosphate 5-phosphotransferase. This enzyme is also called 1D-myo-inositol-tetrakisphosphate 5-kinase. This enzyme participates in inositol phosphate metabolism and phosphatidylinositol signaling system.
References.
<templatestyles src="Reflist/styles.css" />
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14678957
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14679008
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Isocitrate dehydrogenase (NADP+) kinase
|
In enzymology, a [isocitrate dehydrogenase (NADP+)] kinase (EC 2.7.11.5) is an enzyme that catalyzes the chemical reaction:
ATP + [isocitrate dehydrogenase (NADP+)] formula_0 ADP + [isocitrate dehydrogenase (NADP+)] phosphate
Thus, the two substrates of this enzyme are ATP and isocitrate dehydrogenase (NADP+), whereas its two products are ADP and isocitrate dehydrogenase (NADP+) phosphate.
This enzyme belongs to the family of transferases, specifically those transferring a phosphate group to the sidechain oxygen atom of serine or threonine residues in proteins (protein-serine/threonine kinases).
Other names.
The systematic name of this enzyme class is ATP:[isocitrate dehydrogenase (NADP+)] phosphotransferase. Other names in common use include [isocitrate dehydrogenase (NADP+)] kinase, ICDH kinase/phosphatase, IDH kinase, IDH kinase/phosphatase, IDH-K/P, IDHK/P, isocitrate dehydrogenase kinase (phosphorylating), isocitrate dehydrogenase kinase/phosphatase, and STK3.
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{
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"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14679008
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14679061
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L-arabinokinase
|
In enzymology, a L-arabinokinase (EC 2.7.1.46) is an enzyme that catalyzes the chemical reaction
ATP + L-arabinose formula_0 ADP + beta-L-arabinose 1-phosphate
Thus, the two substrates of this enzyme are ATP and L-arabinose, whereas its two products are ADP and beta-L-arabinose 1-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:L-arabinose 1-phosphotransferase. This enzyme is also called L-arabinokinase (phosphorylating). This enzyme participates in nucleotide sugars metabolism.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14679061
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14679102
|
Lombricine kinase
|
In enzymology, a lombricine kinase (EC 2.7.3.5) is an enzyme that catalyzes the chemical reaction
ATP + lombricine formula_0 ADP + N-phospholombricine
The two substrates of this enzyme are ATP and lombricine, and the two products are ADP and N-phospholombricine.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with a nitrogenous group as acceptor. The systematic name of this enzyme class is ATP:lombricine N-phosphotransferase. This enzyme participates in glycine, serine and threonine metabolism.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14679102
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14679135
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Low-density-lipoprotein receptor kinase
|
In enzymology, a low-density-lipoprotein receptor kinase (EC 2.7.11.29) is an enzyme that catalyzes the chemical reaction
ATP + [low-density-lipoprotein receptor]-L-serine formula_0 ADP + [low-density-lipoprotein receptor]-O-phospho-L-serine
Thus, the two substrates of this enzyme are ATP and [low-density-lipoprotein receptor]-L-serine, whereas its two products are ADP and [low-density-lipoprotein receptor]-O-phospho-L-serine.
This enzyme belongs to the family of transferases, specifically those transferring a phosphate group to the sidechain oxygen atom of serine or threonine residues in proteins (protein-serine/threonine kinases). The systematic name of this enzyme class is ATP:[low-density-lipoprotein receptor]-L-serine O-phosphotransferase. Other names in common use include ATP:low-density-lipoprotein-L-serine O-phosphotransferase, LDL receptor kinase, [low-density-lipoprotein] kinase, low-density lipoprotein kinase, low-density-lipoprotein receptor kinase (phosphorylating), and STK7.
References.
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{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14679135
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14679155
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L-xylulokinase
|
In enzymology, a L-xylulokinase (EC 2.7.1.53) is an enzyme that catalyzes the chemical reaction
ATP + L-xylulose formula_0 ADP + L-xylulose 5-phosphate
Thus, the two substrates of this enzyme are ATP and L-xylulose, whereas its two products are ADP and L-xylulose 5-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:L-xylulose 5-phosphotransferase. This enzyme is also called L-xylulokinase (phosphorylating). This enzyme participates in pentose and glucuronate interconversions and ascorbate and aldarate metabolism.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14679155
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14679185
|
Macrolide 2'-kinase
|
In enzymology, a macrolide 2'-kinase (EC 2.7.1.136) is an enzyme that catalyzes the chemical reaction
ATP + oleandomycin formula_0 ADP + oleandomycin 2'-O-phosphate
Thus, the two substrates of this enzyme are ATP and oleandomycin, whereas its two products are ADP and oleandomycin 2'-O-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:macrolide 2'-O-phosphotransferase.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14679185
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14679206
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Mannokinase
|
In enzymology, a mannokinase (EC 2.7.1.7) is an enzyme that catalyzes the chemical reaction
ATP + D-mannose formula_0 ADP + D-mannose 6-phosphate
Thus, the two substrates of this enzyme are ATP and D-mannose, whereas its two products are ADP and D-mannose 6-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:D-mannose 6-phosphotransferase. Other names in common use include mannokinase (phosphorylating), and D-fructose (D-mannose) kinase. This enzyme participates in fructose and mannose metabolism.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14679206
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14679233
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Mannose-1-phosphate guanylyltransferase
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In enzymology, a mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) is an enzyme that catalyzes the chemical reaction
GTP + alpha-D-mannose 1-phosphate formula_0 diphosphate + GDP-mannose
Thus, the two substrates of this enzyme are GTP and alpha-D-mannose 1-phosphate, whereas its two products are diphosphate and GDP-mannose.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing nucleotide groups (nucleotidyltransferases). The systematic name of this enzyme class is GTP:alpha-D-mannose-1-phosphate guanylyltransferase. Other names in common use include GTP-mannose-1-phosphate guanylyltransferase, PIM-GMP (phosphomannose isomerase-guanosine 5'-diphospho-D-mannose, pyrophosphorylase), GDP-mannose pyrophosphorylase, guanosine 5'-diphospho-D-mannose pyrophosphorylase, guanosine diphosphomannose pyrophosphorylase, guanosine triphosphate-mannose 1-phosphate guanylyltransferase, and mannose 1-phosphate guanylyltransferase (guanosine triphosphate). This enzyme participates in fructose and mannose metabolism.
Structural studies.
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code 2CU2.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14679233
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14679259
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Mannose-1-phosphate guanylyltransferase (GDP)
|
In enzymology, a mannose-1-phosphate guanylyltransferase (GDP) (EC 2.7.7.22) is an enzyme that catalyzes the chemical reaction
GDP + alpha-D-mannose 1-phosphate formula_0 phosphate + GDP-mannose
Thus, the two substrates of this enzyme are GDP and alpha-D-mannose 1-phosphate, whereas its two products are phosphate and GDP-mannose.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing nucleotide groups (nucleotidyltransferases). The systematic name of this enzyme class is GDP:alpha-D-mannose-1-phosphate guanylyltransferase. This enzyme participates in fructose and mannose metabolism.
References.
<templatestyles src="Reflist/styles.css" />
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
}
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https://en.wikipedia.org/wiki?curid=14679259
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14679314
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MRNA guanylyltransferase
|
Class of enzymes
In enzymology, a mRNA guanylyltransferase (EC 2.7.7.50) is an enzyme that catalyzes the chemical reaction
GTP + (5')ppPur-mRNA formula_0 diphosphate + G(5')pppPur-mRNA
Thus, the two substrates of this enzyme are GTP and (5')ppPur-mRNA, whereas its two products are diphosphate and G(5')pppPur-mRNA.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing nucleotide groups (nucleotidyltransferases).op The systematic name of this enzyme class is GTP:mRNA guanylyltransferase. Other names in common use include mRNA capping enzyme, messenger RNA guanylyltransferase, and Protein 2.
Structural studies.
As of late 2007, 5 structures have been solved for this class of enzymes, with PDB accession codes 1CKM, 1CKN, 1CKO, 1P16, and 2C46.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14679314
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14679337
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Myosin-heavy-chain kinase
|
In enzymology, a myosin-heavy-chain kinase (EC 2.7.11.7) is an enzyme that catalyzes the chemical reaction
ATP + [myosin heavy-chain] formula_0 ADP + [myosin heavy-chain] phosphate
Thus, the two substrates of this enzyme are ATP and myosin heavy-chain, whereas its two products are ADP and myosin heavy-chain phosphate.
This enzyme belongs to the family of transferases, specifically those transferring a phosphate group to the sidechain oxygen atom of serine or threonine residues in proteins (protein-serine/threonine kinases). The systematic name of this enzyme class is ATP:[myosin heavy-chain] O-phosphotransferase. Other names in common use include
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
}
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https://en.wikipedia.org/wiki?curid=14679337
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14679371
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N-acetylgalactosamine kinase
|
In enzymology, a N-acetylgalactosamine kinase (EC 2.7.1.157) is an enzyme that catalyzes the chemical reaction
ATP + N-acetyl-D-galactosamine formula_0 ADP + N-acetyl-alpha-D-galactosamine 1-phosphate
Thus, the two substrates of this enzyme are ATP and N-acetyl-D-galactosamine, whereas its two products are ADP and N-acetyl-alpha-D-galactosamine 1-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:N-acetyl-D-galactosamine 1-phosphotransferase. Other names in common use include GALK2, GK2, GalNAc kinase, and N-acetylgalactosamine (GalNAc)-1-phosphate kinase.
References.
<templatestyles src="Reflist/styles.css" />
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14679371
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14679393
|
N-acetylglucosamine kinase
|
In enzymology, a N-acetylglucosamine kinase (EC 2.7.1.59) is an enzyme that catalyzes the chemical reaction
ATP + N-acetyl-D-glucosamine formula_0 ADP + N-acetyl-D-glucosamine 6-phosphate
Thus, the two substrates of this enzyme are ATP and N-acetyl-D-glucosamine, whereas its two products are ADP and N-acetyl-D-glucosamine 6-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:N-acetyl-D-glucosamine 6-phosphotransferase. Other names in common use include acetylglucosamine kinase (phosphorylating), ATP:2-acetylamino-2-deoxy-D-glucose 6-phosphotransferase, 2-acetylamino-2-deoxy-D-glucose kinase, and acetylaminodeoxyglucokinase. This enzyme participates in glutamate metabolism and aminosugars metabolism.
References.
<templatestyles src="Reflist/styles.css" />
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
}
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https://en.wikipedia.org/wiki?curid=14679393
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14679417
|
N-acylmannosamine kinase
|
In enzymology, a N-acylmannosamine kinase (EC 2.7.1.60) is an enzyme that catalyzes the chemical reaction
ATP + N-acyl-D-mannosamine formula_0 ADP + N-acyl-D-mannosamine 6-phosphate
Thus, the two substrates of this enzyme are ATP and N-acyl-D-mannosamine, whereas its two products are ADP and N-acyl-D-mannosamine 6-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:N-acyl-D-mannosamine 6-phosphotransferase. Other names in common use include acylmannosamine kinase (phosphorylating), acetylamidodeoxymannokinase, acetylmannosamine kinase, acylaminodeoxymannokinase, acylmannosamine kinase, N-acyl-D-mannosamine kinase, N-acetylmannosamine kinase, and ATP:N-acetylmannosamine 6-phosphotransferase. This enzyme participates in aminosugars metabolism.
Structural studies.
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code 2AA4.
References.
<templatestyles src="Reflist/styles.css" />
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
}
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https://en.wikipedia.org/wiki?curid=14679417
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14679446
|
N-acylneuraminate cytidylyltransferase
|
In enzymology, a N-acylneuraminate cytidylyltransferase (EC 2.7.7.43) is an enzyme that catalyzes the chemical reaction
CTP + N-acylneuraminate formula_0 diphosphate + CMP-N-acylneuraminate
Thus, the two substrates of this enzyme are CTP and N-acylneuraminate, whereas its two products are diphosphate and CMP-N-acylneuraminate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing nucleotide groups (nucleotidyltransferases). The systematic name of this enzyme class is CTP:N-acylneuraminate cytidylyltransferase. Other names in common use include CMP-sialate pyrophosphorylase, CMP-sialate synthase, cytidine 5'-monophosphosialic acid synthetase, CMP-Neu5Ac synthetase, CMP-NeuAc synthetase, acylneuraminate cytidyltransferase, CMP-N-acetylneuraminate synthetase, CMP-N-acetylneuraminate synthase, CMP-N-acetylneuraminic acid synthase, CMP-NANA synthetase, CMP-sialate synthetase, CMP-sialic synthetase, cytidine 5'-monophospho-N-acetylneuraminic acid synthetase, cytidine 5-monophosphate N-acetylneuraminic acid synthetase, cytidine monophosphosialic acid synthetase, cytidine monophosphoacetylneuraminic synthetase, cytidine monophosphosialate pyrophosphorylase, cytidine monophosphosialate synthetase, and acetylneuraminate cytidylyltransferase. This enzyme participates in aminosugars metabolism.
Structural studies.
As of late 2007, three structures have been solved for this class of enzymes, with PDB accession codes 1EYR, 1EZI, and 1QWJ.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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1467946
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Modelica
|
Computer Language for System Modeling
Modelica is an object-oriented, declarative, multi-domain modeling language for component-oriented modeling of complex systems, e.g., systems containing mechanical, electrical, electronic, hydraulic, thermal, control, electric power or process-oriented subcomponents.
The free Modelica language
is developed by the non-profit Modelica Association. The Modelica Association also develops the free Modelica Standard Library that contains about 1400 generic model components and 1200 functions in various domains, as of version 4.0.0.
Characteristics.
While Modelica resembles object-oriented programming languages, such as C++ or Java, it differs in two important respects. First, Modelica is a modeling language rather than a conventional "programming" language. Modelica classes are not compiled in the usual sense, but they are translated into objects which are then exercised by a simulation engine. The simulation engine is not specified by the language, although certain required capabilities are outlined.
Second, although classes may contain algorithmic components similar to statements or blocks in programming languages, their primary content is a set of "equations". In contrast to a typical assignment statement, such as
x := 2 + y;
where the left-hand side of the statement is assigned a value calculated from the expression on the right-hand side, an equation may have expressions on both its right- and left-hand sides, for example,
x + y = 3 * z;
Equations do not describe assignment but "equality". In Modelica terms, equations have no pre-defined "causality". The simulation engine may (and usually must) manipulate the equations symbolically to determine their order of execution and which components in the equation are inputs and which are outputs.
History.
The Modelica design effort was initiated in September 1996 by Hilding Elmqvist.
The goal was to develop an object-oriented language for modeling
of technical systems in order to reuse and exchange dynamic system models in
a standardized format. Modelica 1.0 is based on the
PhD thesis of Hilding Elmqvist and on the experience with the modeling languages Allan,
Dymola, NMF
ObjectMath,
Omola,
SIDOPS+, and Smile. Hilding Elmqvist is the key architect of Modelica, but many other people have contributed as well (see appendix E in the Modelica specification). In September 1997, version 1.0 of the Modelica specification was released which was the basis for a prototype implementation within the commercial Dymola software system. In year 2000, the non-profit Modelica Association was formed to manage the continually evolving Modelica language and the development of the free Modelica Standard Library. In the same year, the usage of Modelica in industrial applications started.
This table presents the timeline of the Modelica specification history:
Implementations.
Commercial front-ends for Modelica include AMESim from the French company Imagine SA (now part of Siemens Digital Industries Software), Dymola from the Swedish company Dynasim AB (now part of Dassault Systemes), Wolfram SystemModeler (formerly "MathModelica") from the Swedish company Wolfram MathCore AB (now part of Wolfram Research), SimulationX from the German company ESI ITI GmbH, MapleSim from the Canadian company Maplesoft,
JModelica.org (open source, discontinued) and Modelon Impact, from the Swedish company Modelon AB, and
CATIA Systems
from Dassault Systemes (CATIA is one of the major CAD systems).
Openmodelica is an open-source Modelica-based modeling and simulation environment intended for industrial and academic usage. Its long-term development is supported by a non-profit organization – the Open Source Modelica Consortium (OSMC). The goal with the OpenModelica effort is to create a comprehensive Open Source Modelica modeling, compilation and simulation environment based on free software distributed in binary and source code form for research, teaching, and industrial usage.
The free simulation environment Scicos uses a subset of Modelica for component modeling. Support for a larger part of the Modelica language is currently under development.
Nevertheless, there is still some incompatibility and diverging interpretation between all the different tools concerning the Modelica language.
Examples.
The following code fragment shows a very simple example of a first order system
(formula_0):
model FirstOrder
parameter Real c=1 "Time constant";
Real x (start=10) "An unknown";
equation
der(x) = -c*x "A first order differential equation";
end FirstOrder;
The following code fragment shows an example to calculate the second derivative of a trigonometric function, using OMShell, as a means to develop the program written below.
model second_derivative
Real l;
Real z=sin(w*time);
Real m;
parameter Real w = 1;
equation
l=der(z);
m=der(l);
end second_derivative;
Interesting things to note about this example are the 'parameter' qualifier, which indicates that a given variable is time-invariant and the 'der' operator, which represents (symbolically) the time derivative of a variable. Also worth noting are the documentation strings that can be associated with declarations and equations.
The main application area of Modelica is the modeling of physical systems. The most basic structuring concepts are shown at hand of simple examples from the electrical domain:
Built-in and user derived types.
Modelica has the four built-in types Real, Integer, Boolean, String. Typically, user-defined types are derived, to associate physical quantity, unit, nominal values, and other attributes:
type Voltage = Real(quantity="ElectricalPotential", unit="V");
type Current = Real(quantity="ElectricalCurrent", unit="A");
Connectors describing physical interaction.
The interaction of a component to other components is defined by physical ports, called connectors, e.g., an electrical pin is defined as
connector Pin "Electrical pin"
Voltage v "Potential at the pin";
flow Current i "Current flowing into the component";
end Pin;
When drawing connection lines between ports, the meaning is that corresponding connector variables without the "flow" prefix are identical (here: "v") and that corresponding connector variables with the "flow" prefix (here: "i") are defined by a zero-sum equation (the sum of all corresponding "flow" variables is zero). The motivation is to automatically fulfill the relevant balance equations at the infinitesimally small connection point.
Basic model components.
A basic model component is defined by a model and contains equations that describe the relationship between the connector variables in a declarative form (i.e., without specifying the calculation order):
model Capacitor
parameter Capacitance C;
Voltage u "Voltage drop between pin_p and pin_n";
Pin pin_p, pin_n;
equation
0 = pin_p.i + pin_n.i;
u = pin_p.v - pin_n.v;
C * der(u) = pin_p.i;
end Capacitor;
The goal is that a connected set of model components leads to a set of differential, algebraic and discrete equations where the number of unknowns and the number of equations is identical. In Modelica, this is achieved by requiring so called balanced models.
The full rules for defining balanced models are rather complex, and can be read from
in section 4.7.
However, for most cases, a simple rule can be issued, that counts variables and equations the same way as most simulation tools do:
given that variables and equations must be counted according to the following rule:
"Note that standard input connectors (such as RealInput or IntegerInput) do not contribute to the count of variables since no new variables are defined inside them."
The reason for this rule can be understood thinking of the capacitor defined above. Its pins contain a flow variable, i.e. a current, each. When we check it, it is connected to nothing. This corresponds to set an equation pin.i=0 for each pin. That's why we must add an equation for each flow variable.
Obviously the example can be extended to other cases, in which other kinds of flow variables are involved (e.g. forces, torques, etc.).
When our capacitor is connected to another (balanced) model through one of its pins, a connection equation will be generated that will substitute the two i=0 equations of the pins being connected. Since the connection equation corresponds to two scalar equations, the connection operation will leave the balanced larger model (constituted by our Capacitor and the model it is connected to).
The Capacitor model above is balanced, since
Verification using OpenModelica of this model gives, in fact
Another example, containing both input connectors and physical connectors is the following component from Modelica Standard Library:
model SignalVoltage
"Generic voltage source using the input signal as source voltage"
Interfaces.PositivePin p;
Interfaces.NegativePin n;
Modelica.Blocks.Interfaces.RealInput v(unit="V")
"Voltage between pin p and n (= p.v - n.v) as input signal";
SI.Current i "Current flowing from pin p to pin n";
equation
v = p.v - n.v;
0 = p.i + n.i;
i = p.i;
end SignalVoltage;
The component SignalVoltage is balanced since
Again, checking with OpenModelica gives
Hierarchical models.
A hierarchical model is built-up from basic models, by instantiating basic models, providing suitable values for the model parameters, and by connecting model connectors. A typical example is the following electrical circuit:
model Circuit
Capacitor C1(C=1e-4) "A Capacitor instance from the model above";
Capacitor C2(C=1e-5) "A Capacitor instance from the model above";
equation
connect(C1.pin_p, C2.pin_n);
end Circuit;
Via the language element annotation(...), definitions can be added to a model that do not have an influence on a simulation. Annotations are used to define graphical layout, documentation and version information. A basic set of graphical annotations is standardized to ensure that the graphical appearance and layout of models in different Modelica tools is the same.
Applications.
Modelica is designed to be domain neutral and, as a result, is used in a wide variety of applications, such as fluid systems (for example, steam power generation, hydraulics, etc.), automotive applications (especially powertrain) and mechanical systems (for example, multi-body systems, mechatronics, etc.).
In the automotive sector, many of the major automotive OEMs are using Modelica. These include Ford, General Motors, Toyota, BMW, and Daimler.
Modelica is also being increasingly used for the simulation of thermo-fluid and energy systems.
The characteristics of Modelica (acausal, object-oriented, domain neutral) make it well suited to system-level simulation, a domain where Modelica is now well established.
Notes.
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[
{
"math_id": 0,
"text": "\\dot x = - c \\cdot x, x(0)=10 "
}
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14679477
|
NADH kinase
|
Class of enzymes
In enzymology, a NADH kinase (EC 2.7.1.86) is an enzyme that catalyzes a chemical reaction.
ATP + NADH formula_0 ADP + NADPH
Explanation.
Thus, the two substrates of this enzyme are ATP and NADH, whereas its two products are ADP and NADPH.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:NADH 2'-phosphotransferase. Other names in common use include reduced nicotinamide adenine dinucleotide kinase (phosphorylating), DPNH kinase, reduced diphosphopyridine nucleotide kinase, and NADH kinase. This enzyme has at least one activator, acetate.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
}
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14679497
|
Nicotinamide-nucleotide adenylyltransferase
|
In enzymology, nicotinamide-nucleotide adenylyltransferase (NMNAT) (EC 2.7.7.1) are enzymes that catalyzes the chemical reaction
ATP + nicotinamide mononucleotide formula_0 diphosphate + NAD+
Thus, the two substrates of this enzyme are ATP and nicotinamide mononucleotide (NMN), whereas its two products are diphosphate and NAD+.
This enzyme participates in nicotinate and nicotinamide metabolism.
Humans have three protein isoforms: NMNAT1 (widespread), NMNAT2 (predominantly in brain), and NMNAT3 (highest in liver, heart, skeletal muscle, and erythrocytes). Mutations in the "NMNAT1" gene lead to the LCA9 form of Leber congenital amaurosis. Mutations in "NMNAT2" or "NMNAT3" genes are not known to cause any human disease. NMNAT2 is critical for neurons: loss of NMNAT2 is associated with neurodegeneration. All NMNAT isoforms reportedly decline with age.
Belongs to.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing nucleotide groups (nucleotidyltransferases). The systematic name of this enzyme class is ATP:nicotinamide-nucleotide adenylyltransferase. Other names in common use include NAD+ pyrophosphorylase, adenosine triphosphate-nicotinamide mononucleotide transadenylase, ATP:NMN adenylyltransferase, diphosphopyridine nucleotide pyrophosphorylase, nicotinamide adenine dinucleotide pyrophosphorylase, nicotinamide mononucleotide adenylyltransferase, and NMN adenylyltransferase.
Structural studies.
As of late 2007, 11 structures have been solved for this class of enzymes, with PDB accession codes 1EJ2, 1GZU, 1HYB, 1KKU, 1KQN, 1KQO, 1KR2, 1M8F, 1M8G, 1M8J, and 1M8K.
Isoform cellular localization.
The three protein isoforms have the following cellular localizations
All three NMNATs compete for the NMN produced by NAMPT.
Clinical significance.
Chronic inflammation due to obesity and other causes reduced NMNAT and NAD+ levels in many tissues.
References.
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{
"math_id": 0,
"text": "\\rightleftharpoons"
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14679527
|
Nicotinate-nucleotide adenylyltransferase
|
In enzymology, a nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18) is an enzyme that catalyzes the chemical reaction
ATP + nicotinate ribonucleotide formula_0 diphosphate + deamido-NAD+
Thus, the two substrates of this enzyme are ATP and nicotinate ribonucleotide, whereas its two products are diphosphate and deamido-NAD+.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing nucleotide groups (nucleotidyltransferases). The systematic name of this enzyme class is ATP:nicotinate-ribonucleotide adenylyltransferase. Other names in common use include deamido-NAD+ pyrophosphorylase, nicotinate mononucleotide adenylyltransferase, deamidonicotinamide adenine dinucleotide pyrophosphorylase, NaMN-ATase, and nicotinic acid mononucleotide adenylyltransferase. This enzyme participates in nicotinate and nicotinamide metabolism.
Structural studies.
As of late 2007, 9 structures have been solved for this class of enzymes, with PDB accession codes 1K4K, 1K4M, 1KAM, 1KAQ, 1YUL, 1YUM, 1YUN, 2H29, and 2H2A.
References.
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14679568
|
N-methylphosphoethanolamine cytidylyltransferase
|
In enzymology, a N-methylphosphoethanolamine cytidylyltransferase (EC 2.7.7.57) is an enzyme that catalyzes the chemical reaction
CTP + N-methylethanolamine phosphate formula_0 diphosphate + CDP-N-methylethanolamine
Thus, the two substrates of this enzyme are CTP and N-methylethanolamine phosphate, whereas its two products are diphosphate and CDP-N-methylethanolamine.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing nucleotide groups (nucleotidyltransferases). The systematic name of this enzyme class is CTP:N-methylethanolamine-phosphate cytidylyltransferase. Other names in common use include monomethylethanolamine phosphate cytidylyltransferase, and CTP:P-MEA cytidylyltransferase.
References.
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14679645
|
Fas-activated serine/threonine kinase
|
In enzymology, a Fas-activated serine/threonine kinase (EC 2.7.11.8) is an enzyme that catalyzes the chemical reaction
ATP + [Fas-activated serine/threonine protein] formula_0 ADP + [Fas-activated serine/threonine phosphoprotein]
Thus, the two substrates of this enzyme are ATP and Fas-activated serine/threonine protein, whereas its two products are ADP and Fas-activated serine/threonine phosphoprotein.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups protein-serine/threonine kinases. The systematic name of this enzyme class is ATP:[Fas-activated serine/threonine protein] phosphotransferase. Other names in common use include FAST, FASTK, and STK10.
References.
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{
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"text": "\\rightleftharpoons"
}
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14679673
|
Nucleoside-phosphate kinase
|
In enzymology, a nucleoside-phosphate kinase (EC 2.7.4.4) is an enzyme that catalyzes the chemical reaction
ATP + nucleoside phosphate formula_0 ADP + nucleoside diphosphate
Thus, the two substrates of this enzyme are ATP and nucleoside monophosphate, whereas its two products are ADP and nucleoside diphosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with a phosphate group as acceptor. The systematic name of this enzyme class is ATP:nucleoside-phosphate phosphotransferase. This enzyme is also called NMP-kinase, or nucleoside-monophosphate kinase.
Structure.
A number of crystal structures have been solved for this class of enzymes, revealing that they share a common ATP binding domain. This section of the enzyme is commonly referred to as the P-loop, in reference to its interaction with the phosphoryl groups on ATP. This binding domain also consists of a β sheet flanked by α helices.
The [P-loop] typically has the amino acid sequence of Gly-X-X-X-X-Gly-Lys. Similar sequences are found in many other nucleotide-binding proteins.
Mechanism.
Metal ion interaction.
To allow for interaction with this class of enzymes, ATP must first bind to a metal ion such as magnesium or manganese. The metal ion forms a complex with the phosphoryl-group, as well as several water molecules. These water molecules then form hydrogen bonds to a conserved aspartate residue on the enzyme.
The metal ion interaction facilitates binding by holding the ATP molecule in a position allowing for specific binding to the active site and by providing additional points for binding between the substrate and the enzyme. This increases the binding energy.
Conformational changes.
Binding of ATP causes the P-loop to move, in turn making the lid domain lower and secure the ATP in place. Nucleoside monophosphate binding induces further changes that render the enzyme catalytically capable of facilitating a transfer of the phosphoryl group from ATP to nucleoside monophosphate.
The necessity of these conformational changes prevents the wasteful hydrolysis of ATP.
This enzyme mechanism is an example of catalysis by approximation: the nucleoside-phosphate kinase binds the substrates to bring them together in the correct position for the phosphoryl group to be transferred.
Biological function.
Similar catalytic domains are present in a variety of proteins, including:
Evolution.
When a phylogenetic tree composed of members of the nucleoside-phosphate kinase family was made, it showed that these enzymes had originally diverged from a common ancestor into long and short varieties. This first change was drastic – the three-dimensional structure of the lid domain changed significantly.
Following the evolution of long and short varieties of NMP-kinases, smaller changes in the amino acid sequences resulted in the differentiation of subcellular localization.
References.
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14679713
|
Nucleoside phosphotransferase
|
In enzymology, a nucleoside phosphotransferase (EC 2.7.1.77) is an enzyme that catalyzes the chemical reaction
a nucleotide + a 2'-deoxynucleoside formula_0 a nucleoside + a 2'-deoxynucleoside 5'-phosphate
Thus, the two substrates of this enzyme are nucleotide and 2'-deoxynucleoside, whereas its two products are nucleoside and 2'-deoxynucleoside 5'-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is nucleotide:nucleoside 5'-phosphotransferase. Other names in common use include nonspecific nucleoside phosphotransferase, and nucleotide:3'-deoxynucleoside 5'-phosphotransferase.
References.
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14679737
|
Nucleoside-triphosphate—adenylate kinase
|
In enzymology, a nucleoside-triphosphate-adenylate kinase (EC 2.7.4.10) is an enzyme that catalyzes the chemical reaction
nucleoside triphosphate + AMP formula_0 nucleoside diphosphate + ADP
Thus, the two substrates of this enzyme are nucleoside triphosphate and AMP, whereas its two products are nucleoside diphosphate and ADP.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with a phosphate group as acceptor. The systematic name of this enzyme class is nucleoside-triphosphate:AMP phosphotransferase. Other names in common use include guanosine triphosphate-adenylate kinase, nucleoside triphosphate-adenosine monophosphate transphosphorylase, GTP:AMP phosphotransferase, and isozyme 3 of adenylate kinase. This enzyme participates in pyrimidine metabolism.
Structural studies.
As of late 2007, two structures have been solved for this class of enzymes, with PDB accession codes 1ZD8 and 2AK3.
References.
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{
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14679765
|
Nucleoside-triphosphate-aldose-1-phosphate nucleotidyltransferase
|
In enzymology, a nucleoside-triphosphate-aldose-1-phosphate nucleotidyltransferase (EC 2.7.7.28) is an enzyme that catalyzes the chemical reaction
nucleoside triphosphate + alpha-D-aldose 1-phosphate formula_0 diphosphate + NDP-hexose
Thus, the two substrates of this enzyme are nucleoside triphosphate and alpha-D-aldose 1-phosphate, whereas its two products are diphosphate and NDP-hexose.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing nucleotide groups (nucleotidyltransferases). The systematic name of this enzyme class is NTP:alpha-D-aldose-1-phosphate nucleotidyltransferase. Other names in common use include NDP hexose pyrophosphorylase, hexose 1-phosphate nucleotidyltransferase, hexose nucleotidylating enzyme, nucleoside diphosphohexose pyrophosphorylase, hexose-1-phosphate guanylyltransferase, GTP:alpha-D-hexose-1-phosphate guanylyltransferase, GDP hexose pyrophosphorylase, guanosine diphosphohexose pyrophosphorylase, nucleoside-triphosphate-hexose-1-phosphate nucleotidyltransferase, and NTP:hexose-1-phosphate nucleotidyltransferase.
References.
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{
"math_id": 0,
"text": "\\rightleftharpoons"
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14679797
|
Nucleotide diphosphokinase
|
Class of enzymes
In enzymology, a nucleotide diphosphokinase (EC 2.7.6.4) is an enzyme that catalyzes the chemical reaction
ATP + nucleoside 5'-phosphate formula_0 AMP + 5'-phosphonucleoside 3'-diphosphate
Thus, the two substrates of this enzyme are ATP and nucleoside 5'-phosphate, whereas its two products are AMP and 5'-phosphonucleoside 3'-diphosphate.
This enzyme belongs to the family of transferases, specifically those transferring two phosphorus-containing groups (diphosphotransferases). The systematic name of this enzyme class is ATP:nucleoside-5'-phosphate diphosphotransferase. Other names in common use include nucleotide pyrophosphokinase, ATP:nucleotide pyrophosphotransferase, ATP nucleotide 3'-pyrophosphokinase, and nucleotide 3'-pyrophosphokinase.
References.
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{
"math_id": 0,
"text": "\\rightleftharpoons"
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14679831
|
Opheline kinase
|
In enzymology, an opheline kinase (EC 2.7.3.7) is an enzyme that catalyzes the chemical reaction
ATP + guanidinoethyl methyl phosphate formula_0 ADP + N'-phosphoguanidinoethyl methylphosphate
Thus, the two substrates of this enzyme are ATP and guanidinoethyl methyl phosphate, whereas its two products are ADP and N'-phosphoguanidinoethyl methylphosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with a nitrogenous group as acceptor. The systematic name of this enzyme class is ATP:guanidinoethyl-methyl-phosphate phosphotransferase.
References.
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{
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14679868
|
Phosphatidylglycerol—membrane-oligosaccharide glycerophosphotransferase
|
In enzymology, a phosphatidylglycerol-membrane-oligosaccharide glycerophosphotransferase (EC 2.7.8.20) is an enzyme that catalyzes the chemical reaction
phosphatidylglycerol + membrane-derived-oligosaccharide D-glucose formula_0 1,2-diacyl-sn-glycerol + membrane-derived-oligosaccharide 6-(glycerophospho)-D-glucose
Thus, the two substrates of this enzyme are phosphatidylglycerol and membrane-derived-oligosaccharide D-glucose, whereas its two products are 1,2-diacyl-sn-glycerol and membrane-derived-oligosaccharide 6-(glycerophospho)-D-glucose.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups transferases for other substituted phosphate groups. The systematic name of this enzyme class is phosphatidylglycerol:membrane-derived-oligosaccharide-D-glucose glycerophosphotransferase. Other names in common use include phosphoglycerol transferase, oligosaccharide glycerophosphotransferase, and phosphoglycerol transferase I. This enzyme participates in glycerolipid metabolism.
References.
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14679874
|
Pantetheine kinase
|
Class of enzymes
In enzymology, a pantetheine kinase (EC 2.7.1.34) is an enzyme that catalyzes the chemical reaction
ATP + pantetheine formula_0 ADP + pantetheine 4'-phosphate
Thus, the two substrates of this enzyme are ATP and pantetheine, whereas its two products are ADP and pantetheine 4'-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:pantetheine 4'-phosphotransferase. This enzyme is also called pantetheine kinase (phosphorylating). This enzyme participates in pantothenate and coa biosynthesis.
References.
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{
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14679903
|
Pantetheine-phosphate adenylyltransferase
|
In enzymology, a pantetheine-phosphate adenylyltransferase (EC 2.7.7.3) is an enzyme that catalyzes the chemical reaction
ATP + 4'-Phosphopantetheineformula_0 diphosphate + 3'-dephospho-CoA
Thus, the two substrates of this enzyme are ATP and 4'-Phosphopantetheine, whereas its two products are diphosphate and 3'-dephospho-CoA.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing nucleotide groups (nucleotidyltransferases). The systematic name of this enzyme class is ATP:pantetheine-4'-phosphate adenylyltransferase. Other names in common use include dephospho-CoA pyrophosphorylase, pantetheine phosphate adenylyltransferase, dephospho-coenzyme A pyrophosphorylase, and 3'-dephospho-CoA pyrophosphorylase. This enzyme participates in pantothenate and coa biosynthesis.
Structural studies.
As of late 2007, 8 structures have been solved for this class of enzymes, with PDB accession codes 1B6T, 1GN8, 1H1T, 1O6B, 1OD6, 1QJC, 1TFU, and 1VLH.
References.
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{
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https://en.wikipedia.org/wiki?curid=14679903
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14679939
|
Phenylalanine adenylyltransferase
|
In enzymology, a phenylalanine adenylyltransferase (EC 2.7.7.54) is an enzyme that catalyzes the chemical reaction
ATP + L-phenylalanine formula_0 diphosphate + N-adenylyl-L-phenylalanine
Thus, the two substrates of this enzyme are ATP and L-phenylalanine, whereas its two products are diphosphate and N-adenylyl-L-phenylalanine.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing nucleotide groups (nucleotidyltransferases). The systematic name of this enzyme class is ATP:L-phenylalanine adenylyltransferase. This enzyme is also called L-phenylalanine adenylyltransferase.
References.
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"math_id": 0,
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https://en.wikipedia.org/wiki?curid=14679939
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14679961
|
Phosphatidate cytidylyltransferase
|
Phosphatidate cytidylyltransferase (EC 2.7.7.41) (also known as CDP- diacylglycerol synthase) (CDS) is the enzyme that catalyzes the synthesis of CDP-diacylglycerol from cytidine triphosphate and phosphatidate.
CTP + phosphatidate formula_0 diphosphate + CDP-diacylglycerol
Thus, the two substrates of this enzyme are cytidine triphosphate, or CTP, and phosphatidate, whereas its two products are diphosphate and CDP-diacylglycerol.
CDP-diacylglycerol is an important branch point intermediate in both prokaryotic and eukaryotic organisms. CDS is a membrane-bound enzyme.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing nucleotide groups (nucleotidyltransferases). The systematic name of this enzyme class is CTP:phosphatidate cytidylyltransferase. Other names in common use include CDP diglyceride pyrophosphorylase, CDP-diacylglycerol synthase, CDP-diacylglyceride synthetase, cytidine diphosphoglyceride pyrophosphorylase, phosphatidate cytidyltransferase, phosphatidic acid cytidylyltransferase, CTP:1,2-diacylglycerophosphate-cytidyl transferase, CTP-diacylglycerol synthetase, DAG synthetase, and CDP-DG. This enzyme participates in glycerophospholipid metabolism and phosphatidylinositol signaling system.
References.
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https://en.wikipedia.org/wiki?curid=14679961
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14679992
|
Phosphatidylcholine synthase
|
In enzymology, a phosphatidylcholine synthase (EC 2.7.8.24) is an enzyme that catalyzes the chemical reaction
CDP-diacylglycerol + choline formula_0 CMP + phosphatidylcholine
Thus, the two substrates of this enzyme are CDP-diacylglycerol and choline, whereas its two products are CMP and phosphatidylcholine.
This enzyme belongs to the family of transferases, specifically those transferring non-standard substituted phosphate groups. The systematic name of this enzyme class is CDP-diacylglycerol:choline O-phosphatidyltransferase. This enzyme is also called CDP-diglyceride-choline O-phosphatidyltransferase. This enzyme participates in glycerophospholipid metabolism.
References.
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[
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https://en.wikipedia.org/wiki?curid=14679992
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14680021
|
Phosphatidylinositol-4,5-bisphosphate 3-kinase
|
In enzymology, a phosphatidylinositol-4,5-bisphosphate 3-kinase (EC 2.7.1.153) is an enzyme that catalyzes the chemical reaction:
ATP + 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate formula_0 ADP + 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate
Thus, the two substrates of this enzyme are ATP and 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate, whereas its two products are ADP and 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:1-phosphatidyl-1D-myo-inositol-4,5-bisphosphate 3-phosphotransferase. This enzyme is also called type I phosphoinositide 3-kinase. This enzyme participates in 29 metabolic pathways: inositol phosphate metabolism, erbb signaling pathway, phosphatidylinositol signaling system, mtor signaling pathway, apoptosis, VEGF signaling pathway, focal adhesion, toll-like receptor signaling pathway, jak-stat signaling pathway, natural killer cell mediated cytotoxicity, t cell receptor signaling pathway, b cell receptor signaling pathway, fc epsilon ri signaling pathway, leukocyte transendothelial migration, regulation of actin cytoskeleton, insulin signaling pathway, progesterone-mediated oocyte maturation, Type II diabetes mellitus, colorectal cancer, renal cell carcinoma, pancreatic cancer, endometrial cancer, glioma, prostate cancer, melanoma, chronic myeloid leukemia, acute myeloid leukemia, small cell lung cancer, and non-small cell lung cancer.
Structural studies.
As of late 2007, 6 structures have been solved for this class of enzymes, with PDB accession codes 2A4Z, 2A5U, 2CHW, 2CHX, 2CHZ, and 2V1Y.
Examples.
Human genes encoding proteins with phosphatidylinositol-4,5-bisphosphate 3-kinase activity include:
References.
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https://en.wikipedia.org/wiki?curid=14680021
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14680049
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Phosphatidylinositol-4-phosphate 3-kinase
|
In enzymology, a phosphatidylinositol-4-phosphate 3-kinase (EC 2.7.1.154) is an enzyme that catalyzes the chemical reaction
ATP + 1-phosphatidyl-1D-myo-inositol 4-phosphate formula_0 ADP + 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphate
Thus, the two substrates of this enzyme are ATP and 1-phosphatidyl-1D-myo-inositol 4-phosphate, whereas its two products are ADP and 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:1-phosphatidyl-1D-myo-inositol-4-phosphate 3-phosphotransferase. Other names in common use include type II phosphoinositide 3-kinase, C2-domain-containing phosphoinositide 3-kinase, and phosphoinositide 3-kinase. This enzyme participates in phosphatidylinositol signaling system.
Structural studies.
As of late 2007, 3 structures have been solved for this class of enzymes, with PDB accession codes 2AR5, 2B3R, and 2IWL.
References.
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https://en.wikipedia.org/wiki?curid=14680049
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14680077
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Phosphoenolpyruvate—glycerone phosphotransferase
|
Enzyme
In enzymology, a phosphoenolpyruvate-glycerone phosphotransferase (EC 2.7.1.121) is an enzyme that catalyzes the chemical reaction
phosphoenolpyruvate + glycerone formula_0 pyruvate + glycerone phosphate
Thus, the two substrates of this enzyme are phosphoenolpyruvate and glycerone, whereas its two products are pyruvate and glycerone phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is phosphoenolpyruvate:glycerone phosphotransferase.
References.
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https://en.wikipedia.org/wiki?curid=14680077
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14680106
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Phosphoenolpyruvate—protein phosphotransferase
|
Enzyme
In enzymology, a phosphoenolpyruvate-protein phosphotransferase (EC 2.7.3.9) is an enzyme that catalyzes the chemical reaction
phosphoenolpyruvate + protein histidine formula_0 pyruvate + protein Npi-phospho-L-histidine
Thus, the two substrates of this enzyme are phosphoenolpyruvate and protein histidine, whereas its two products are pyruvate and protein Npi-phospho-L-histidine.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with a nitrogenous group as acceptor. This enzyme participates in phosphotransferase system (pts).
Nomenclature.
The systematic name of this enzyme class is phosphoenolpyruvate:protein-L-histidine Npi-phosphotransferase. Other names in common use include phosphoenolpyruvate sugar phosphotransferase enzyme I, phosphopyruvate-protein factor phosphotransferase, phosphopyruvate-protein phosphotransferase, sugar-PEP phosphotransferase enzyme I, and phosphoenolpyruvate:protein-L-histidine N-pros-phosphotransferase.
References.
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https://en.wikipedia.org/wiki?curid=14680106
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14680131
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Phosphoglucan, water dikinase
|
In enzymology, a phosphoglucan, water dikinase (EC 2.7.9.5) is an enzyme that catalyzes the chemical reaction
ATP + [phospho-alpha-glucan] + H2O formula_0 AMP + O-phospho-[phospho-alpha-glucan] + phosphate
The 3 substrates of this enzyme are ATP, phospho-alpha-glucan, and H2O, whereas its 3 products are AMP, O-phospho-[phospho-alpha-glucan], and phosphate.
This enzyme belongs to the family of transferases, to be specific, those transferring phosphorus-containing groups (phosphotransferases) with paired acceptors (dikinases). The systematic name of this enzyme class is ATP:phospho-alpha-glucan, water phosphotransferase. Other names in common use include PWD, and OK1.
References.
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https://en.wikipedia.org/wiki?curid=14680131
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14680147
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UDP-N-acetylglucosamine—dolichyl-phosphate N-acetylglucosaminephosphotransferase
|
Class of enzymes
In enzymology, an UDP-N-acetylglucosamine—dolichyl-phosphate N-acetylglucosaminephosphotransferase (EC 2.7.8.15) is an enzyme that catalyzes the chemical reaction
UDP-N-acetyl-D-glucosamine + dolichyl phosphate formula_0 UMP + N-acetyl-D-glucosaminyl-diphosphodolichol
Thus, the two substrates of this enzyme are UDP-N-acetyl-D-glucosamine and dolichyl phosphate, whereas its two products are UMP and N-acetyl-D-glucosaminyl-diphosphodolichol.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups transferases for other substituted phosphate groups. The systematic name of this enzyme class is UDP-N-acetyl-D-glucosamine:dolichyl-phosphate N-acetyl-D-glucosaminephosphotransferase. Other names in common use include UDP-D-N-acetylglucosamine N-acetylglucosamine 1-phosphate transferase, UDP-GlcNAc:dolichyl-phosphate GlcNAc-1-phosphate transferase, UDP-N-acetyl-D-glucosamine:dolichol phosphate N-acetyl-D-glucosamine-1-phosphate transferase, uridine diphosphoacetylglucosamine-dolichyl phosphate acetylglucosamine-1-phosphotransferase, chitobiosylpyrophosphoryldolichol synthase, dolichol phosphate N-acetylglucosamine-1-phosphotransferase, UDP-acetylglucosamine-dolichol phosphate acetylglucosamine phosphotransferase, and UDP-acetylglucosamine-dolichol phosphate acetylglucosamine-1-phosphotransferase. This enzyme participates in the biosynthesis of N-glycan and glycan structures.
References.
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https://en.wikipedia.org/wiki?curid=14680147
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14680160
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Phosphoglucokinase
|
In enzymology, a phosphoglucokinase (EC 2.7.1.10) is an enzyme that catalyzes the chemical reaction
ATP + alpha-D-glucose 1-phosphate formula_0 ADP + alpha-D-glucose 1,6-bisphosphate
Thus, the two substrates of this enzyme are ATP and alpha-D-glucose 1-phosphate, whereas its two products are ADP and alpha-D-glucose 1,6-bisphosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:alpha-D-glucose-1-phosphate 6-phosphotransferase. Other names in common use include glucose-phosphate kinase, phosphoglucokinase (phosphorylating), and ATP:D-glucose-1-phosphate 6-phosphotransferase. This enzyme participates in starch and sucrose metabolism.
References.
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https://en.wikipedia.org/wiki?curid=14680160
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14680173
|
UDP-N-acetylglucosamine—lysosomal-enzyme N-acetylglucosaminephosphotransferase
|
Class of enzymes
In enzymology, an UDP-N-acetylglucosamine—lysosomal-enzyme N-acetylglucosaminephosphotransferase (EC 2.7.8.17) is an enzyme that catalyzes the chemical reaction
UDP-N-acetyl-D-glucosamine + lysosomal-enzyme D-mannose formula_0 UMP + lysosomal-enzyme N-acetyl-D-glucosaminyl-phospho-D-mannose
Thus, the two substrates of this enzyme are UDP-N-acetyl-D-glucosamine and lysosomal-enzyme D-mannose, whereas its two products are UMP and lysosomal-enzyme N-acetyl-D-glucosaminyl-phospho-D-mannose.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups transferases for other substituted phosphate groups. The systematic name of this enzyme class is UDP-N-acetyl-D-glucosamine:lysosomal-enzyme N-acetylglucosaminephosphotransferase. Other names in common use include UDP-N-acetylglucosamine:lysosomal enzyme N-acetylglucosamine-1-phosphotransferase, UDP-GlcNAc:glycoprotein N-acetylglucosamine-1-phosphotransferase, uridine diphosphoacetylglucosamine-lysosomal enzyme precursor acetylglucosamine-1-phosphotransferase, uridine diphosphoacetylglucosamine-glycoprotein acetylglucosamine-1-phosphotransferase, lysosomal enzyme precursor acetylglucosamine-1-phosphotransferase, UDP-acetylglucosamine:lysosomal enzyme N-acetylglucosamine-1-phosphotransferase, UDP-GlcNAc:lysosomal enzyme N-acetylglucosamine-1-phosphotransferase, UDP-N-acetylglucosamine:glycoprotein N-acetylglucosamine-1-phosphotransferase, and UDP-N-acetylglucosamine:glycoprotein N-acetylglucosaminyl-1-phosphotransferase.
References.
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https://en.wikipedia.org/wiki?curid=14680173
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14680198
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Phosphoglycerate kinase (GTP)
|
In enzymology, a phosphoglycerate kinase (GTP) (EC 2.7.2.10) is an enzyme that catalyzes the chemical reaction
GTP + 3-phospho-D-glycerate formula_0 GDP + 3-phospho-D-glyceroyl phosphate
Thus, the two substrates of this enzyme are GTP and 3-phospho-D-glycerate, whereas its two products are GDP and 3-phospho-D-glyceroyl phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with a carboxy group as acceptor. The systematic name of this enzyme class is GTP:3-phospho-D-glycerate 1-phosphotransferase.
References.
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https://en.wikipedia.org/wiki?curid=14680198
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14680222
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UDP-galactose—UDP-N-acetylglucosamine galactose phosphotransferase
|
In enzymology, an UDP-galactose—UDP-N-acetylglucosamine galactose phosphotransferase (EC 2.7.8.18) is an enzyme that catalyzes the chemical reaction
UDP-galactose + UDP-N-acetyl-D-glucosamine formula_0 UMP + UDP-N-acetyl-6-(D-galactose-1-phospho)-D-glucosamine
Thus, the two substrates of this enzyme are UDP-galactose and UDP-N-acetyl-D-glucosamine, whereas its two products are UMP and UDP-N-acetyl-6-(D-galactose-1-phospho)-D-glucosamine.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups transferases for other substituted phosphate groups. The systematic name of this enzyme class is UDP-galactose:UDP-N-acetyl-D-glucosamine galactose phosphotransferase. Other names in common use include uridine diphosphogalactose-uridine diphosphoacetylglucosamine galactose-1-phosphotransferase, galactose-1-phosphotransferase, and galactosyl phosphotransferase.
References.
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https://en.wikipedia.org/wiki?curid=14680222
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14680233
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Phosphomannan mannosephosphotransferase
|
In enzymology, a phosphomannan mannosephosphotransferase (EC 2.7.8.9) is an enzyme that catalyzes the chemical reaction
GDP-mannose + (phosphomannan)n formula_0 GMP + (phosphomannan)n+1
Thus, the two substrates of this enzyme are GDP-mannose and (phosphomannan)n, whereas its two products are GMP and (phosphomannan)n+1.
This enzyme belongs to the family of transferases, specifically those transferring non-standard substituted phosphate groups. The systematic name of this enzyme class is GDP-mannose:phosphomannan mannose phosphotransferase.
References.
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https://en.wikipedia.org/wiki?curid=14680233
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14680266
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Phosphomethylpyrimidine kinase
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In enzymology, a phosphomethylpyrimidine kinase (EC 2.7.4.7) is an enzyme that catalyzes the chemical reaction
ATP + (4-amino-2-methylpyrimidin-5-yl)methyl phosphate formula_0 ADP + (4-amino-2-methylpyrimidin-5-yl)methyl diphosphate
Thus, the two substrates of this enzyme are ATP and (4-amino-2-methylpyrimidin-5-yl)methyl phosphate, whereas its two products are ADP and (4-amino-2-methylpyrimidin-5-yl)methyl diphosphate.
This enzyme belongs to the family of transferases, to be specific, those transferring phosphorus-containing groups (phosphotransferases) with a phosphate group as acceptor. The systematic name of this enzyme class is ATP:(4-amino-2-methylpyrimidin-5-yl)methyl-phosphate phosphotransferase. Other names in common use include hydroxymethylpyrimidine phosphokinase, and ATP:4-amino-2-methyl-5-phosphomethylpyrimidine phosphotransferase. This enzyme participates in thiamine metabolism.
Structural studies.
As of late 2007, 4 structures have been solved for this class of enzymes, with PDB accession codes 1JXH, 1JXI, 1UB0, and 2I5B.
References.
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https://en.wikipedia.org/wiki?curid=14680266
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14680298
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Phospho-N-acetylmuramoyl-pentapeptide-transferase
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In enzymology, a phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13) is an enzyme that catalyzes the chemical reaction
UDP-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala) + undecaprenyl phosphate formula_0 UMP + Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol
Thus, the two substrates of this enzyme are UDP-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala) and undecaprenyl phosphate, whereas its 2 products are UMP and Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol.
This enzyme participates in peptidoglycan biosynthesis. It can be expressed efficiently by a cell-free protein expression system.
Nomenclature.
This enzyme belongs to the family of transferases, specifically those transferring non-standard substituted phosphate groups. The systematic name of this enzyme class is UDP-MurAc(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala): undecaprenyl-phosphate phospho-N-acetylmuramoyl-pentapeptide-transferase. Other names in common use include translocase I, MraY transferase, UDP-MurNAc-L-Ala-D-gamma-Glu-L-Lys-D-Ala-D-Ala:C55-isoprenoid, alcohol transferase, UDP-MurNAc-Ala-gammaDGlu-Lys-DAla-DAla:undecaprenylphosphate, transferase, phospho-N-acetylmuramoyl pentapeptide translocase, phospho-MurNAc-pentapeptide transferase, phospho-NAc-muramoyl-pentapeptide translocase (UMP), phosphoacetylmuramoylpentapeptide translocase, and phosphoacetylmuramoylpentapeptidetransferase.
References.
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Further reading.
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https://en.wikipedia.org/wiki?curid=14680298
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14680323
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Phosphoramidate—hexose phosphotransferase
|
In enzymology, a phosphoramidate-hexose phosphotransferase (EC 2.7.1.62) is an enzyme that catalyzes the chemical reaction
phosphoramidate + hexose formula_0 NH3 + alpha-D-hexose 1-phosphate
Thus, the two substrates of this enzyme are phosphoramidate and hexose, whereas its two products are NH3 and alpha-D-hexose 1-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is phosphoramidate:hexose 1-phosphotransferase. Other names in common use include phosphoramidate-hexose transphosphorylase, and phosphoramidic-hexose transphosphorylase.
References.
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https://en.wikipedia.org/wiki?curid=14680323
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14680336
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Phosphoribokinase
|
In enzymology, a phosphoribokinase (EC 2.7.1.18) is an enzyme that catalyzes the chemical reaction
ATP + D-ribose 5-phosphate formula_0 ADP + D-ribose 1,5-bisphosphate
Thus, the two substrates of this enzyme are ATP and D-ribose 5-phosphate, whereas its two products are ADP and D-ribose 1,5-bisphosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:D-ribose-5-phosphate 1-phosphotransferase. This enzyme is also called phosphoribokinase (phosphorylating).
References.
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https://en.wikipedia.org/wiki?curid=14680336
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14680360
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Phosphoribulokinase
|
Phosphoribulokinase (PRK) (EC 2.7.1.19) is an essential photosynthetic enzyme that catalyzes the ATP-dependent phosphorylation of ribulose 5-phosphate (RuP) into ribulose 1,5-bisphosphate (RuBP), both intermediates in the Calvin Cycle. Its main function is to regenerate RuBP, which is the initial substrate and CO2-acceptor molecule of the Calvin Cycle. PRK belongs to the family of transferase enzymes, specifically those transferring phosphorus-containing groups (phosphotransferases) to an alcohol group acceptor. Along with ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo), phosphoribulokinase is unique to the Calvin Cycle. Therefore, PRK activity often determines the metabolic rate in organisms for which carbon fixation is key to survival. Much initial work on PRK was done with spinach leaf extracts in the 1950s; subsequent studies of PRK in other photosynthetic prokaryotic and eukaryotic organisms have followed. The possibility that PRK might exist was first recognized by Weissbach et al. in 1954; for example, the group noted that carbon dioxide fixation in crude spinach extracts was enhanced by the addition of ATP. The first purification of PRK was conducted by Hurwitz and colleagues in 1956.
ATP + Mg2+ - D-ribulose 5-phosphate formula_0 ADP + D-ribulose 1,5-bisphosphate
The two substrates of PRK are ATP and D-ribulose 5-phosphate, whereas its two products are ADP and D-ribulose 1,5-bisphosphate. PRK activity requires the presence of a divalent metal cation like Mg2+, as indicated in the reaction above.
Structure.
The structure of PRK is different in prokaryotes and eukaryotes. Prokaryotic PRK's typically exist as octamers of 32 kDa subunits, while eukaryotic PRK's are often dimers of 40 kDa subunits. Structural determinations for eukaryotic PRK have yet to be conducted, but prokaryotic PRK structures are still useful for rationalizing the regulation and mechanism of PRK. As of 2018, only two crystal structures have been resolved for this class of enzymes in "Rhodobacter sphaeroides" and "Methanospirillum hungatei", with the respective PDB accession codes 1A7J and 5B3F.
"Rhodobacter sphaeroides".
In "Rhodobacter sphaeroides", PRK (or RsPRK) exists as a homooctomer with protomers composed of seven-stranded mixed β-sheets, seven α-helices, and an auxiliary pair of anti-parallel β-strands. The RsPRK subunit exhibits a protein folding analogous to the folding of nucleotide monophosphate (NMP) kinases. Mutagenesis studies suggest that either Asp 42 or Asp 169 acts as the catalytic base that deprotonates the O1 hydroxyl oxygen on RuP for nucleophilic attack of ATP, while the other acts a ligand for a metal cation like Mg2+ (read mechanism below for more details). Other residues present at the active site for RsPRK include His 45, Arg 49, Arg 168, and Arg 173, which are purportedly involved in RuP binding. (See image at right).
"Methanospirillum hungatei".
In archaeal PRK of "Methanospirillum hungatei," PRK (or MhPRK) exists as a homodimer of two protomers, each consisting of eight-stranded mixed β-sheets surrounded by α-helices and β-strands—similar to the structure of bacterial PRK from "R. sphaeroides" (see info. box above)"." Although their quaternary structures differ and they have low amino acid sequence identity, MhPRK and RsPRK have structurally similar N-terminal domains as well as sequentially conserved residues like His 55, Lys 151, and Arg 154.
Mechanism and Activity.
PRK catalyzes the phosphorylation of RuP into RuBP. A catalytic residue in the enzyme (i.e. aspartate in RsPRK) deprotonates the O1 hydroxyl oxygen on RuP and activates it for nucleophilic attack of the γ-phosphoryl group of ATP. As the γ-phosphoryl group is transferred from ATP to RuP, its stereochemistry inverts. To allow for such inversion, the catalytic mechanism of PRK must not involve a phosphoryl-enzyme intermediate.
Some studies suggest that both substrates (ATP and RuP) bind simultaneously to PRK and form a ternary complex. Others suggest that the substrate addition is sequential; the particular order by which substrates are added is still disputed, and may in fact, vary for different organisms. In addition to binding its substrates, PRK also requires ligation to divalent metal cations like Mg2+ or Mn2+ for activity; Hg2+ has been demonstrated to inactivate the enzyme.
Enzyme specificity.
PRK shows high specificity for ribulose 5-phosphate. It does not act on any of the following substrates: D-xylulose 5-phosphate, fructose 6-phosphate, and sedoheptulose 7-phosphate. However, at high concentrations, PRK may sometimes phosphorylate ribose 5-phosphate, a compound upstream the RuBP regeneration step in the Calvin Cycle. Furthermore, PRK isolated from "Alcaligenes eutrophus" has been shown to use uridine triphosphate (UTP) and guanosine triphosphate (GTP) as alternative substrates to ATP.
pH effects.
The phosphorylation reaction proceeds with maximal velocity at pH 7.9, with no detectable activity at pH's below 5.5 or above 9.0.
Regulation.
The mechanisms by which prokaryotic and eukaryotic PRK's are regulated vary. Prokaryotic PRK's are typically subject to allosteric regulation while eukaryotic PRK's are often regulated by reversible thiol/disulfide exchange. These differences are likely due to structural differences in their C-terminal domains
Allosteric regulation of prokaryotic PRK.
NADH is known to stimulate PRK activity, while AMP and phosphoenolpyruvate (PEP) are known to inhibit activity. AMP has been shown to be involved in competitive inhibition in "Thiobacillus ferrooxidans" PRK. On the other hand, PEP acts as a non-competitive inhibitor of PRK.
Regulation of eukaryotic PRK.
Eukaryotic PRK is typically regulated through the reversible oxidation/reduction of its cysteine sulfhydryl groups, but studies suggests that its activity can be regulated by other proteins or metabolites in the chloroplast. Of such metabolites, 6-phosphogluconate has been shown to be the most effective inhibitor of eukaryotic PRK by competing with RuP for the enzyme's active site. This phenomenon may arise from the similarity in molecular structure between 6-phosphogluconate and RuP.
More recent work on the regulation of eukaryotic PRK has focused on its ability to form multi-enzyme complexes with other Calvin cycle enzymes such as glyceraldehyde 3-phosphate dehydrogenase (G3PDH) or RuBisCo. In "Chlamydomonas reinhardtii", chloroplast PRK and G3PDH exist as a bi-enzyme complex of 2 molecules of dimeric PRK and 2 molecules of tetrameric G3PDH thorough association by an Arg 64 residue, which may potentially transfer information between the two enzymes as well.
Multi-enzyme complexes are likely to have more intricate regulatory mechanisms, and studies have already probed such processes. For example, it has been shown that PRK-glyceraldehyde 3-phosphate dehydrogenase complexes in "Scenedesmus obliquus" only dissociate to release activated forms of its constituent enzymes in the presence of NADPH, dithiothreitol (DTT), and thioredoxin. Another topic of interest has been to compare the relative levels of PRK activity for when it is complexed to when it is not. For different photosynthetic eukaryotes, the enzyme activity of complexed PRK may be enhanced as opposed to free PRK, and vice versa.
Other names.
The systematic name of this enzyme class is ATP:D-ribulose-5-phosphate 1-phosphotransferase. Other names in common use include phosphopentokinase, ribulose-5-phosphate kinase, phosphopentokinase, phosphoribulokinase (phosphorylating), 5-phosphoribulose kinase, ribulose phosphate kinase, PKK, PRuK, and PRK.
References.
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14680393
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Polo kinase
|
Class of enzymes
In enzymology, a polo kinase (EC 2.7.11.21) is a kinase enzyme i.e. one that catalyzes the chemical reaction
ATP + a protein formula_0 ADP + a phosphoprotein
Thus, the two substrates of these enzymes are ATP and protein, whereas their two products are ADP and phosphoprotein.
These enzymes belong to the family of transferases, specifically those transferring a phosphate group to the sidechain oxygen atom of serine or threonine residues in proteins (protein-serine/threonine kinases).
The systematic name of this [polo[-like] kinase] enzyme class is ATP:protein phosphotransferase (spindle-pole-dependent).
Examples and other names in common use include Cdc5, Cdc5p, Plk, PLK, Plk1, Plo1, POLO kinase, polo serine-threonine kinase, polo-like kinase, polo-like kinase 1, serine/threonine-specific Drosophila kinase polo, and STK21.
These enzymes participate in 3 metabolic pathways: cell cycle, cell cycle - yeast, and progesterone-mediated oocyte maturation.
Structural studies.
As of late 2007, 5 structures have been solved for this class of enzymes, with PDB accession codes 2OGQ, 2OJS, 2OJX, 2OU7, and 2OWB.
References.
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14680428
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Polynucleotide 5'-hydroxyl-kinase
|
In enzymology, a polynucleotide 5'-hydroxyl-kinase (EC 2.7.1.78) is an enzyme that catalyzes the chemical reaction
ATP + 5'-dephospho-DNA formula_0 ADP + 5'-phospho-DNA
Thus, the two substrates of this enzyme are ATP and 5'-dephospho-DNA, whereas its two products are ADP and 5'-phospho-DNA. Polynucleotide kinase is a T7 bacteriophage (or T4 bacteriophage) enzyme that catalyzes the transfer of a gamma-phosphate from ATP to the free hydroxyl end of the 5' DNA or RNA. The resulting product could be used to end-label DNA or RNA, or in ligation reactions.
Nomenclature.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as an acceptor. The systematic name of this enzyme class is ATP:5'-dephosphopolynucleotide 5'-phosphotransferase. Other names in common use include:
References.
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14680463
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Polynucleotide adenylyltransferase
|
Class of enzymes
In enzymology, a polynucleotide adenylyltransferase (EC 2.7.7.19) is an enzyme that catalyzes the chemical reaction
ATP + RNA-3'OH formula_0 pyrophosphate + RNApA-3'OH
Thus, the two substrates of this enzyme are ATP and RNA, whereas its two products are pyrophosphate and RNA with an extra adenosine nucleotide at its 3' end.
Human genes with this activity include TUT1, MTPAP, PAPOLA, PAPOLB, PAPOLG, TENT2, TENT4A, TENT4B, TENT5C, TENT5D.
Function.
This enzyme is responsible for the addition of the 3' polyadenine tail to a newly synthesized pre-messenger RNA (pre-mRNA) molecule during the process of gene transcription. The protein is the final addition to a large protein complex that also contains smaller assemblies known as the cleavage and polyadenylation specificity factor (CPSF) and cleavage stimulatory factor (CtSF) and its binding is a necessary prerequisite to the cleavage of the 3' end of the pre-mRNA. After cleavage of the 3' signaling region that directs the assembly of the complex, polyadenylate polymerase (PAP) adds the polyadenine tail to the new 3' end.
The rate at which PAP adds adenine nucleotides is dependent on the presence of another regulatory protein, PABPII (poly-adenine binding protein II). The first few nucleotides added by PAP are added very slowly, but the short polyadenine tail is then bound by PABPII, which accelerates the rate of adenine addition by PAP. The final tail is about 200-250 adenine nucleotides long in mammals.
PAP is phosphorylated by mitosis-promoting factor, a key regulator of the cell cycle. High phosphorylation levels decrease PAP activity.
Structural studies.
As of late 2007, 27 structures have been solved for this class of enzymes, with PDB accession codes 1AV6, 1B42, 1BKY, 1EAM, 1EQA, 1F5A, 1FA0, 1JSZ, 1JTE, 1JTF, 1P39, 1Q78, 1Q79, 1V39, 1VFG, 1VP3, 1VP9, 1VPT, 2GA9, 2GAF, 2HHP, 2O1P, 2Q66, 2VP3, 3MAG, 3MCT, and 4DCG.
References.
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14680487
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Polyphosphate—glucose phosphotransferase
|
In enzymology, a polyphosphate-glucose phosphotransferase (EC 2.7.1.63) is an enzyme that catalyzes the chemical reaction.
(phosphate)n + D-glucose formula_0 (phosphate)n-1 + D-glucose 6-phosphate
Thus, the two substrates of this enzyme are (phosphate)n and D-glucose, whereas its two products are (phosphate)n-1 and D-glucose 6-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is polyphosphate:D-glucose 6-phosphotransferase. Other names in common use include polyphosphate glucokinase, polyphosphate-D-(+)-glucose-6-phosphotransferase, and polyphosphate-glucose 6-phosphotransferase. This enzyme participates in glycolysis / gluconeogenesis. It employs one cofactor, neutral salt.
References.
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14680518
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Polyphosphate kinase
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Enzyme
In enzymology, a polyphosphate kinase (EC 2.7.4.1), or polyphosphate polymerase, is an enzyme that catalyzes the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate moieties.
ATP + (phosphate)n formula_0 ADP + (phosphate)n+1
Thus, the two substrates of this enzyme are ATP and polyphosphate [(phosphate)n], whereas its two products are ADP and polyphosphate extended by one phosphate moiety [(phosphate)n+1].
This enzyme is a membrane protein and goes through an intermediate stage during the reaction where it is autophosphorylated with a phosphate group covalently linked to a basic amino acyl residue through an N-P bond.
Several enzymes catalyze polyphosphate polymerization. Some of these enzymes couple phosphotransfer to transmembrane transport. These enzyme/transporters are categorized in the Transporter Classification Database (TCDB) under the Polyphosphate Polymerase/YidH Superfamily (TC# 4.E.1) and are transferases that transfer phosphoryl groups (phosphotransferases) with polyphosphate as the acceptor. The systematic name of this enzyme class is ATP:polyphosphate phosphotransferase. This enzyme is also called polyphosphoric acid kinase.
Families.
The Polyphosphate Polymerase Superfamily (TC# 4.E.1) includes the following families:
The Vacuolar (Acidocalcisome) Polyphosphate Polymerase (V-PPP) Family.
Eukaryotes contain inorganic polyphosphate (polyP) and acidocalcisomes, which sequester polyP and store amino acids and divalent cations. Gerasimaitė et al. showed that polyP produced in the cytosol of yeast is toxic. Reconstitution of polyP translocation with purified vacuoles, the acidocalcisomes of yeast, showed that cytosolic polyP cannot be imported whereas polyP produced by the vacuolar transporter chaperone (VTC) complex, an endogenous vacuolar polyP polymerase, is efficiently imported and does not interfere with growth. PolyP synthesis and import require an electrochemical gradient, probably as a (partial) driving force for polyP translocation. VTC exposes its catalytic domain to the cytosol and has nine vacuolar transmembrane segments (TMSs). Mutations in the VTC transmembrane regions, which may constitute the translocation channel, block not only polyP translocation but also synthesis. Since these mutations are far from the cytosolic catalytic domain of VTC, this suggests that the VTC complex obligatorily couples synthesis of polyP to its vesicular import in order to avoid toxic intermediates in the cytosol. The process therefore conforms to the classical definition of Group Translocation, where the substrate is modified during transport. Sequestration of otherwise toxic polyP may be one reason for the existence of this mechanism in acidocalcisomes. The vacuolar polyphosphate kinase (polymerase) is described in TCDB with family TC# 4.E.1.
Function.
CYTH-like superfamily enzymes, which include polyphosphate polymerases, hydrolyze triphosphate-containing substrates and require metal cations as cofactors. They have a unique active site located at the center of an eight-stranded antiparallel beta barrel tunnel (the triphosphate tunnel). The name CYTH originated from the gene designation for bacterial class IV adenylyl cyclases (CyaB), and from thiamine triphosphatase (THTPA). Class IV adenylate cyclases catalyze the conversion of ATP to 3',5'-cyclic AMP (cAMP) and PPi. Thiamine triphosphatase is a soluble cytosolic enzyme which converts thiamine triphosphate to thiamine diphosphate. This domain superfamily also contains RNA triphosphatases, membrane-associated polyphosphate polymerases, tripolyphosphatases, nucleoside triphosphatases, nucleoside tetraphosphatases and other proteins with unknown functions.
The generalized reaction catalyzed by the vectorial polyphosphate polymerases is:
ATP + (phosphate)n in the cytoplasm formula_0 ADP + (phosphate)n+1 in the vacuolar lumen
Structure.
VTC2 has three recognized domains: an N-terminal SPX domain, a large central CYTH-like domain and a smaller transmembrane VTC1 (DUF202) domain. The SPX domain is found in Syg1, Pho81, XPR1 (SPX), and related proteins. This domain is found at the amino termini of a variety of proteins. In the yeast protein, Syg1, the N-terminus directly binds to the G-protein beta subunit and inhibits transduction of the mating pheromone signal. Similarly, the N-terminus of the human XPR1 protein binds directly to the beta subunit of the G-protein heterotrimer, leading to increased production of cAMP. Thus, this domain is involved in G-protein associated signal transduction. The N-termini of several proteins involved in the regulation of phosphate transport, including the putative phosphate level sensors, Pho81 from "Saccharomyces cerevisiae" and NUC-2 from "Neurospora crassa", have this domain.
The SPX domains of the "S. cerevisiae" low-affinity phosphate transporters, Pho87 and Pho90, auto-regulate uptake and prevent efflux. This SPX-dependent inhibition is mediated by a physical interaction with Spl2. NUC-2 contains several ankyrin repeats. Several members of this family are annotated as XPR1 proteins: the xenotropic and polytropic retrovirus receptor confers susceptibility to infection with xenotropic and polytropic murine leukaemia viruses (MLV). Infection by these retroviruses can inhibit XPR1-mediated cAMP signaling and result in cell toxicity and death. The similarity between Syg1 phosphate regulators and XPR1 sequences has been noted, as has the additional similarity to several predicted proteins of unknown function, from "Drosophila melanogaster", "Arabidopsis thaliana", "Caenorhabditis elegans", "Schizosaccharomyces pombe", "S. cerevisiae", and many other diverse organisms.
As of 2015, several structures have been solved for this class of enzymes, with PDB accession codes 1XDO, 1XDP, 2O8R, 3CZP, 3CZQ, 3RHF.
The Uncharacterized DUF202/YidH (YidH) Family.
Members of the YidH Family are found in bacteria, archaea and eukaryotes. Members of this family include YidH of "E. coli" (TC# 9.B.51.1.1) which has 115 amino acyl residues and 3 TMSs of α-helical nature. The first TMS has a low level of hydrophobicity, the second has a moderate level of hydrophobicity, and the third has very hydrophobic character. These traits appear to be characteristic of all members of this family. A representative list of proteins belonging to this family can be found in the Transporter Classification Database. In fungi, a long homologue of 351 aas has a similar 3 TMS DUF202 domain at its extreme C-terminus.
References.
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Further reading.
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14680551
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Protein-histidine pros-kinase
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In enzymology, a protein-histidine pros-kinase (EC 2.7.13.1) is an enzyme that catalyzes the chemical reaction
ATP + protein -histidine formula_0 ADP + protein "Nπ"-phospho--histidine
Thus, the two substrates of this enzyme are ATP and protein L-histidine, whereas its two products are ADP and protein Npi-phospho-L-histidine.
This enzyme belongs to the family of transferases, specifically those transferring a phosphate group to the sidechain of histidine residues in proteins (protein-histidine kinases). The systematic name of this enzyme class is ATP:protein-L-histidine Npi-phosphotransferase. Other names in common use include "ATP:protein-L-histidine N-pros-phosphotransferase", "histidine kinase", "histidine protein kinase", "protein histidine kinase", "protein kinase (histidine)", and "HK2".
References.
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14680590
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Protein-histidine tele-kinase
|
In enzymology, a protein-histidine tele-kinase (EC 2.7.13.2) is an enzyme that catalyzes the chemical reaction
ATP + protein -histidine formula_0 ADP + protein "Nτ"-phospho--histidine
Thus, the two substrates of this enzyme are ATP and protein L-histidine, whereas its two products are ADP and protein Ntau-phospho-L-histidine.
This enzyme belongs to the family of transferases, specifically those transferring a phosphate group to the sidechain of histidine residues in proteins (protein-histidine kinases). The systematic name of this enzyme class is "ATP:protein-L-histidine Ntau-phosphotransferase". Other names in common use include "ATP:protein-L-histidine N-tele-phosphotransferase", "histidine kinase", "histidine protein kinase", "protein histidine kinase", "protein kinase (histidine)", and "HK3".
References.
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146806
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Recurrence relation
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Pattern defining an infinite sequence of numbers
In mathematics, a recurrence relation is an equation according to which the formula_0th term of a sequence of numbers is equal to some combination of the previous terms. Often, only formula_1 previous terms of the sequence appear in the equation, for a parameter formula_1 that is independent of formula_0; this number formula_1 is called the "order" of the relation. If the values of the first formula_1 numbers in the sequence have been given, the rest of the sequence can be calculated by repeatedly applying the equation.
In "linear recurrences", the nth term is equated to a linear function of the formula_1 previous terms. A famous example is the recurrence for the Fibonacci numbers,
formula_2
where the order formula_1 is two and the linear function merely adds the two previous terms. This example is a linear recurrence with constant coefficients, because the coefficients of the linear function (1 and 1) are constants that do not depend on formula_3 For these recurrences, one can express the general term of the sequence as a closed-form expression of formula_0. As well, linear recurrences with polynomial coefficients depending on formula_0 are also important, because many common elementary and special functions have a Taylor series whose coefficients satisfy such a recurrence relation (see holonomic function).
Solving a recurrence relation means obtaining a closed-form solution: a non-recursive function of formula_0.
The concept of a recurrence relation can be extended to multidimensional arrays, that is, indexed families that are indexed by tuples of natural numbers.
Definition.
A "recurrence relation" is an equation that expresses each element of a sequence as a function of the preceding ones. More precisely, in the case where only the immediately preceding element is involved, a recurrence relation has the form
formula_4
where
formula_5
is a function, where X is a set to which the elements of a sequence must belong. For any formula_6, this defines a unique sequence with formula_7 as its first element, called the "initial value".
It is easy to modify the definition for getting sequences starting from the term of index 1 or higher.
This defines recurrence relation of "first order". A recurrence relation of "order" k has the form
formula_8
where formula_9 is a function that involves k consecutive elements of the sequence.
In this case, k initial values are needed for defining a sequence.
Examples.
Factorial.
The factorial is defined by the recurrence relation
formula_10
and the initial condition
formula_11
This is an example of a "linear recurrence with polynomial coefficients" of order 1, with the simple polynomial (in n)
formula_0
as its only coefficient.
Logistic map.
An example of a recurrence relation is the logistic map defined by
formula_12
for a given constant formula_13 The behavior of the sequence depends dramatically on formula_14 but is stable when the initial condition formula_15 varies.
Fibonacci numbers.
The recurrence of order two satisfied by the Fibonacci numbers is the canonical example of a homogeneous linear recurrence relation with constant coefficients (see below). The Fibonacci sequence is defined using the recurrence
formula_16
with initial conditions
formula_17
formula_18
Explicitly, the recurrence yields the equations
formula_19
formula_20
formula_21
etc.
We obtain the sequence of Fibonacci numbers, which begins
0, 1, 1, 2, 3, 5, 8, 13, 21, 34, 55, 89, ...
The recurrence can be solved by methods described below yielding Binet's formula, which involves powers of the two roots of the characteristic polynomial formula_22; the generating function of the sequence is the rational function
formula_23
Binomial coefficients.
A simple example of a multidimensional recurrence relation is given by the binomial coefficients formula_24, which count the ways of selecting formula_1 elements out of a set of formula_0 elements.
They can be computed by the recurrence relation
formula_25
with the base cases formula_26. Using this formula to compute the values of all binomial coefficients generates an infinite array called Pascal's triangle. The same values can also be computed directly by a different formula that is not a recurrence, but uses factorials, multiplication and division, not just additions:
formula_27
The binomial coefficients can also be computed with a uni-dimensional recurrence:
formula_28
with the initial value formula_29 (The division is not displayed as a fraction for emphasizing that it must be computed after the multiplication, for not introducing fractional numbers).
This recurrence is widely used in computers because it does not require to build a table as does the bi-dimensional recurrence, and does involve very large integers as does the formula with factorials (if one uses formula_30 all involved integers are smaller than the final result).
Difference operator and difference equations.
The <templatestyles src="Template:Visible anchor/styles.css" />difference operator is an operator that maps sequences to sequences, and, more generally, functions to functions. It is commonly denoted formula_31 and is defined, in functional notation, as
formula_32
It is thus a special case of finite difference.
When using the index notation for sequences, the definition becomes
formula_33
The parentheses around formula_34 and formula_35 are generally omitted, and formula_36 must be understood as the term of index n in the sequence formula_37 and not formula_38 applied to the element formula_39
Given sequence formula_40 the <templatestyles src="Template:Visible anchor/styles.css" />first difference of a is formula_41
The <templatestyles src="Template:Visible anchor/styles.css" />second difference is
formula_42 A simple computation shows that
formula_43
More generally: the k"th difference" is defined recursively as formula_44 and one has
formula_45
This relation can be inverted, giving
formula_46
A <templatestyles src="Template:Visible anchor/styles.css" />difference equation of order k is an equation that involves the k first differences of a sequence or a function, in the same way as a differential equation of order k relates the k first derivatives of a function.
The two above relations allow transforming a recurrence relation of order k into a difference equation of order k, and, conversely, a difference equation of order k into recurrence relation of order k. Each transformation is the inverse of the other, and the sequences that are solution of the difference equation are exactly those that satisfies the recurrence relation.
For example, the difference equation
formula_47
is equivalent to the recurrence relation
formula_48
in the sense that the two equations are satisfied by the same sequences.
As it is equivalent for a sequence to satisfy a recurrence relation or to be the solution of a difference equation, the two terms "recurrence relation" and "difference equation" are sometimes used interchangeably. See Rational difference equation and Matrix difference equation for example of uses of "difference equation" instead of "recurrence relation"
Difference equations resemble differential equations, and this resemblance is often used to mimic methods for solving differentiable equations to apply to solving difference equations, and therefore recurrence relations.
Summation equations relate to difference equations as integral equations relate to differential equations. See time scale calculus for a unification of the theory of difference equations with that of differential equations.
From sequences to grids.
Single-variable or one-dimensional recurrence relations are about sequences (i.e. functions defined on one-dimensional grids). Multi-variable or n-dimensional recurrence relations are about formula_0-dimensional grids. Functions defined on formula_0-grids can also be studied with partial difference equations.
Solving.
Solving first-order non-homogeneous recurrence relations with variable coefficients.
Moreover, for the general first-order non-homogeneous linear recurrence relation with variable coefficients:
formula_49
there is also a nice method to solve it:
formula_50
formula_51
formula_52
Let
formula_53
Then
formula_54
formula_55
formula_56
formula_57
If we apply the formula to formula_58 and take the limit formula_59, we get the formula for first order linear differential equations with variable coefficients; the sum becomes an integral, and the product becomes the exponential function of an integral.
Solving general homogeneous linear recurrence relations.
Many homogeneous linear recurrence relations may be solved by means of the generalized hypergeometric series. Special cases of these lead to recurrence relations for the orthogonal polynomials, and many special functions. For example, the solution to
formula_60
is given by
formula_61
the Bessel function, while
formula_62
is solved by
formula_63
the confluent hypergeometric series. Sequences which are the solutions of linear difference equations with polynomial coefficients are called P-recursive. For these specific recurrence equations algorithms are known which find polynomial, rational or hypergeometric solutions.
Solving first-order rational difference equations.
A first order rational difference equation has the form formula_64. Such an equation can be solved by writing formula_65 as a nonlinear transformation of another variable formula_66 which itself evolves linearly. Then standard methods can be used to solve the linear difference equation in formula_66.
Stability.
Stability of linear higher-order recurrences.
The linear recurrence of order formula_67,
formula_68
has the characteristic equation
formula_69
The recurrence is stable, meaning that the iterates converge asymptotically to a fixed value, if and only if the eigenvalues (i.e., the roots of the characteristic equation), whether real or complex, are all less than unity in absolute value.
Stability of linear first-order matrix recurrences.
In the first-order matrix difference equation
formula_70
with state vector formula_71 and transition matrix formula_72, formula_71 converges asymptotically to the steady state vector formula_73 if and only if all eigenvalues of the transition matrix formula_72 (whether real or complex) have an absolute value which is less than 1.
Stability of nonlinear first-order recurrences.
Consider the nonlinear first-order recurrence
formula_74
This recurrence is locally stable, meaning that it converges to a fixed point formula_73 from points sufficiently close to formula_73, if the slope of formula_75 in the neighborhood of formula_73 is smaller than unity in absolute value: that is,
formula_76
A nonlinear recurrence could have multiple fixed points, in which case some fixed points may be locally stable and others locally unstable; for continuous "f" two adjacent fixed points cannot both be locally stable.
A nonlinear recurrence relation could also have a cycle of period formula_1 for formula_77. Such a cycle is stable, meaning that it attracts a set of initial conditions of positive measure, if the composite function
formula_78
with formula_75 appearing formula_1 times is locally stable according to the same criterion:
formula_79
where formula_73 is any point on the cycle.
In a chaotic recurrence relation, the variable formula_71 stays in a bounded region but never converges to a fixed point or an attracting cycle; any fixed points or cycles of the equation are unstable. See also logistic map, dyadic transformation, and tent map.
Relationship to differential equations.
When solving an ordinary differential equation numerically, one typically encounters a recurrence relation. For example, when solving the initial value problem
formula_80
with Euler's method and a step size formula_81, one calculates the values
formula_82
by the recurrence
formula_83
Systems of linear first order differential equations can be discretized exactly analytically using the methods shown in the discretization article.
Applications.
Mathematical biology.
Some of the best-known difference equations have their origins in the attempt to model population dynamics. For example, the Fibonacci numbers were once used as a model for the growth of a rabbit population.
The logistic map is used either directly to model population growth, or as a starting point for more detailed models of population dynamics. In this context, coupled difference equations are often used to model the interaction of two or more populations. For example, the Nicholson–Bailey model for a host-parasite interaction is given by
formula_84
formula_85
with formula_86 representing the hosts, and formula_87 the parasites, at time formula_88.
Integrodifference equations are a form of recurrence relation important to spatial ecology. These and other difference equations are particularly suited to modeling univoltine populations.
Computer science.
Recurrence relations are also of fundamental importance in analysis of algorithms. If an algorithm is designed so that it will break a problem into smaller subproblems (divide and conquer), its running time is described by a recurrence relation.
A simple example is the time an algorithm takes to find an element in an ordered vector with formula_0 elements, in the worst case.
A naive algorithm will search from left to right, one element at a time. The worst possible scenario is when the required element is the last, so the number of comparisons is formula_0.
A better algorithm is called binary search. However, it requires a sorted vector. It will first check if the element is at the middle of the vector. If not, then it will check if the middle element is greater or lesser than the sought element. At this point, half of the vector can be discarded, and the algorithm can be run again on the other half. The number of comparisons will be given by
formula_89
formula_90
the time complexity of which will be formula_91.
Digital signal processing.
In digital signal processing, recurrence relations can model feedback in a system, where outputs at one time become inputs for future time. They thus arise in infinite impulse response (IIR) digital filters.
For example, the equation for a "feedforward" IIR comb filter of delay formula_92 is:
formula_93
where formula_66 is the input at time formula_88, formula_94 is the output at time formula_88, and formula_95 controls how much of the delayed signal is fed back into the output. From this we can see that
formula_96
formula_97
etc.
Economics.
Recurrence relations, especially linear recurrence relations, are used extensively in both theoretical and empirical economics. In particular, in macroeconomics one might develop a model of various broad sectors of the economy (the financial sector, the goods sector, the labor market, etc.) in which some agents' actions depend on lagged variables. The model would then be solved for current values of key variables (interest rate, real GDP, etc.) in terms of past and current values of other variables.
References.
Footnotes.
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{
"math_id": 0,
"text": "n"
},
{
"math_id": 1,
"text": "k"
},
{
"math_id": 2,
"text": "F_n=F_{n-1}+F_{n-2}"
},
{
"math_id": 3,
"text": "n."
},
{
"math_id": 4,
"text": "u_n=\\varphi(n, u_{n-1})\\quad\\text{for}\\quad n>0,"
},
{
"math_id": 5,
"text": "\\varphi:\\mathbb N\\times X \\to X"
},
{
"math_id": 6,
"text": "u_0\\in X"
},
{
"math_id": 7,
"text": "u_0"
},
{
"math_id": 8,
"text": "u_n=\\varphi(n, u_{n-1}, u_{n-2}, \\ldots, u_{n-k})\\quad\\text{for}\\quad n\\ge k,"
},
{
"math_id": 9,
"text": "\\varphi: \\mathbb N\\times X^k \\to X"
},
{
"math_id": 10,
"text": "n!=n\\cdot (n-1)!\\quad\\text{for}\\quad n>0,"
},
{
"math_id": 11,
"text": "0!=1."
},
{
"math_id": 12,
"text": "x_{n+1} = r x_n (1 - x_n),"
},
{
"math_id": 13,
"text": "r."
},
{
"math_id": 14,
"text": "r,"
},
{
"math_id": 15,
"text": "x_0"
},
{
"math_id": 16,
"text": "F_n = F_{n-1}+F_{n-2}"
},
{
"math_id": 17,
"text": "F_0 = 0"
},
{
"math_id": 18,
"text": "F_1 = 1."
},
{
"math_id": 19,
"text": "F_2 = F_1 + F_0"
},
{
"math_id": 20,
"text": "F_3 = F_2 + F_1"
},
{
"math_id": 21,
"text": "F_4 = F_3 + F_2"
},
{
"math_id": 22,
"text": "t^2 = t + 1"
},
{
"math_id": 23,
"text": "\\frac{t}{1-t-t^2}."
},
{
"math_id": 24,
"text": "\\tbinom{n}{k}"
},
{
"math_id": 25,
"text": "\\binom{n}{k}=\\binom{n-1}{k-1}+\\binom{n-1}{k},"
},
{
"math_id": 26,
"text": "\\tbinom{n}{0}=\\tbinom{n}{n}=1"
},
{
"math_id": 27,
"text": "\\binom{n}{k}=\\frac{n!}{k!(n-k)!}."
},
{
"math_id": 28,
"text": "\\binom n k = \\binom n{k-1}(n-k+1)/k,"
},
{
"math_id": 29,
"text": "\\binom n 0 =1"
},
{
"math_id": 30,
"text": "\\binom nk= \\binom n{n-k}, "
},
{
"math_id": 31,
"text": "\\Delta,"
},
{
"math_id": 32,
"text": "(\\Delta f)(x)=f(x+1)-f(x)."
},
{
"math_id": 33,
"text": "(\\Delta a)_n= a_{n+1} - a_n."
},
{
"math_id": 34,
"text": "\\Delta f"
},
{
"math_id": 35,
"text": "\\Delta a"
},
{
"math_id": 36,
"text": "\\Delta a_n"
},
{
"math_id": 37,
"text": "\\Delta a,"
},
{
"math_id": 38,
"text": "\\Delta"
},
{
"math_id": 39,
"text": "a_n."
},
{
"math_id": 40,
"text": "a=(a_n)_{n\\in \\N},"
},
{
"math_id": 41,
"text": "\\Delta a."
},
{
"math_id": 42,
"text": "\\Delta^2 a=(\\Delta\\circ\\Delta)a= \\Delta(\\Delta a)."
},
{
"math_id": 43,
"text": "\\Delta^2 a_n= a_{n+2} - 2a_{n+1} + a_n."
},
{
"math_id": 44,
"text": "\\Delta^k=\\Delta\\circ \\Delta^{k-1},"
},
{
"math_id": 45,
"text": "\\Delta^k a_n = \\sum_{t=0}^k (-1)^t \\binom{k}{t} a_{n+k-t}."
},
{
"math_id": 46,
"text": "a_{n+k} = a_n + {k\\choose 1} \\Delta a_n + \\cdots + {k\\choose k} \\Delta^k(a_n)."
},
{
"math_id": 47,
"text": "3\\Delta^2 a_n + 2\\Delta a_n + 7a_n = 0"
},
{
"math_id": 48,
"text": "3a_{n+2} = 4a_{n+1} - 8a_n,"
},
{
"math_id": 49,
"text": "a_{n+1} = f_n a_n + g_n, \\qquad f_n \\neq 0,"
},
{
"math_id": 50,
"text": "a_{n+1} - f_n a_n = g_n"
},
{
"math_id": 51,
"text": "\\frac{a_{n+1}}{\\prod_{k=0}^n f_k} - \\frac{f_n a_n}{\\prod_{k=0}^n f_k} = \\frac{g_n}{\\prod_{k=0}^n f_k}"
},
{
"math_id": 52,
"text": "\\frac{a_{n+1}}{\\prod_{k=0}^n f_k} - \\frac{a_n}{\\prod_{k=0}^{n-1} f_k} = \\frac{g_n}{\\prod_{k=0}^n f_k}"
},
{
"math_id": 53,
"text": "A_n = \\frac{a_n}{\\prod_{k=0}^{n-1} f_k},"
},
{
"math_id": 54,
"text": "A_{n+1} - A_n = \\frac{g_n}{\\prod_{k=0}^n f_k}"
},
{
"math_id": 55,
"text": "\\sum_{m=0}^{n-1}(A_{m+1} - A_m) = A_n - A_0 = \\sum_{m=0}^{n-1}\\frac{g_m}{\\prod_{k=0}^m f_k}"
},
{
"math_id": 56,
"text": "\\frac{a_n}{\\prod_{k=0}^{n-1} f_k} = A_0 + \\sum_{m=0}^{n-1}\\frac{g_m}{\\prod_{k=0}^m f_k}"
},
{
"math_id": 57,
"text": "a_n = \\left(\\prod_{k=0}^{n-1} f_k \\right) \\left(A_0 + \\sum_{m=0}^{n-1}\\frac{g_m}{\\prod_{k=0}^m f_k}\\right)"
},
{
"math_id": 58,
"text": "a_{n+1} = (1 + h f_{nh}) a_n + hg_{nh}"
},
{
"math_id": 59,
"text": "h \\to 0"
},
{
"math_id": 60,
"text": "J_{n+1}=\\frac{2n}{z}J_n-J_{n-1}"
},
{
"math_id": 61,
"text": "J_n=J_n(z), "
},
{
"math_id": 62,
"text": "(b-n)M_{n-1} +(2n-b+z)M_n - nM_{n+1}=0 "
},
{
"math_id": 63,
"text": "M_n=M(n,b;z) "
},
{
"math_id": 64,
"text": "w_{t+1} = \\tfrac{aw_t+b}{cw_t+d}"
},
{
"math_id": 65,
"text": "w_t"
},
{
"math_id": 66,
"text": "x_t"
},
{
"math_id": 67,
"text": "d"
},
{
"math_id": 68,
"text": "a_n = c_1a_{n-1} + c_2a_{n-2}+\\cdots+c_da_{n-d}, "
},
{
"math_id": 69,
"text": "\\lambda^d - c_1 \\lambda^{d-1} - c_2 \\lambda^{d-2} - \\cdots - c_d \\lambda^0 =0. "
},
{
"math_id": 70,
"text": "[x_t - x^*] = A[x_{t-1}-x^*]"
},
{
"math_id": 71,
"text": "x"
},
{
"math_id": 72,
"text": "A"
},
{
"math_id": 73,
"text": "x^*"
},
{
"math_id": 74,
"text": "x_n=f(x_{n-1})."
},
{
"math_id": 75,
"text": "f"
},
{
"math_id": 76,
"text": "| f' (x^*) | < 1. "
},
{
"math_id": 77,
"text": "k > 1"
},
{
"math_id": 78,
"text": "g(x) := f \\circ f \\circ \\cdots \\circ f(x)"
},
{
"math_id": 79,
"text": "| g' (x^*) | < 1,"
},
{
"math_id": 80,
"text": "y'(t) = f(t,y(t)), \\ \\ y(t_0)=y_0,"
},
{
"math_id": 81,
"text": "h"
},
{
"math_id": 82,
"text": "y_0=y(t_0), \\ \\ y_1=y(t_0+h), \\ \\ y_2=y(t_0+2h), \\ \\dots"
},
{
"math_id": 83,
"text": "\\, y_{n+1} = y_n + hf(t_n,y_n), t_n = t_0 + nh "
},
{
"math_id": 84,
"text": "N_{t+1} = \\lambda N_t e^{-aP_t} "
},
{
"math_id": 85,
"text": "P_{t+1} = N_t(1-e^{-aP_t}), "
},
{
"math_id": 86,
"text": "N_t"
},
{
"math_id": 87,
"text": "P_t"
},
{
"math_id": 88,
"text": "t"
},
{
"math_id": 89,
"text": "c_1=1"
},
{
"math_id": 90,
"text": "c_n=1+c_{n/2}"
},
{
"math_id": 91,
"text": "O(\\log_2(n))"
},
{
"math_id": 92,
"text": "T"
},
{
"math_id": 93,
"text": "y_t = (1 - \\alpha) x_t + \\alpha y_{t - T},"
},
{
"math_id": 94,
"text": "y_t"
},
{
"math_id": 95,
"text": "\\alpha"
},
{
"math_id": 96,
"text": "y_t = (1 - \\alpha) x_t + \\alpha ((1-\\alpha) x_{t-T} + \\alpha y_{t - 2T})"
},
{
"math_id": 97,
"text": "y_t = (1 - \\alpha) x_t + (\\alpha-\\alpha^2) x_{t-T} + \\alpha^2 y_{t - 2T}"
}
] |
https://en.wikipedia.org/wiki?curid=146806
|
14680625
|
Protein-Npi-phosphohistidine-sugar phosphotransferase
|
In enzymology, a protein-Npi-phosphohistidine-sugar phosphotransferase (EC 2.7.1.69) is an enzyme that catalyzes the chemical reaction
protein Npi-phospho-L-histidine + sugar formula_0 protein histidine + sugar phosphate
Thus, the two substrates of this enzyme are protein Npi-phospho-L-histidine and sugar, whereas its two products are protein histidine and sugar phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is protein-Npi-phosphohistidine:sugar Npi-phosphotransferase. Other names in common use include glucose permease, PTS permease, phosphotransferase, phosphohistidinoprotein-hexose, enzyme IIl4ac, gene glC proteins, gene bglC RNA formation factors, PEP-dependent phosphotransferase enzyme II, PEP-sugar phosphotransferase enzyme II, phosphoenolpyruvate-sugar phosphotransferase enzyme II, phosphohistidinoprotein-hexose phosphotransferase, phosphohistidinoprotein-hexose phosphoribosyltransferase, phosphoprotein factor-hexose phosophotransferase, protein, specific or class, gene bglC, ribonucleic acid formation factor, gene glC, sucrose phosphotransferase system II, and protein-Npi-phosphohistidine:sugar N-pros-phosphotransferase. This enzyme participates in 7 metabolic pathways: glycolysis / gluconeogenesis, fructose and mannose metabolism, galactose metabolism, ascorbate and aldarate metabolism, starch and sucrose metabolism, aminosugars metabolism, and phosphotransferase system (pts).
Structural studies.
As of late 2007, 29 structures have been solved for this class of enzymes, with PDB accession codes 1A3A, 1A6J, 1AX3, 1BLE, 1E2A, 1E2B, 1F3Z, 1GGR, 1GLA, 1GLB, 1GLC, 1GLD, 1GLE, 1GPR, 1H9C, 1IBA, 1IIB, 1NRZ, 1O2F, 1O53, 1PDO, 1TVM, 1VRC, 1WCR, 2A0J, 2E2A, 2F3G, 2FEW, and 2GPR.
References.
<templatestyles src="Reflist/styles.css" />
|
[
{
"math_id": 0,
"text": "\\rightleftharpoons"
}
] |
https://en.wikipedia.org/wiki?curid=14680625
|
14680663
|
(protein-PII) uridylyltransferase
|
Class of enzymes
In enzymology, a [protein-PII] uridylyltransferase (EC 2.7.7.59) is an enzyme that catalyzes the chemical reaction
UTP + [protein-PII] formula_0 diphosphate + uridylyl-[protein-PII]
Thus, the two substrates of this enzyme are UTP and protein-PII, whereas its two products are diphosphate and uridylyl-[protein-PII].
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing nucleotide groups (nucleotidyltransferases). The systematic name of this enzyme class is UTP:[protein-PII] uridylyltransferase. Other names in common use include PII uridylyl-transferase, and uridyl removing enzyme. This enzyme participates in two-component system - general.
References.
<templatestyles src="Reflist/styles.css" />
|
[
{
"math_id": 0,
"text": "\\rightleftharpoons"
}
] |
https://en.wikipedia.org/wiki?curid=14680663
|
14680695
|
Pseudouridine kinase
|
Class of enzymes
In enzymology, a pseudouridine kinase (EC 2.7.1.83) is an enzyme that catalyzes the chemical reaction
ATP + pseudouridine formula_0 ADP + pseudouridine 5'-phosphate
Thus, the two substrates of this enzyme are ATP and pseudouridine, whereas its two products are ADP and pseudouridine 5'-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:pseudouridine 5'-phosphotransferase. This enzyme is also called pseudouridine kinase (phosphorylating). This enzyme participates in pyrimidine metabolism.
References.
<templatestyles src="Reflist/styles.css" />
|
[
{
"math_id": 0,
"text": "\\rightleftharpoons"
}
] |
https://en.wikipedia.org/wiki?curid=14680695
|
14680725
|
Pyridoxal kinase
|
In enzymology, a pyridoxal kinase (EC 2.7.1.35) is an enzyme that catalyzes the chemical reaction
ATP + pyridoxal formula_0 ADP + pyridoxal 5'-phosphate
Thus, the two substrates of this enzyme are ATP and pyridoxal, whereas its two products are ADP and pyridoxal 5'-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:pyridoxal 5'-phosphotransferase. Other names in common use include pyridoxal kinase (phosphorylating), pyridoxal 5-phosphate-kinase, pyridoxal phosphokinase, and pyridoxine kinase. This enzyme participates in vitamin B6 metabolism.
Structural studies.
As of late 2007, 15 structures have been solved for this class of enzymes, with PDB accession codes 1LHP, 1LHR, 1RFT, 1RFU, 1RFV, 1TD2, 1VI9, 1YGJ, 1YGK, 1YHJ, 2AJP, 2DDM, 2DDO, 2DDW, and 2F7K.
References.
<templatestyles src="Reflist/styles.css" />
|
[
{
"math_id": 0,
"text": "\\rightleftharpoons"
}
] |
https://en.wikipedia.org/wiki?curid=14680725
|
14680754
|
Pyruvate, phosphate dikinase
|
Pyruvate, phosphate dikinase, or PPDK (EC 2.7.9.1) is an enzyme in the family of transferases that catalyzes the chemical reaction
ATP + pyruvate + phosphate formula_0 AMP + phosphoenolpyruvate + diphosphate
This enzyme has been studied primarily in plants, but it has been studied in some bacteria as well. It is a key enzyme in gluconeogenesis and photosynthesis that is responsible for reversing the reaction performed by pyruvate kinase in Embden-Meyerhof-Parnas glycolysis. It should not be confused with pyruvate, water dikinase.
It belongs to the family of transferases, to be specific, those transferring phosphorus-containing groups (phosphotransferases) with paired acceptors (dikinases). This enzyme participates in pyruvate metabolism and carbon fixation.
Nomenclature.
The systematic name of this enzyme class is ATP:pyruvate, phosphate phosphotransferase. Other names in common use include pyruvate, orthophosphate dikinase, pyruvate-phosphate dikinase (phosphorylating), pyruvate phosphate dikinase, pyruvate-inorganic phosphate dikinase, pyruvate-phosphate dikinase, pyruvate-phosphate ligase, pyruvic-phosphate dikinase, pyruvic-phosphate ligase, pyruvate, Pi dikinase, and PPDK.
Reaction mechanism.
PPDK catalyses the conversion of pyruvate to phosphoenolpyruvate (PEP), consuming 1 molecule of ATP, and producing one molecule of AMP in the process. The mechanism consists of 3 reversible reactions:
The reaction is similar to the reaction catalysed by pyruvate kinase, which also converts pyruvate to PEP. However, pyruvate kinase catalyses an irreversible reaction, and does not consume ATP. By contrast, PPDK catalyses a reversible reaction, and consumes 1 molecule of ATP for each molecule of pyruvate converted.
Currently, the details of each mechanistic step is unknown
Structure.
In its active form, PPDK is a homotetramer with subunits about 95 kDa
There are two different reaction centres about 45 Angstroms apart, in which different substrates bind. The nucleotide (ATP) binding site is on the N-terminus, has 240 amino acids, and a characteristic ATP-grasp. The pyruvate/PEP binding site is on the C-terminus, has 340 amino acids, and an α/β-barrel fold. There is also a central domain, which contains His455, the primary residue responsible for catalysis. His455 is the phosphoryl acceptor or donor residue. The structure of the enzyme suggests that the His455 arm undergoes a swivelling motion to shuttle a phosphoryl group between the two reaction centres. During this swivelling, the central domain rotates at least 92 degrees, and translates 0.5 Angstroms.
Studies of crystal structures of PPDK show that the central domain is located in different proximity to the two other domains depending on the source of the enzyme. In maize, it is closer to the C-terminal, while in "Clostridium symbiosum", it is closer to the N-terminal.
Research has shown that the PPDK binding mechanisms are similar to that of D-Ala-D-Ala ligase and pyruvate kinase. In particular, PPDK is very similar to pyruvate kinase, which also catalyses the conversion of pyruvate to phosphoenolpyruvate; however, it does so without a phosphorylated-enzyme intermediate. Though their amino acid sequences are different, residues key to catalysis are preserved in both enzymes. Point-mutagenesis experiments have shown that catalytic residues include Arg561, Arg617, Glu745, Asn768, and Cys831 (numbering relative to the "C, symbiosum" protein, PDB: 1KBL, 1KC7).
Biological function and evolution.
PPDK is used in the C4 pathway, to improve the efficiency of carbon dioxide fixation. In environments where there is a lot of light, the rate of photosynthesis in plants is limited by the rate of carbon dioxide (CO2) uptake. This can be improved by using a series of chemical reactions to transport CO2 from mesophyll cells (which are located on the outside of a leaf) to bundle sheath cells (which are located inside the cells). PPDK converts pyruvate to PEP, which reacts with CO2 to produce oxaloacetate. When CO2 is released in the bundle sheath cells, pyruvate is regenerated, and the cycle continues.
Though the reaction catalysed by PPDK is reversible, PEP is favoured as the product in biological conditions. This is due to the basic pH in the stroma, where the reaction occurs, as well as high concentrations of adenylate kinase and pyrophosphatase. Because these two enzymes catalyse exergonic reactions involving AMP, and disphosphate, respectively, they drive the PPDK-catalysed reaction forward. Because PPDK consumes ATP, the C4 pathway is unfavourable for plants in environments with little access to light, as they are unable to produce large quantities of ATP.
PPDK is highly abundant in C4 leaves, comprising up to 10% of total protein. Research has shown that the enzyme is about 96% identical in different species of plants. Hybridization experiments revealed that the genetic differences correlate with the extent to which the plants perform the C4 pathway – the uncommon sequences exist in plants which also display C3 characteristics. PPDK is also found in small quantities in C3 plants. Evolutionary history suggests that it once had a role in glycolysis like the similar pyruvate kinase, and eventually evolved into the C4 pathway.
Besides plants, PPDK is also found in the parasitic ameoba "Entamoeba histolytica" (P37213) and the bacteria "Clostridium symbiosum" (P22983; as well as other bacteria). In those two organisms PPDK functions similarly to (and sometimes in place of) pyruvate kinase, catalyzing the reaction in the ATP-producing direction as a part of glycolysis. Inhibitors for the "Entamoeba" PPDK have been proposed as amebicides against this organism.
Regulation.
Plant PPDK is regulated by the pyruvate, phosphate dikinase regulatory protein (PDRP). When levels of light are high, PDRP dephosphorylates Thr456 on PPDK using AMP, thus activating the enzyme. PDRP deactivates PPDK by phosphorylating the same threonine residue, using diphosphate. PDRP is a unique regulator because it catalyses both activation and deactivation of PPDK, through two different mechanisms.
Research on maize PPDK suggests that introns, terminator sequences, and perhaps other enhancer sequences, act cooperatively to increase the level of functional and stable mRNA. PPDK cDNA was expressed only slightly in transgenic rice, compared to intact DNA which saw significant expression.
Structural studies.
As of early 2018, 14 structures have been solved for this class of enzymes, with PDB accession codes 1DIK, 1GGO, 1H6Z, 1JDE, 1KBL, 1KC7, 1VBG, 1VBH, 2DIK, 2FM4, 5JVJ, 5JVL, 5JVN, 5LU4.
References.
<templatestyles src="Reflist/styles.css" />
Further reading.
<templatestyles src="Refbegin/styles.css" />
|
[
{
"math_id": 0,
"text": "\\rightleftharpoons"
}
] |
https://en.wikipedia.org/wiki?curid=14680754
|
14680782
|
Pyruvate, water dikinase
|
In enzymology, a pyruvate, water dikinase (EC 2.7.9.2) is an enzyme that catalyzes the chemical reaction
ATP + pyruvate + H2O formula_0 AMP + phosphoenolpyruvate + phosphate
The 3 substrates of this enzyme are ATP, pyruvate, and H2O, whereas its 3 products are AMP, phosphoenolpyruvate, and phosphate. This reaction catalyzed by pyruvate, water dikinase can run in both directions, but has a strong preference for AMP, phosphate, and phosphoenolpyruvate as substrate and typically runs in the ATP producing direction.
This enzyme belongs to the family of transferases, to be specific, those transferring phosphorus-containing groups (phosphotransferases) with paired acceptors (dikinases). The systematic name of this enzyme class is ATP:pyruvate, water phosphotransferase. Other names in common use include phosphoenolpyruvate synthase, pyruvate-water dikinase (phosphorylating), PEP synthetase, PEP synthase, PEPS, phoephoenolpyruvate synthetase, phosphoenolpyruvic synthase, and phosphopyruvate synthetase. This enzyme participates in pyruvate metabolism and reductive carboxylate cycle (CO2 fixation). It employs one cofactor, manganese.
Studied organisms.
According to the BRENDA database, pyruvate, water dikinase has been studied in nine unique bacterial and archaea species under a wide range of names. Many of the studied organisms are thermophilic or hyperthermophilic, meaning they live and function in very high temperatures in their natural environments, and have been found in hot springs, volcanos, and deep sea hydrothermal vents.
One of the most widely studied organisms for pyruvate, water dikninase is "Pyrococcus furiosus". "Pyrococcus furiosus" is a deep sea hyperthermophilic archaea that is commonly found living in extremely hot waters around hydrothermal vents. This species is heterotrophic and anaerobic (grows and metabolizes without the presence of oxygen), and has an optimal growth temperature of 100˚C. The enzymes and proteins in this species are studied and of note because of their thermal stability. "Pyrococcus furiosus" organisms use the fermentation of carbohydrates and glycolysis to produce energy.
Structure.
As of 2023, only one structure has been solved for this class of enzymes, with the PDB accession code 2OLS. The crystalline structure from "Neisseria meningitidis" was computed through x-ray diffraction techniques at a resolution of 2.40 Å. Pyruvate, water dikinase in "Neisseria meningitidis" is 794 amino acids in length and has two active sites: one at at position 422 and position 752.
In "Pyrococcus furiosus", the pyruvate, water dikinase enzyme has a subunit molecular mass of 92 kDa, and each subunit contains one calcium and one phosphorus atom. This enzyme has a octomeric structure, meaning that pyruvate, water dikinase in "Pyrococcus furiosus" is an oligomer protein consisting of eight subunits in its quaternary structure. This eight subunit protein structure might help this enzyme function at high temperatures. This enzyme comes in two protein types, one phosphorylated and one non phosphorylated version. The N terminal amino acid sequences the same in both versions, which shows these two forms are phosphorylated and non phosphorylated versions of pyruvate, water dikinase.
Reaction pathway and biological function.
In "Pyrococcus furiosus," pyruvate, water dikinase is the enzyme that catalyzes the first step of gluconeogenesis from pyruvate in the modified Embden-Meyerhof pathway (M-EMP) and is an important ATP producing reaction in the metabolism pathway. The modified Embden-Meyerhof pathway is a glycolytic pathway that converts glucose into pyruvate and energy products for the cell. This enzyme participates in catalyzing reactions that are important for both gluconeogenesis and the reverse, glycolysis. For their metabolism, "Pyrococcus furiosus" uses carbon sources like maltose, cellobiose, laminarin, and starches in this sugar metabolic pathway to produce energy for the organism.
Pyruvate, water dikinase in "Pyrococcus furiosus" primarily catalyzes the reaction that goes from phosphoenolpyruvate and AMP to pyruvate and ATP, but can also catalyze the reverse reaction. This reaction is thought to be important because it converts AMP into usable ATP energy during this sugar M-EMP metabolism. Two sugar kinase enzymes (glucokinase and phosphofructokinase) were found in the M-EMP pathway in "Pyrococcus furiosus" that catalyze the reaction that used ADP and produces AMP. In order for the AMP to be usable as ATP in the cell, the pyruvate, water dikinase enzyme catalyzes the phosphate dependent formation of pyruvate reaction pathway to convert AMP to ATP. This enzyme uses phosphoenolpyruvate as the phosphoryl group donor and then forms ATP in the presence of phosphate.
One study determined that pyruvate, water dikinase in "Pyrococcus furiosus" can act in a futile cycle between phosphoenolpyruvate and pyruvate as substrates/products. These two reactions can run through the metabolic pathways at the same time in opposite directions, which will dissipate energy as heat without other effects. This can remove unwanted energy, as the energy produced from glycolysis is much more than the energy required for growth and cellular repairs. This is possibly a mode of "energy spilling" in "Pyrococcus furiosus". This is in part hypothesized because of to the high concentrations of this enzyme (~5% of protein in the cytoplasm) in "Pyrococcus furiosus" cells.
Enzyme kinematics.
The hyperthermostable pyruvate, water dikinase enzyme in "Pyrococcus furiosus" is encoded by the mlrA gene, which was found to be regulated by at least in part by maltose at a transcription level. Pyruvate, water dikinase catalyzes the reaction that converts phosphoenolpyruvate, AMP, and phosphate to pyruvate, ATP, and water. This enzyme also catalyzes the reverse reaction, but reaction rates and equilibrium constants show that the ATP production reaction direction is highly favorable. Pyruvate, water dikinase in "Pyrococcus furiosus" is sensitive to oxygen, with no enzyme activity measured in aerobic conditions. The purified pyruvate, water dikinase in "Pyrococcus furiosus" has a pH optimum between 6.5 and 9, and a temperature optimum around 90˚C. In the PEP formation reaction, pyruvate has an apparent Km of 0.11mM, apparent kcat of 1,573(s-1) and apparent kcat/Km of 1.43 x 10^4 (mM-1• s-1), and ATP has an apparent Km of 0.39mM, apparent kcat of 1,326(s-1) and apparent kcat/Km of 3.40 x 10^3 (mM-1 • s-1). In the pyruvate formation reaction, PEP has an apparent Km of 0.40mM, apparent kcat of 12.6(s-1) and apparent kcat/Km of 31.5 (mM-1 • s-1), AMP has an apparent Km of 1.00mM, apparent kcat of 8.7(s-1) and apparent kcat/Km of 8.7 (mM-1 • s-1), and phosphate has an apparent Km of 38.4mM, apparent kcat of 11.9(s-1) and apparent kcat/Km of 0.315(mM-1 • s-1). The equilibrium constant Keq of the reaction is 1.07 at 50˚C, and the change in Gibbs free energy (ΔG˚) is -0.04 kcal/mol at experimental conditions.
References.
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14680810
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Rhamnulokinase
|
In enzymology, a rhamnulokinase (EC 2.7.1.5) is an enzyme that catalyzes the chemical reaction
ATP + L-rhamnulose formula_0 ADP + L-rhamnulose 1-phosphate
Thus, the two substrates of this enzyme are ATP and L-rhamnulose, whereas its two products are ADP and L-rhamnulose 1-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:L-rhamnulose 1-phosphotransferase. Other names in common use include RhuK, rhamnulokinase (phosphorylating), L-rhamnulokinase, L-rhamnulose kinase, and rhamnulose kinase. This enzyme participates in pentose and glucuronate interconversions and fructose and mannose metabolism. This enzyme can catalyze the xylulose phosphorilation:
ATP + L-Xylulose formula_0 ADP + L-Xylulose 1-phosphate
Structural studies.
As of late 2007, 4 structures have been solved for this class of enzymes by Grueninger and Schulz with PDB accession codes 2CGJ, 2CGK, 2CGL, and 2UYT.
References.
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14680834
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Riboflavin kinase
|
Class of enzymes
In enzymology, a riboflavin kinase (EC 2.7.1.26) is an enzyme that catalyzes the chemical reaction
ATP + riboflavin formula_0 ADP + FMN
Thus, the two substrates of this enzyme are ATP and riboflavin, whereas its two products are ADP and FMN.
Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (EC 2.7.1.26), which converts it into FMN, and FAD synthetase (EC 2.7.7.2), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme, the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases.
This enzyme belongs to the family of transferases, to be specific, those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:riboflavin 5'-phosphotransferase. This enzyme is also called flavokinase. This enzyme participates in riboflavin metabolism.
However, archaeal riboflavin kinases (EC 2.7.1.161) in general utilize CTP rather than ATP as the donor nucleotide, catalyzing the reaction
CTP + riboflavin formula_0 CDP + FMN
Riboflavin kinase can also be isolated from other types of bacteria, all with similar function but a different number of amino acids.
Structure.
The complete enzyme arrangement can be observed with X-ray crystallography and with NMR.
The riboflavin kinase enzyme isolated from "Thermoplasma acidophilum" contains 220 amino acids. The structure of this enzyme has been determined X-ray crystallography at a resolution of 2.20 Å. Its secondary structure contains 69 residues (30%) in alpha helix form, and 60 residues (26%) a beta sheet conformation. The enzyme contains a magnesium binding site at amino acids 131 and 133, and a Flavin mononucleotide binding site at amino acids 188 and 195.
As of late 2007, 14 structures have been solved for this class of enzymes, with PDB accession codes 1N05, 1N06, 1N07, 1N08, 1NB0, 1NB9, 1P4M, 1Q9S, 2P3M, 2VBS, 2VBT, 3CTA, 2VBU, and 2VBV.
References.
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Further reading.
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14680861
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Riboflavin phosphotransferase
|
In enzymology, a riboflavin phosphotransferase (EC 2.7.1.42) is an enzyme that catalyzes the chemical reaction
alpha-D-glucose 1-phosphate + riboflavin formula_0 D-glucose + FMN
Thus, the two substrates of this enzyme are alpha-D-glucose 1-phosphate and riboflavin, whereas its two products are D-glucose and FMN.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is alpha-D-glucose-1-phosphate:riboflavin 5'-phosphotransferase. Other names in common use include riboflavine phosphotransferase, glucose-1-phosphate phosphotransferase, G-1-P phosphotransferase, and D-glucose-1-phosphate:riboflavin 5'-phosphotransferase.
References.
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14680916
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Ribose 1,5-bisphosphate phosphokinase
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In enzymology, a ribose 1,5-bisphosphate phosphokinase (EC 2.7.4.23) is an enzyme that catalyzes the chemical reaction
ATP + ribose 1,5-bisphosphate formula_0 ADP + 5-phospho-alpha-D-ribose 1-diphosphate
Thus, the two substrates of this enzyme are ATP and ribose 1,5-bisphosphate, whereas its two products are ADP and 5-phospho-alpha-D-ribose 1-diphosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with a phosphate group as acceptor. The systematic name of this enzyme class is ATP:ribose-1,5-bisphosphate phosphotransferase. Other names in common use include ribose 1,5-bisphosphokinase, and PhnN. This enzyme participates in pentose phosphate pathway.
References.
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14680944
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Ribose-5-phosphate adenylyltransferase
|
In enzymology, a ribose-5-phosphate adenylyltransferase (EC 2.7.7.35) is an enzyme that catalyzes the chemical reaction
ADP + D-ribose 5-phosphate formula_0 phosphate + ADP-ribose
Thus, the two substrates of this enzyme are ADP and D-ribose 5-phosphate, whereas its two products are phosphate and ADP-ribose.
This enzyme belongs to the family of transferases, specifically ones transferring phosphorus-containing nucleotide groups (nucleotidyltransferases). The systematic name of this enzyme class is ADP:D-ribose-5-phosphate adenylyltransferase. Other names in common use include ADP ribose phosphorylase, and adenosine diphosphoribose phosphorylase.
References.
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14680967
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Ribosylnicotinamide kinase
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In enzymology, a ribosylnicotinamide kinase (EC 2.7.1.22) is an enzyme that catalyzes the chemical reaction
ATP + N-ribosylnicotinamide formula_0 ADP + nicotinamide ribonucleotide
Thus, the two substrates of this enzyme are ATP and N-ribosylnicotinamide, whereas its two products are ADP and nicotinamide ribonucleotide.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:N-ribosylnicotinamide 5'-phosphotransferase. This enzyme is also called ribosylnicotinamide kinase (phosphorylating). This enzyme participates in nicotinate and nicotinamide metabolism.
Health.
Studies show potential for obesity treatment and for longer healthier life. Ribosylnicotinamide kinase seems to activate similar genes that Resveratrol does.
Food.
The enzyme can be found in milk and beer. Since the molecules are difficult to detect, it is expected that there are a lot more food products containing ribosylnicotinamide kinase.
References.
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14680993
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Ribulokinase
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In enzymology, a ribulokinase (EC 2.7.1.16) is an enzyme that catalyzes the chemical reaction
ATP + L(or D)-ribulose formula_0 ADP + L(or D)-ribulose 5-phosphate
The 3 substrates of this enzyme are ATP, L-ribulose, and D-ribulose, whereas its 3 products are ADP, L-ribulose 5-phosphate, and D-ribulose 5-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:L(or D)-ribulose 5-phosphotransferase. Other names in common use include ribulokinase (phosphorylating), and L-ribulokinase. This enzyme participates in pentose and glucuronate interconversions.
References.
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14681016
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(RNA-polymerase)-subunit kinase
|
Class of enzymes
In enzymology, an [RNA-polymerase]-subunit kinase (EC 2.7.11.23) is an enzyme that catalyzes the chemical reaction
ATP + [DNA-directed RNA polymerase] formula_0 ADP + phospho-[DNA-directed RNA polymerase]
Thus, the two substrates of this enzyme are ATP and DNA-directed RNA polymerase, whereas its two products are ADP and phospho-DNA-directed RNA polymerase.
This enzyme belongs to the family of transferases, specifically those transferring a phosphate group to the sidechain oxygen atom of serine or threonine residues in proteins (protein-serine/threonine kinases). The systematic name of this enzyme class is ATP:[DNA-directed RNA polymerase] phosphotransferase. Other names in common use include CTD kinase, and STK9.
References.
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14681038
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RNA uridylyltransferase
|
Class of enzymes
In enzymology, a RNA uridylyltransferase (EC 2.7.7.52) is an enzyme that catalyzes the chemical reaction
UTP + RNAn formula_0 diphosphate + RNAn+1
Thus, the two substrates of this enzyme are UTP and RNAn, whereas its two products are diphosphate and RNAn+1.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing nucleotide groups (nucleotidyltransferases). The systematic name of this enzyme class is UTP:RNA uridylyltransferase. Other names in common use include terminal uridylyltransferase, and TUT.
Structural studies.
As of late 2007, 8 structures have been solved for this class of enzymes, with PDB accession codes 2E5G, 2IKF, 2NOM, 2Q0C, 2Q0D, 2Q0E, 2Q0F, and 2Q0G.
References.
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14681072
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Scyllo-inosamine 4-kinase
|
Enzyme
In enzymology, a scyllo-inosamine 4-kinase (EC 2.7.1.65) is an enzyme that catalyzes the chemical reaction
ATP + 1-amino-1-deoxy-scyllo-inositol formula_0 ADP + 1-amino-1-deoxy-scyllo-inositol 4-phosphate
Thus, the two substrates of this enzyme are ATP and 1-amino-1-deoxy-scyllo-inositol, whereas its two products are ADP and 1-amino-1-deoxy-scyllo-inositol 4-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:1-amino-1-deoxy-scyllo-inositol 4-phosphotransferase. Other names in common use include scyllo-inosamine kinase (phosphorylating), scyllo-inosamine kinase, and ATP:inosamine phosphotransferase. This enzyme participates in streptomycin biosynthesis.
References.
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14681098
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Sedoheptulokinase
|
In enzymology, a sedoheptulokinase (EC 2.7.1.14) is an enzyme that catalyzes the chemical reaction
ATP + sedoheptulose formula_0 ADP + sedoheptulose 7-phosphate
Thus, the two substrates of this enzyme are ATP and sedoheptulose, whereas its two products are ADP and sedoheptulose 7-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:sedoheptulose 7-phosphotransferase. Other names in common use include heptulokinase, and sedoheptulokinase (phosphorylating). This enzyme participates in carbon fixation.
References.
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14681128
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Selenide, water dikinase
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In enzymology, a selenide, water dikinase (EC 2.7.9.3) is an enzyme that catalyzes the chemical reaction
ATP + selenide + H2O formula_0 AMP + selenophosphate + phosphate
The 3 substrates of this enzyme are ATP, selenide, and H2O, whereas its 3 products are AMP, selenophosphate, and phosphate.
This enzyme belongs to the family of transferases, to be specific, those transferring phosphorus-containing groups (phosphotransferases) with paired acceptors (dikinases). The systematic name of this enzyme class is ATP:selenide, water phosphotransferase. This enzyme is also called selenophosphate synthetase. This enzyme participates in selenoamino acid metabolism.
References.
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14681153
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Serine-phosphoethanolamine synthase
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In enzymology, a serine-phosphoethanolamine synthase (EC 2.7.8.4) is an enzyme that catalyzes the chemical reaction
CDP-ethanolamine + L-serine formula_0 CMP + L-serine-phosphoethanolamine
Thus, the two substrates of this enzyme are CDP-ethanolamine and L-serine, whereas its two products are CMP and L-serine-phosphoethanolamine.
This enzyme belongs to the family of transferases, specifically those transferring non-standard substituted phosphate groups. The systematic name of this enzyme class is CDP-ethanolamine:L-serine ethanolamine phosphotransferase. Other names in common use include serine ethanolamine phosphate synthetase, serine ethanolamine phosphodiester synthase, serine ethanolaminephosphotransferase, serine-phosphinico-ethanolamine synthase, and serinephosphoethanolamine synthase. This enzyme participates in glycerophospholipid metabolism.
References.
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14681202
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S-methyl-5-thioribose kinase
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In enzymology, a S-methyl-5-thioribose kinase (EC 2.7.1.100) is an enzyme that catalyzes the chemical reaction
ATP + S-methyl-5-thio-D-ribose formula_0 ADP + S-methyl-5-thio-alpha-D-ribose 1-phosphate
Thus, the two substrates of this enzyme are ATP and S-methyl-5-thio-D-ribose, whereas its two products are ADP and S-methyl-5-thio-alpha-D-ribose 1-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:S-methylmethyl-5-thio-D-ribose 1-phosphotransferase. Other names in common use include 5-methylthioribose kinase (phosphorylating), methylthioribose kinase, 5-methylthioribose kinase, and ATP:S5-methyl-5-thio-D-ribose 1-phosphotransferase. This enzyme participates in methionine metabolism.
Structural studies.
As of late 2007, 6 structures have been solved for this class of enzymes, with PDB accession codes 2OLC, 2PU8, 2PUI, 2PUL, 2PUN, and 2PUP.
References.
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14681256
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Sphingomyelin synthase
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In enzymology, a sphingomyelin synthase (EC 2.7.8.27) is an enzyme that catalyzes the chemical reaction
a ceramide + a phosphatidylcholine formula_0 a sphingomyelin + a 1,2-diacyl-sn-glycerol
or the reaction using phosphatidylethanolamine instead of phosphatidylcholine to generate ceramide phosphoethanolamine (CPE), a sphingomyelin analog rich in invertebrates, such as insects.
Thus, the two substrates of this enzyme are ceramide and phosphatidylcholine, whereas its two products are sphingomyelin and 1,2-diacyl-sn-glycerol.
This enzyme belongs to the family of transferases, specifically those transferring non-standard substituted phosphate groups. The systematic name of this enzyme class is ceramide:phosphatidylcholine cholinephosphotransferase. Other names in common use include SM synthase, SMS1, and SMS2. SM synthase family also includes the enzyme catalyzing CPE synthesis, named SMSr (SMS-related).
Structure of SM synthases.
The high sequence identities shared among the three members of the Sphingomyelin Synthase (SMS) family have intrigued researchers for years. Recent cryo-electron microscopic studies have unveiled a fascinating hexameric organization specifically for SMSr, while biochemical investigations have highlighted the formation of stable dimers by SMS1 and SMS2. Within this hexameric structure, each monomeric unit of SMSr functions as an independent catalytic entity, characterized by six transmembrane helices.
The structural analysis has revealed the presence of a sizable chamber within the helical bundle of SMSr. This chamber serves as the site for catalytic activity, with researchers pinpointing a catalytic pentad, denoted as E-H/D-H-D, strategically positioned at the interface between the lipophilic and hydrophilic segments of the reaction chamber. Furthermore, the elucidation of SMSr's catalytic mechanism has uncovered an intricate two-step synthesis process for SM synthesis. Initially, phosphoethanolamine (or phosphatidylcholine in case of SMS1/2) is hydrolyzed from phosphatidylethanolamine (PE-PLC hydrolysis), followed by the subsequent transfer of the phosphoethanolamine moiety to ceramide.
References.
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14681286
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Sphingosine cholinephosphotransferase
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In enzymology, a sphingosine cholinephosphotransferase (EC 2.7.8.10) is an enzyme that catalyzes the chemical reaction
CDP-choline + sphingosine formula_0 CMP + sphingosyl-phosphocholine
Thus, the two substrates of this enzyme are CDP-choline and sphingosine, whereas its two products are CMP and sphingosyl-phosphocholine.
This enzyme belongs to the family of transferases, specifically those transferring non-standard substituted phosphate groups. The systematic name of this enzyme class is CDP-choline:sphingosine cholinephosphotransferase. Other names in common use include CDP-choline-sphingosine cholinephosphotransferase, phosphorylcholine-sphingosine transferase, cytidine diphosphocholine-sphingosine cholinephosphotransferase, and sphingosine choline phosphotransferase. This enzyme participates in sphingolipid metabolism.
References.
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14681319
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Streptomycin 3"-adenylyltransferase
|
In enzymology, a streptomycin 3"-adenylyltransferase (EC 2.7.7.47) is an enzyme that catalyzes the chemical reaction:
ATP + streptomycin formula_0 diphosphate + 3"-adenylylstreptomycin
Thus, the two substrates of this enzyme are ATP and streptomycin, whereas its two products are diphosphate and 3"-adenylylstreptomycin.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing nucleotide groups (nucleotidyltransferases). The systematic name of this enzyme class is ATP:streptomycin 3"-adenylyltransferase. Other names in common use include streptomycin adenylate synthetase, streptomycin adenyltransferase, streptomycin adenylylase, streptomycin adenylyltransferase, streptomycin-spectinomycin adenylyltransferase, AAD (3"), and aminoglycoside 3"-adenylyltransferase.
References.
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14681361
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Streptomycin 3"-kinase
|
In enzymology, a streptomycin 3"-kinase (EC 2.7.1.87) is an enzyme that catalyzes the chemical reaction
ATP + streptomycin formula_0 ADP + streptomycin 3"-phosphate
Thus, the two substrates of this enzyme are ATP and streptomycin, whereas its two products are ADP and streptomycin 3"-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:streptomycin 3"-phosphotransferase. Other names in common use include streptomycin 3"-kinase (phosphorylating), and streptomycin 3"-phosphotransferase.
References.
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14681387
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Streptomycin 6-kinase
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In enzymology, a streptomycin 6-kinase (EC 2.7.1.72) is an enzyme that catalyzes the chemical reaction
ATP + streptomycin formula_0 ADP + streptomycin 6-phosphate
Thus, the two substrates of this enzyme are ATP and streptomycin, whereas its two products are ADP and streptomycin 6-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:streptomycin 6-phosphotransferase. Other names in common use include streptidine kinase, SM 6-kinase, streptomycin 6-kinase (phosphorylating), streptidine kinase (phosphorylating), streptomycin 6-O-phosphotransferase, and streptomycin 6-phosphotransferase. This enzyme participates in streptomycin biosynthesis.
References.
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14681411
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Sulfate adenylyltransferase
|
In enzymology, a sulfate adenylyltransferase (EC 2.7.7.4) is an enzyme that catalyzes the chemical reaction
ATP + sulfate formula_0pyrophosphate + adenylyl sulfate
Thus, the two substrates of this enzyme are ATP and sulfate, whereas its two products are pyrophosphate and adenylyl sulfate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing nucleotide groups (nucleotidyltransferases). The systematic name of this enzyme class is ATP:sulfate adenylyltransferase. Other names in common use include adenosine-5'-triphosphate sulfurylase, adenosinetriphosphate sulfurylase, adenylylsulfate pyrophosphorylase, ATP sulfurylase, ATP-sulfurylase, and sulfurylase. This enzyme participates in 3 metabolic pathways: purine metabolism, selenoamino acid metabolism, and sulfur metabolism.
Some sulfate adenylyltransferases are part of a bifunctional polypeptide chain associated with adenosyl phosphosulfate (APS) kinase. Both enzymes are required for PAPS (phosphoadenosine-phosphosulfate) synthesis from inorganic sulfate.
Within the cell Sulfate adenylyltransferase plays a key role in both assimilatory sulfur reduction and dissimilatory sulfur oxidation and reduction (DSR) and participates in the biogeochemically relevant sulfur cycle. In dissimilatory sulfate reduction the SAT enzyme, acts as the first priming step in the reduction converting sulfate(+6) to Adenosine 5'-phosphosulfate (APS) via adenylation at the cost of an ATP. If the organisms participating in the DSR pathway possess the full suite of genes necessary, APS can then be further stepwise reduced to sulfite(+4) and then sulfide (-2). Conversely in the process of dissimilatory sulfate oxidation, pyrophosphate combines with APS in a sulfate adenylyltransferase catalyzed reaction to form sulfate. In either direction in which the Sulfate adenylyltransferase (reduction or oxidation) proceeds along DSR in bacterial cells, the associated pathways are participating in cellular respiration necessary for the growth of the organism.
Structural studies.
As of late 2007, 18 structures have been solved for this class of enzymes, with PDB accession codes 1G8F, 1G8G, 1G8H, 1I2D, 1J70, 1JEC, 1JED, 1JEE, 1JHD, 1M8P, 1R6X, 1TV6, 1V47, 1X6V, 1XJQ, 1XNJ, 1ZUN, and 2GKS.
In yeast other fungi and bacteria participating in assimilatory sulfate reduction, the sulfate adenylyltransferase is in the form a of a homohexamer. Its shape is that of a homotetramer in plants. In Saccharomyces cerevisiae sulfate adenylyltransferase is composed of four domains. Domain I features the N-terminus with beta-barrels similar to pyruvate kinase. A right handed alpha/beta fold makes of the shape of Domain II, and it also contains the active site and substrate-binding pocket. Domain III is composed of a region linking the terminal domain to Domain I & II. Domain IV contains the C-terminus of the protein and forms a typical alpha/beta-fold. The active site of Sulfate adenylyltransferase is composed mostly of portions of the Domain II specifically, H9, S9, S10, S12, and the conserved RNP-Loop and GRD-Loop. The active site is located in the center of the Sulfate adenylyltransferase above the Domain II between the other domains I & II. The core of the groove in which the active site is located is mostly composed of hydrophobic residues, but towards the outside of the groove are positive and hydrophilic residues necessary for substrate binding.
Applications.
ATP sulfurylase is one of the enzymes used in pyrosequencing.
References.
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14681434
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Sulfate adenylyltransferase (ADP)
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In enzymology, a sulfate adenylyltransferase (ADP) (EC 2.7.7.5) is an enzyme that catalyzes the chemical reaction
ADP + sulfate formula_0 phosphate + adenylyl sulfate
Thus, the two substrates of this enzyme are ADP and sulfate, whereas its two products are phosphate and adenylyl sulfate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing nucleotide groups (nucleotidyltransferases). The systematic name of this enzyme class is ADP:sulfate adenylyltransferase. Other names in common use include ADP-sulfurylase, sulfate (adenosine diphosphate) adenylyltransferase, and adenosine diphosphate sulfurylase. This enzyme participates in sulfur metabolism.
References.
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14681464
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T2-induced deoxynucleotide kinase
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Class of enzymes
In enzymology, a T2-induced deoxynucleotide kinase (EC 2.7.4.12) is an enzyme that catalyzes the chemical reaction
ATP + dGMP (or dTMP) formula_0 ADP + dGDP (or dTDP)
The 3 substrates of this enzyme are ATP, dGMP, and dTMP, whereas its 3 products are ADP, dGDP, and dTDP.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with a phosphate group as acceptor. The systematic name of this enzyme class is ATP:(d)NMP phosphotransferase.
References.
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14681489
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Tagatose-6-phosphate kinase
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In enzymology, a tagatose-6-phosphate kinase (EC 2.7.1.144) is an enzyme that catalyzes the chemical reaction
ATP + D-tagatose 6-phosphate formula_0 ADP + D-tagatose 1,6-bisphosphate
Thus, the two substrates of this enzyme are ATP and D-tagatose 6-phosphate, whereas its two products are ADP and D-tagatose 1,6-bisphosphate.
This enzyme belongs to the phosphofructokinase B (PfkB) or Ribokinase family of sugar kinases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:D-tagatose-6-phosphate 1-phosphotransferase. The members of the PfkB/RK family are identified by the presence of three conserved sequence motifs and their enzymatic activity generally shows a dependence on the presence of pentavalent ions. Pentavalent ions dependency is a conserved property of adenosine kinase from diverse sources: identification of a novel motif implicated in phosphate and magnesium ion binding and substrate inhibition. Biochemistry 2002, 41: 4059-4069.</ref> This enzyme participates in galactose metabolism.
Structural studies.
As of late 2007, five structures have been solved for this class of enzymes, with PDB accession codes 2AWD, 2F02, 2JG1, 2JGV, and 2Q5R.
References.
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14681513
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Tagatose kinase
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In enzymology, a tagatose kinase (EC 2.7.1.101) is an enzyme that catalyzes the chemical reaction
ATP + D-tagatose formula_0 ADP + D-tagatose 6-phosphate
Thus, the two substrates of this enzyme are ATP and D-tagatose, whereas its two products are ADP and D-tagatose 6-phosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:D-tagatose 6-phosphotransferase. Other names in common use include tagatose 6-phosphate kinase (phosphorylating), D-tagatose 6-phosphate kinase, and tagatose-6-phosphate kinase. This enzyme participates in galactose metabolism.
Structural studies.
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code 2FIQ.
References.
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14681543
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Tau-protein kinase
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Class of enzymes
In enzymology, a tau-protein kinase (EC 2.7.11.26) is an enzyme that catalyzes the chemical reaction
ATP + tau protein formula_0 ADP + O-phospho-tau-protein
Thus, the two substrates of this enzyme are ATP and tau protein, whereas its two products are ADP and O-phospho-tau-protein.
This enzyme belongs to the family of transferases, specifically, those transferring a phosphate group to the sidechain oxygen atom of serine or threonine residues in proteins (protein-serine/threonine kinases). This enzyme participates in 14 metabolic pathways: erbb signaling pathway, cell cycle, wnt signaling pathway, hedgehog signaling pathway, axon guidance, focal adhesion, b cell receptor signaling pathway, insulin signaling pathway, melanogenesis, alzheimer's disease, colorectal cancer, endometrial cancer, prostate cancer, and basal cell carcinoma.
Nomenclature.
The systematic name of this enzyme class is ATP:[tau-protein] O-phosphotransferase. Other names in common use include ATP:tau-protein O-hosphotransferase, brain protein kinase PK40erk, cdk5/p20, CDK5/p23, glycogen synthase kinase-3beta, GSK, protein tau kinase, STK31, tau kinase, [tau-protein] kinase, tau-protein kinase I, tau-protein kinase II, tau-tubulin kinase, TPK, TPK I, TPK II, and TTK.
Structural studies.
As of late 2007, 3 structures have been solved for this class of enzymes, with PDB accession codes 2JDO, 2JDR, and 2UW9.
Examples.
Human genes encoding proteins with Tau-protein kinase activity include:
References.
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14681569
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Taurocyamine kinase
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In enzymology, a taurocyamine kinase (EC 2.7.3.4) is an enzyme that catalyzes the chemical reaction
ATP + taurocyamine formula_0 ADP + N-phosphotaurocyamine
Thus, the two substrates of this enzyme are ATP and taurocyamine, whereas its two products are ADP and N-phosphotaurocyamine.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with a nitrogenous group as acceptor. The systematic name of this enzyme class is ATP:taurocyamine N-phosphotransferase. Other names in common use include taurocyamine phosphotransferase, and ATP:taurocyamine phosphotransferase. This enzyme participates in taurine and hypotaurine metabolism.
References.
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14681593
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Tetraacyldisaccharide 4'-kinase
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Tetraacyldisaccharide 4'-kinase is an enzyme that phosphorylates the 4'-position of a tetraacyldisaccharide 1-phosphate precursor (DS-1-P) of lipopolysaccharide lipid A. This lipid forms outer membranes of Gram-negative bacteria. This enzyme catalyzes the chemical reaction
ATP + [2-N,3-O-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl]-(1->6)-[2- N,3-O-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl phosphate] formula_0 ADP + [2-N,3-O-bis(3-hydroxytetradecanoyl)-4-O-phosphono-beta-D- glucosaminyl]-(1->6)-[2-N,3-O-bis(3-hydroxytetradecanoyl)-beta-D- glucosaminyl phosphate]
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor.
References.
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