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14284082
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Dimethylaniline-N-oxide aldolase
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The enzyme dimethylaniline-"N"-oxide aldolase (EC 4.1.2.24) catalyzes the chemical reaction
"N,N"-dimethylaniline "N"-oxide formula_0 "N"-methylaniline + formaldehyde
This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is N,N-dimethylaniline-N-oxide formaldehyde-lyase (N-methylaniline-forming). Other names in common use include microsomal oxidase II, microsomal N-oxide dealkylase, and N,N-dimethylaniline-N-oxide formaldehyde-lyase.
References.
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14284098
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Diphosphomevalonate decarboxylase
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InterPro Family
Diphosphomevalonate decarboxylase (EC 4.1.1.33), most commonly referred to in scientific literature as mevalonate diphosphate decarboxylase, is an enzyme that catalyzes the chemical reaction
ATP + (R)-5-diphosphomevalonate formula_0 ADP + phosphate + isopentenyl diphosphate + CO2
This enzyme converts mevalonate 5-diphosphate (MVAPP) to isopentenyl diphosphate (IPP) through ATP dependent decarboxylation. The two substrates of this enzyme are ATP and mevalonate 5-diphosphate, whereas its 4 products are ADP, phosphate, isopentenyl diphosphate, and CO2.
Mevalonate diphosphate decarboxylase catalyzes the final step in the mevalonate pathway. The mevalonate pathway is responsible for the biosynthesis of isoprenoids from acetate. This pathway plays a key role in multiple cellular processes by synthesizing sterol isoprenoids, such as cholesterol, and non-sterol isoprenoids, such as dolichol, heme A, tRNA isopentenyltransferase, and ubiquinone.
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is ATP:(R)-5-diphosphomevalonate carboxy-lyase (adding ATP isopentenyl-diphosphate-forming). Other names in common use include pyrophosphomevalonate decarboxylase, mevalonate-5-pyrophosphate decarboxylase, pyrophosphomevalonic acid decarboxylase, 5-pyrophosphomevalonate decarboxylase, mevalonate 5-diphosphate decarboxylase, and ATP:(R)-5-diphosphomevalonate carboxy-lyase (dehydrating).
Enzyme mechanism.
Mevalonate diphosphate decarboxylase recognizes and binds two substrates: ATP and mevalonate 5-diphosphate. After binding, the enzyme performs three types of reactions that can be separated into two main stages. First, phosphorylation occurs. This creates a reactive intermediate, which in the second stage undergoes concerted dephosphorylation and decarboxylation. Many enzyme residues in the active site play important roles in this concerted mechanism. An aspartic acid residue deprotonates the C3 hydroxyl on MVAPP and facilitates the oxygen to attack a phosphate from ATP. As a result, intermediate 1, 3-phosphoMVAPP, now has a much better leaving group, which helps to produce intermediate 2. This third intermediate is a transient beta carboxy carbonium intermediate and provides an "electron sink" that helps drives the decarboxylation reaction.
Enzyme structure.
The exact enzyme apparatus of mevalonate diphosphate decarboxylase is not completely understood. Structures of both the yeast and human mevalonate diphosphate decarboxylase have been solved with X-ray crystallography, but scientists have experienced difficulties in obtaining structures of bound metabolites. Scientists have classified mevalonate diphosphate decarboxylase as an enzyme in the GHMP kinase family (galactokinase, homoserine kinase, mevalonate kinase, and phosphomevalonate kinase). Both mevalonate kinase and mevalonate diphosphate decarboxylase probably evolved from a common ancestor since they have a similar fold and catalyze phosphorylation of similar substrates. Due to these commonalities, both enzymes are often studied comparatively, and especially in reference to inhibitors.
Though there is limited information, some important residues have been identified and are highlighted in the active site structure and mechanism. Due to the difficulty of obtaining crystal structures of bound substrates, a sulfate ion and water molecules were used to better understand the residues role in substrate binding.
When investigating the human form of mevalonate diphosphate decarboxylase, the following specific residues were identified: arginine-161 (Arg-161), serine-127 (Ser-127), aspartate-305 (Asp-305), and asparagine-17 (Asn-17). Arg-161 interacts with the C1 carbonyl of MVAPP, and Asn-17 is important for hydrogen bonding with this same arginine residue. Asp-305 is positioned about 4 Å from the C3 hydroxyl on MVAPP and acts as a general base catalyst in the active site. Ser-127 aids in orientation of the phosphoryl chain for the phosphate transfer to MVAPP. Mevalonate diphosphate decarboxylase also has a phosphate-binding loop (‘P-loop’) where amino acid residues provide key interactions that stabilize the nucleotide triphosphoryl moiety. The residues from the P-loop are conserved across enzymes in the GHMP kinase family and include Ala-105, Ser-106, Ser-107 and Ala-108.
Biological function.
Many different organisms utilize the mevalonate pathway and mevalonate diphosphate decarboxylase, but for different purposes. In gram positive bacteria, isopentenyl diphosphate, the end product of mevalonate diphosphate decarboxylase, is an essential intermediate in peptidoglycan and polyisoprenoid biosynethesis. Therefore, targeting the mevalonate pathway, and mevalonate diphosphate decarboxylase, could be a potential antimicrobial drug.
The mevalonate pathway is also used in higher order eukaryotes and plants. Mevalonate diphosphate decarboxylase is mainly present in the liver of mammals where the majority of mevalonate is converted to cholesterol. Some of the cholesterol is converted to steroid hormones, bile acids, and vitamin D. Mevalonate is also converted into many other important intermediates in mammalian cells: dolichols (carriers in the assembly of carbohydrate chains in glycoproteins), ubiquinones (important for electron transport), tRNA isopentenyltransferase (used in protein synthesis), and franesylated and geranylgeranylated proteins (membrane associated proteins that appear to be involved in intracellular signaling). The main point of regulation in cholesterol and nonsterol isoprene biosynethsis is HMGCoA reductase, the third enzyme in the mevalonate pathway.
Disease relevance.
Coronary artery disease is the leading cause of death in the US general population. Hypercholesterolemia or high cholesterol is considered a major risk factor in coronary artery disease. Therefore, major efforts are focused toward understanding regulation and developing inhibitors of cholesterol biosynthesis. Mevalonate diphosphate decarboxylase is a potential enzyme to be targeted in the cholesterol synthesis pathway. Scientists discovered a molecule, 6-fluoromevalonate (6-FMVA), to be a strong competitive inhibitor of mevalonate diphosphate decarboxylase. The addition of 6-FMVA results in a decrease in cholesterol levels.
Spontaneously hypertensive rats (stroke-prone) (SHRSP) are affected by severe hypertension and cerebral hemorrhage. Scientists have found a low serum cholesterol level in rats with this condition. In SHRSP, mevalonate diphosphate decarboxylase has a much lower activity while HMG-CoA reductase remains unchanged; therefore, mevalonate diphosphate decarboxylase may be responsible for the lower cholesterol biosynthesis in this condition. In humans, it is hypothesized that cholesterol deficiency may make the plasma membranes fragile and, as a result, induce angionecrosis in the brain. Reduced serum cholesterol, resulting from a low activity of mevalonate diphosphate decarboxylase, may be the cause of cerebral hemorrhage in some cases.
Structural studies.
As of 2015, at least 15 structures have been solved for this class of enzymes, including PDB accession codes 1FI4, 2HK2, 2HK3, and 2HKE.
References.
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14284119
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Fructose-6-phosphate phosphoketolase
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The enzyme fructose-6-phosphate phosphoketolase (EC 4.1.2.22) catalyzes the chemical reaction
-fructose 6-phosphate + phosphate formula_0 acetyl phosphate + -erythrose 4-phosphate + H2O
This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is D-fructose-6-phosphate D-erythrose-4-phosphate-lyase (adding phosphate; acetyl-phosphate-forming). Other names in common use include D-fructose-6-phosphate D-erythrose-4-phosphate-lyase, and (phosphate-acetylating). This enzyme participates in pentose phosphate pathway.
References.
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14284128
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Fucosterol-epoxide lyase
|
The enzyme fucosterol-epoxide lyase (EC 4.1.2.33) catalyzes the chemical reaction
(24"R",24′"R")-fucosterol epoxide formula_0 desmosterol + acetaldehyde
This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is (24R,24'R)-fucosterol-epoxide acetaldehyde-lyase (desmosterol-forming). This enzyme is also called (24R,24'R)-fucosterol-epoxide acetaldehyde-lyase.
References.
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{
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14284154
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Gallate decarboxylase
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The enzyme gallate decarboxylase (EC 4.1.1.59) catalyzes the chemical reaction
3,4,5-trihydroxybenzoate formula_0 pyrogallol + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is 3,4,5-trihydroxybenzoate carboxy-lyase (pyrogallol-forming). Other names in common use include gallic acid decarboxylase and gallate carboxy-lyase. This enzyme participates in benzoate degradation via CoA ligation.
References.
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https://en.wikipedia.org/wiki?curid=14284154
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14284176
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Gentisate decarboxylase
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The enzyme gentisate decarboxylase (EC 4.1.1.62) catalyzes the chemical reaction
2,5-dihydroxybenzoate formula_0 hydroquinone + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is 2,5-dihydroxybenzoate carboxy-lyase (hydroquinone-forming). Other names in common use include 2,5-dihydroxybenzoate decarboxylase, and gentisate carboxy-lyase. This enzyme participates in tyrosine metabolism.
References.
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{
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14284197
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Glutaconyl-CoA decarboxylase
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In enzymology, a glutaconyl-CoA decarboxylase (EC 7.2.4.5) is an enzyme that catalyzes the chemical reaction
(2"E")-glutaconyl-CoA + H+ + Na+ formula_0 (2"E")-butenoyl-CoA + CO2 + Na+
Hence, this enzyme has one substrate, (2"E")-glutaconyl-CoA, and two products, (2"E")-butenoyl-CoA and CO2. During the process, an sodium ion is transported across the membrane. Previously, this enzyme was classified as EC 4.1.1.70.
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is 4-carboxybut-2-enoyl-CoA carboxy-lyase (but-2-enoyl-CoA-forming). Other names in common use include glutaconyl coenzyme A decarboxylase, pent-2-enoyl-CoA carboxy-lyase, and 4-carboxybut-2-enoyl-CoA carboxy-lyase. This enzyme participates in benzoate degradation via coa ligation and butanoate metabolism.
As a decarboxylase, the enzyme requires biotin for its function.
Structural studies.
As of mid-2024, five structures have been solved for this class of enzymes, with the PDB accession codes 1PIX, 3GF3, 3GF7, 3GLM and 3GMA.
References.
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14284215
|
Hydroxyglutamate decarboxylase
|
The enzyme hydroxyglutamate decarboxylase (EC 4.1.1.16) catalyzes the chemical reaction
3-hydroxy-L-glutamate formula_0 4-amino-3-hydroxybutanoate + CO2
Hence, this enzyme has one substrate, 3-hydroxy-L-glutamate, and two products, 4-amino-3-hydroxybutanoate and CO2.
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is 3-hydroxy-L-glutamate 1-carboxy-lyase (4-amino-3-hydroxybutanoate-forming). This enzyme is also called 3-hydroxy-L-glutamate 1-carboxy-lyase. It employs one cofactor, pyridoxal phosphate.
References.
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14284225
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Hydroxymandelonitrile lyase
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The enzyme hydroxymandelonitrile lyase (EC 4.1.2.11) catalyzes the chemical reaction
(S)-4-hydroxymandelonitrile formula_0 cyanide + 4-hydroxybenzaldehyde
This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is (S)-4-hydroxymandelonitrile 4-hydroxybenzaldehyde-lyase (cyanide-forming). Other names in common use include hydroxynitrile lyase, oxynitrilase, Sorghum hydroxynitrile lyase, and (S)-4-hydroxymandelonitrile hydroxybenzaldehyde-lyase. This enzyme participates in cyanoamino acid metabolism.
Structural studies.
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code 1GXS.
References.
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14284241
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Hydroxynitrilase
|
In enzymology, a hydroxynitrilase (EC 4.1.2.37) is an enzyme that catalyzes the chemical reaction
acetone cyanohydrin formula_0 cyanide + acetone
Hence, this enzyme has one substrate, acetone cyanohydrin, and two products, cyanide and acetone.
This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is acetone-cyanohydrin acetone-lyase (cyanide-forming). Other names in common use include alpha-hydroxynitrile lyase, hydroxynitrile lyase, acetone-cyanhydrin lyase [mis-spelt], acetone-cyanohydrin acetone-lyase, oxynitrilase, 2-hydroxyisobutyronitrile acetone-lyase, 2-hydroxyisobutyronitrile acetone-lyase (cyanide-forming), and acetone-cyanohydrin lyase.
References.
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14284255
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Hydroxypyruvate decarboxylase
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The enzyme hydroxypyruvate decarboxylase (EC 4.1.1.40) catalyzes the chemical reaction
hydroxypyruvate formula_0 glycolaldehyde + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is hydroxypyruvate carboxy-lyase (glycolaldehyde-forming). This enzyme is also called hydroxypyruvate carboxy-lyase. This enzyme participates in glyoxylate and dicarboxylate metabolism.
References.
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14284271
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Indole-3-glycerol-phosphate lyase
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Class of enzymes
The enzyme indole-3-glycerol-phosphate lyase (EC 4.1.2.8) catalyzes the chemical reaction
(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate formula_0 indole + D-glyceraldehyde 3-phosphate
This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is (1S,2R)-1-C-(indol-3-yl)glycerol-3-phosphate D-glyceraldehyde-3-phosphate-lyase (indole-forming). Other names in common use include tryptophan synthase alpha, TSA, indoleglycerolphosphate aldolase, indole glycerol phosphate hydrolase, indole synthase, indole-3-glycerolphosphate D-glyceraldehyde-3-phosphate-lyase, indole-3-glycerol phosphate lyase, IGL, BX1, (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate, and D-glyceraldehyde-3-phosphate-lyase. This enzyme participates in benzoxazinone biosynthesis.
References.
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14284288
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Indole-3-glycerol-phosphate synthase
|
Class of enzymes
The enzyme indole-3-glycerol-phosphate synthase (IGPS) (EC 4.1.1.48) catalyzes the chemical reaction
1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate formula_0 1-C-(indol-3-yl)-glycerol 3-phosphate + CO2 + H2O
This enzyme belongs to the family of lyases, to be specific, the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose-5-phosphate carboxy-lyase [cyclizing 1-C-(indol-3-yl)glycerol-3-phosphate-forming]. Other names in common use include indoleglycerol phosphate synthetase, indoleglycerol phosphate synthase, indole-3-glycerophosphate synthase, 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose-5-phosphate, and carboxy-lyase (cyclizing). This enzyme participates in phenylalanine, tyrosine and tryptophan biosynthesis and two-component system - general. It employs one cofactor, pyruvate.
Structural studies.
In some bacteria, IGPS is a single chain enzyme. In others, such as "Escherichia coli", it is the N-terminal domain of a bifunctional enzyme that also catalyses N-(5'-phosphoribosyl)anthranilate isomerase (EC 5.3.1.24) (PRAI) activity, the third step of tryptophan biosynthesis. In fungi, IGPS is the central domain of a trifunctional enzyme that contains a PRAI C-terminal domain and a glutamine amidotransferase (EC 2.4.2.-) (GATase) N-terminal domain.
A structure of the IGPS domain of the bifunctional enzyme from the mesophilic bacterium "E. coli" (eIGPS) has been compared with the monomeric indole-3-glycerol phosphate synthase from the hyperthermophilic archaeon "Sulfolobus solfataricus" (sIGPS). Both are single-domain (beta/alpha)8 barrel proteins, with one (eIGPS) or two (sIGPS) additional helices inserted before the first beta strand.
As of late 2007, 11 structures have been solved for this class of enzymes, with PDB accession codes 1A53, 1I4N, 1J5T, 1JCM, 1JUK, 1JUL, 1LBF, 1LBL, 1PII, 1VC4, and 2C3Z.
References.
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14284302
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Indolepyruvate decarboxylase
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The enzyme indolepyruvate decarboxylase (EC 4.1.1.74) catalyzes the chemical reaction
3-(indol-3-yl)pyruvate formula_0 2-(indol-3-yl)acetaldehyde + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is 3-(indol-3-yl)pyruvate carboxy-lyase [(2-indol-3-yl)acetaldehyde-forming]. Other names in common use include indol-3-yl-pyruvate carboxy-lyase, and 3-(indol-3-yl)pyruvate carboxy-lyase. This enzyme participates in tryptophan metabolism.
Structural studies.
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code 1OVM.
References.
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14284327
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Ketotetrose-phosphate aldolase
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The enzyme ketotetrose-phosphate aldolase (EC 4.1.2.2) catalyzes the chemical reaction
erythrulose 1-phosphate formula_0 glycerone phosphate + formaldehyde
Hence, this enzyme has one substrate, erythrulose 1-phosphate, and two products, dihydroxyacetone phosphate and formaldehyde.
This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is erythrulose-1-phosphate formaldehyde-lyase (glycerone-phosphate-forming). Other names in common use include phosphoketotetrose aldolase, erythrulose-1-phosphate synthetase, erythrose-1-phosphate synthase, and erythrulose-1-phosphate formaldehyde-lyase.
References.
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14284342
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Lactate aldolase
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The enzyme lactate aldolase (EC 4.1.2.36) catalyzes the chemical reaction
("S")-lactate formula_0 formate + acetaldehyde
This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is (S)-lactate acetaldehyde-lyase (formate-forming). Other names in common use include lactate synthase, and (S)-lactate acetaldehyde-lyase. This enzyme participates in pyruvate metabolism.
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14284357
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L-fuculose-phosphate aldolase
|
The enzyme -fuculose-phosphate aldolase (EC 4.1.2.17) catalyzes the chemical reaction
-fuculose-1-phosphate formula_0 glycerone phosphate + ("S")-lactaldehyde
This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is L-fuculose-1-phosphate (S)-lactaldehyde-lyase (glycerone-phosphate-forming). Other names in common use include L-fuculose 1-phosphate aldolase, fuculose aldolase, and L-fuculose-1-phosphate lactaldehyde-lyase. This enzyme participates in fructose and mannose metabolism.
Structural studies.
As of late 2007, 20 structures have been solved for this class of enzymes, with PDB accession codes 1DZU, 1DZV, 1DZW, 1DZX, 1DZY, 1DZZ, 1E46, 1E47, 1E48, 1E49, 1E4A, 1E4B, 1E4C, 1FUA, 2FK5, 2FLF, 2FUA, 2OPI, 3FUA, and 4FUA.
References.
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14284376
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Malyl-CoA lyase
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The enzyme malyl-CoA lyase (EC 4.1.3.24) catalyzes the chemical reaction
(3"S")-3-carboxy-3-hydroxypropanoyl-CoA formula_0 acetyl-CoA + glyoxylate
This enzyme belongs to the family of lyases, specifically the oxo-acid-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is (3S)-3-carboxy-3-hydroxypropanoyl-CoA glyoxylate-lyase (acetyl-CoA-forming). Other names in common use include malyl-coenzyme A lyase, and (3S)-3-carboxy-3-hydroxypropanoyl-CoA glyoxylate-lyase. This enzyme participates in glyoxylate and dicarboxylate metabolism.
References.
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14284394
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Mandelonitrile lyase
|
Class of enzymes
The enzyme ("R")-mandelonitrile lyase (EC 4.1.2.10, "(R)-HNL", "(R)-oxynitrilase", "(R)-hydroxynitrile lyase") catalyzes the chemical reaction
mandelonitrile formula_0 hydrogen cyanide + benzaldehyde
This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is mandelonitrile benzaldehyde-lyase (hydrogen cyanide-forming). Other names in common use include hydroxynitrile lyase, (R)-oxynitrilase, oxynitrilase, D-oxynitrilase, D-alpha-hydroxynitrile lyase, and mandelonitrile benzaldehyde-lyase. This enzyme participates in cyanoamino acid metabolism. It has 2 cofactors: flavin, and flavoprotein.
Historical perspective.
Mandelonitrile lyases, more colloquially referred to as HNLs (hydroxynitrile lyases) were first characterized by Wöhler in 1938, based on their high activity in almond. Since then, HNLs have been isolated from a wide variety of plants including stone fruits, sorghum grains, millipedes, and passion fruits.
HNLs are peculiar in that, within the same organism and even the same sample, there exist a variety of different isoforms of this enzyme. These isoforms are not able to be determined from one another based on factors influencing activity. This variety also results from macro-heterogeneity, as some isoforms bind FAD at their N-terminus while others are unable to bind FAD. It is understood that this is the case because the N-terminal fold is a region known to bind FAD as a needed cofactor. Also curious is that FAD plays no observed role in active site oxidation-reduction reactions of this enzyme. Those HNLs that bind FAD do so at a hydrophobic region neighboring the active site where it is believed that the binding of FAD confers structural stability that allows for enzymatic action. These HNL, referred to as HNL Class I (or HNL I) are also noted to have N-terminus glycosylation and the distinct heterogeneity and presence of isoforms within the same organism. HNL Class II (HNL II), on the other hand, afford a wider variety of substrates, and in general favor (S) stereochemistry, whereas HNL I stereo-selectively produce (R)-mandelonitrile.
Structure and action.
Due to the simple purification of this enzyme (5-30 fold purification is sufficient to reach homogeneity), its biological and biochemical analysis have been very thoroughly studied. In addition to the study of many isoforms within a given organism, there has been study dedicated to the understanding of HNL localization, the physical structure of the enzyme and its active site, and the mechanisms by which it is able to mediate this important set of reactions. Upon the purification of Black Cherry HNL, research from Wu and Poulton raised antiserum to these specific HNL, which were then applied (with colloidal gold particles in tow) to Black Cherry cotyledon and endosperm. Here it was found that HNL overwhelmingly localizes to the cell walls of these developing plants. It was so enriched in these regions that it was noted upwards of 5% of the cell wall images taken via Electron Microscopy imaged the gold particles that were indirectly labelling these proteins.
Knowing where this protein is highly localized, Figure 1 details work that highlights the structure of this protein and the residues in its active site respectively. Of specific interest, HNLs make use of a catalytically active Cys residue. While Cysteine residues are conserved throughout species in three separate locations (at the N-terminal FAD binding site, and two at the C-terminal active site), it appears that the catalytically active residue lies near the active site, suggesting an important role in HNL catalytic action. Other structural features indicative of HNL are split based on their class. While Class II HNL are known to be more heterogenous and more often seen in grains, Class I HNL are more typically FAD-binding and function as seed storage proteins. This action allows for increased amino acid metabolism in developing seeds. Because the enzyme is able to quickly reverse this reaction to create hydrogen cyanide, HNLs play an essential role in defense of the seed
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code 1JU2.
Mechanism of action.
HNLs are known to be stereospecific, giving the action of this enzyme a major advantage in effectively creating precursors essential to the metabolic development of amino acids and a wide range of clinically relevant small molecules. The wide variety of organisms and isoforms that constitute the HNL family however, has been determined to yield a variety of different mechanisms that facilitate this reaction in a stereospecific way. Figures 2 and 3 detail the typical synthetic and solved biochemical mechanisms for the formation of this key metabolic intermediate. Key differences between these pathways rely mostly on the lack of enantiomeric specificity conferred through the synthetic pathways despite the use of similar classes of reactions. In addition, most of the synthetic methods for facilitating this set of reactions take place in organic solvent, whereas it has been shown that HNL activity is highest at a polar-nonpolar interface.
Disease relevance.
HNLs and the action they mediate is a key target for study of protein engineering, as the formation of mandelonitrile is a key step in a wide variety of organic syntheses with medical and therapeutic potential. The step mediated by these enzymes is essential to the synthesis of stereospecific bond formation in (R)-Salbutamol bronchodilators, (S)-amphetamines, (1R, 2S)-(-)-ephedrine bronchodilators, in addition to many others, including Lipitor, Thalidomide, and the semi-synthesis of cephalosporin antibiotics. The importance of these mandelonitrile synthons makes the HNL class of enzymes a major target for controlled catalysis that has been optimized through work at the interface of polar and non-polar solvent conditions.
References.
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[
{
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"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14284394
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14284407
|
Methionine decarboxylase
|
The enzyme methionine decarboxylase (EC 4.1.1.57) catalyzes the chemical reaction
L-methionine formula_0 3-methylthiopropyl amine + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is L-methionine carboxy-lyase (3-methylthiopropyl amine-forming). Other names in common use include L-methionine decarboxylase and L-methionine carboxy-lyase.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14284407
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14284416
|
Methylisocitrate lyase
|
The enzyme methylisocitrate lyase (EC 4.1.3.30) catalyzes the chemical reaction
(2"S",3"R")-3-hydroxybutane-1,2,3-tricarboxylate formula_0 pyruvate + succinate
The reaction is similar to that of isocitrate lyase, except that an additional methyl group (marked with an asterisk in the above scheme) is present, meaning that citrate is replaced by methylcitrate and glyoxylate by pyruvate. In fact, in some bacteria such as "Mycobacterium tuberculosis", isocitrate lyase actually plays the role of methylisocitrate lyase.
This enzyme belongs to the family of lyases, specifically the oxo-acid-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate pyruvate-lyase (succinate-forming). Other names in common use include 2-methylisocitrate lyase, MICL, and (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate pyruvate-lyase. This enzyme participates in propanoate metabolism.
Methylisocitrate lyase was discovered in 1976.
Structural studies.
As of late 2007, 6 structures have been solved for this class of enzymes, with PDB accession codes 1MUM, 1O5Q, 1OQF, 1UJQ, 1XG3, and 1XG4. The structure is very similar to that of phosphoenolpyruvate mutase. A homotetrameric biological unit is composed of beta barrels with the active site at one end. A magnesium ion is present in the active site, and an active-site "gating loop" moves inward toward it when substrate binds and away with no substrate bound, thus shielding the reaction from solvent. Helices are present all around the beta barrels; in particular, a C-terminal helical domain splits off from the barrel to interact with the barrel of a neighboring subunit, in a "helix swapping" motif (see phosphoenolpyruvate mutase).
The following still shot from a ribbon kinemage shows one subunit from the crystal structure 1MUM, which includes a magnesium ion (gray) but no substrate; helices are red while loops are white and beta strands are green.
Function.
Methylisocitrate lyase is used in the methylcitrate cycle, a modified version of the Krebs cycle that metabolizes propionyl coenzyme A instead of acetyl coenzyme A. The enzyme 2-methylcitrate synthase adds propionyl coenzyme A to oxaloacetate, yielding methylcitrate instead of citrate. But isomerizing methylcitrate to methylisocitrate and then subjecting it to MICL regenerates succinate, which proceeds as in the Krebs cycle, and pyruvate, which is easily metabolized by other pathways (e.g. decarboxylated to form acetyl coenzyme A and oxidized in the Krebs cycle). This allows catabolism of propionic acid—and, using beta oxidation, other fatty acids with odd numbers of carbons—without relying on coenzyme B12, a complex cofactor often used to metabolize propionate. The methylcitrate cycle is found in many microorganisms.
Methylisocitrate lyase plays a regulatory function in this cycle; it is activated by NAD but inhibited noncompetitively by NADH and NADPH.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14284416
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14284431
|
Methylmalonyl-CoA decarboxylase
|
In enzymology, a methylmalonyl-CoA decarboxylase (EC 7.2.4.3) is an enzyme that catalyzes the chemical reaction
(S)-methylmalonyl-CoA formula_0 propanoyl-CoA + CO2
Hence, this enzyme has one substrate, (S)-methylmalonyl-CoA, and two products, propanoyl-CoA and CO2. Along with this reaction, this enzyme transports sodium cations across the membrane, creating a gradient which can be used for synthesis of ATP, hence its classification as a translocase.
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is (S)-methylmalonyl-CoA carboxy-lyase (propanoyl-CoA-forming). Other names in common use include propionyl-CoA carboxylase, propionyl coenzyme A carboxylase, methylmalonyl-coenzyme A decarboxylase, (S)-2-methyl-3-oxopropanoyl-CoA carboxy-lyase [incorrect], and (S)-methylmalonyl-CoA carboxy-lyase. This enzyme participates in propanoate metabolism.
Structural studies.
As of late 2007, two structures have been solved for this class of enzymes, with PDB accession codes 1EF8 and 1EF9.
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=14284431
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14284448
|
N-acetylneuraminate lyase
|
The enzyme "N"-acetylneuraminate lyase (EC 4.1.3.3) catalyzes the chemical reaction
"N"-acetylneuraminate formula_0 N-acetyl-D-mannosamine + pyruvate
This enzyme belongs to the family of lyases, specifically the oxo-acid-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is N-acetylneuraminate pyruvate-lyase (N-acetyl-D-mannosamine-forming). Other names in common use include N-acetylneuraminic acid aldolase, acetylneuraminate lyase, sialic aldolase, sialic acid aldolase, sialate lyase, N-acetylneuraminic aldolase, neuraminic aldolase, N-acetylneuraminate aldolase, neuraminic acid aldolase, N-acetylneuraminic acid aldolase, neuraminate aldolase, N-acetylneuraminic lyase, N-acetylneuraminic acid lyase, NPL, NALase, NANA lyase, acetylneuraminate pyruvate-lyase, and N-acetylneuraminate pyruvate-lyase. This enzyme participates in aminosugars metabolism.
Structural studies.
As of late 2007, 10 structures have been solved for this class of enzymes, with PDB accession codes 1F5Z, 1F6K, 1F6P, 1F73, 1F74, 1F7B, 1FDY, 1FDZ, 1HL2, and 1NAL.
References.
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[
{
"math_id": 0,
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https://en.wikipedia.org/wiki?curid=14284448
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14284488
|
Octadecanal decarbonylase
|
The enzyme octadecanal decarbonylase (EC 4.1.99.5) catalyzes the chemical reaction
octadecanal formula_0 heptadecane + CO
This enzyme belongs to the family of lyases, specifically in the "catch-all" class of carbon-carbon lyases. The systematic name of this enzyme class is octadecanal alkane-lyase. Other names in common use include decarbonylase, and aldehyde decarbonylase. At least one compound, EDTA is known to inhibit this enzyme.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14284488
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14284506
|
O-pyrocatechuate decarboxylase
|
The enzyme "o"-pyrocatechuate decarboxylase (EC 4.1.1.46) catalyzes the chemical reaction
2,3-dihydroxybenzoate formula_0 catechol + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is 2,3-dihydroxybenzoate carboxy-lyase (catechol-forming). This enzyme is also called 2,3-dihydroxybenzoate carboxy-lyase. This enzyme participates in benzoate degradation via hydroxylation and carbazole degradation.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14284506
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14284527
|
Orsellinate decarboxylase
|
The enzyme orsellinate decarboxylase (EC 4.1.1.58) catalyzes the chemical reaction
2,4-dihydroxy-6-methylbenzoate formula_0 orcinol + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is 2,4-dihydroxy-6-methylbenzoate carboxy-lyase (orcinol-forming). This enzyme is also called orsellinate carboxy-lyase.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14284527
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14284539
|
Oxalate decarboxylase
|
In enzymology, an oxalate decarboxylase (EC 4.1.1.2) is an oxalate degrading enzyme that catalyzes the chemical reaction
oxalate + H+ formula_0 formate + CO2
Thus, the two substrates of this enzyme are oxalate and H+, whereas its two products are formate and CO2.
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is oxalate carboxy-lyase (formate-forming). This enzyme is also called oxalate carboxy-lyase. This enzyme participates in glyoxylate and dicarboxylate metabolism.
Structural studies.
As of late 2007, 5 structures have been solved for this class of enzymes, with PDB accession codes 1UW8, 2UY8, 2UY9, 2UYA, and 2UYB.
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=14284539
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14284547
|
Oxalomalate lyase
|
The enzyme oxalomalate lyase (EC 4.1.3.13) catalyzes the chemical reaction
3-oxalomalate formula_0 oxaloacetate + glyoxylate
This enzyme belongs to the family of lyases, specifically the oxo-acid-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is 3-oxalomalate glyoxylate-lyase (oxaloacetate-forming). This enzyme is also called 3-oxalomalate glyoxylate-lyase. This enzyme participates in glyoxylate and dicarboxylate metabolism.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14284547
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14284563
|
Oxalyl-CoA decarboxylase
|
The enzyme oxalyl-CoA decarboxylase (OXC) (EC 4.1.1.8), primarily produced by the gastrointestinal bacterium "Oxalobacter formigenes", catalyzes the chemical reaction
oxalyl-CoA formula_0 formyl-CoA + CO2
OXC belongs to the family of lyases, specifically the carboxy-lyases (decarboxylases), which cleave carbon-carbon bonds. The systematic name of this enzyme class is oxalyl-CoA carboxy-lyase (formyl-CoA-forming). Other names in common use include oxalyl coenzyme A decarboxylase, and oxalyl-CoA carboxy-lyase. This enzyme participates in glyoxylate and dicarboxylate metabolism. It employs one cofactor, thiamin diphosphate (TPP), and plays a key role in catabolism of oxalate, a highly toxic compound that is a product of the oxidation of carbohydrates in many bacteria and plants. Oxalyl-CoA decarboxylase is extremely important for the elimination of ingested oxalates found in human foodstuffs like coffee, tea, and chocolate, and the ingestion of such foods in the absence of "Oxalobacter formigenes" in the gut can result in kidney disease or even death as a result of oxalate poisoning.
Evolution.
Oxalyl-CoA decarboxylase is hypothesized to be evolutionarily related to acetolactate synthase, a TPP-dependent enzyme responsible for the biosynthesis of branched chain amino acids in certain organisms. Sequence alignments between the two enzymes support this claim, as do the presence of vestigial FAD-binding pockets that play no role in either enzyme's catalytic activity. The binding of FAD at this site in acetolactate synthase and the binding of ADP at a cognate site in OXC are thought to play roles in the stabilization of the tertiary structures of the proteins. No FAD binding is observed in oxalyl-CoA decarboxylase, but an excess of coenzyme A in the crystal structure has led to the hypothesis that the binding site was co-opted during OXC evolution to bind the CoA moiety of its substrate.> Despite their similarities, only oxalyl-CoA decarboxylase is necessary for the formation of ATP in "Oxalobacter formigenes", and exogenous ADP has been demonstrated to increase the decarboxylase activity of OXC, but not acetolactate synthase.
Reaction mechanism.
A key feature of the cofactor TPP is the relatively acidic proton bound to the carbon atom between the nitrogen and sulfur in the thiazole ring, which has a pKa near 10. This carbon center ionizes to form a carbanion, which adds to the carbonyl group of oxalyl-CoA. This addition is followed by the decarboxylation of oxalyl-CoA, and then the oxidation and removal of formyl-CoA to regenerate the carbanion form of TPP. While the reaction mechanism is shared with other TPP-dependent enzymes, the residues found in the active site of OXC are unique, which has raised questions about whether TDP must be deprotonated by a basic amino acid at a second site away from the carbanion-forming site to activate the cofactor.
Structure.
Oxalyl-CoA decarboxylase is tetrameric, and each monomer consists of three α/β-type domains. The thiamine diphosphate-binding site rests on the subunit-subunit interface between two of the domains, which is commonly seen in its class of enzymes. Oxalyl-CoA decarboxylase is structurally homologous to acetolactate synthase found in plants and other microorganisms, but OXC binds ADP in a region that is similar to the FAD-binding site in acetolactate synthase.
References.
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[
{
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https://en.wikipedia.org/wiki?curid=14284563
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14284588
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Pantothenoylcysteine decarboxylase
|
The enzyme pantothenoylcysteine decarboxylase (EC 4.1.1.30) catalyzes the chemical reaction
N-[(R)-pantothenoyl]-L-cysteine formula_0 pantetheine + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is N-[(R)-pantothenoyl]-L-cysteine carboxy-lyase (pantetheine-forming). Other names in common use include pantothenylcysteine decarboxylase, and N-[(R)-pantothenoyl]-L-cysteine carboxy-lyase. This enzyme participates in pantothenate and coa biosynthesis.
References.
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[
{
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https://en.wikipedia.org/wiki?curid=14284588
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14284640
|
Phenylalanine decarboxylase
|
The enzyme phenylalanine decarboxylase (EC 4.1.1.53) catalyzes the chemical reaction
-phenylalanine formula_0 phenethylamine + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is -phenylalanine carboxy-lyase (phenylethylamine-forming). Other names in common use include -phenylalanine decarboxylase, aromatic -amino acid decarboxylase, and -phenylalanine carboxy-lyase. This enzyme participates in phenylalanine metabolism. It employs one cofactor, pyridoxal phosphate.
References.
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[
{
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"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14284640
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14284654
|
Phenylpyruvate decarboxylase
|
The enzyme phenylpyruvate decarboxylase (EC 4.1.1.43) catalyzes the chemical reaction
phenylpyruvate formula_0 phenylacetaldehyde + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is phenylpyruvate carboxy-lyase (phenylacetaldehyde-forming). This enzyme is also called phenylpyruvate carboxy-lyase. This enzyme participates in phenylalanine and tryptophan metabolism.
Structural studies.
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code 2NXW.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14284654
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14284666
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Phenylserine aldolase
|
The enzyme phenylserine aldolase (EC 4.1.2.26) catalyzes the chemical reaction
-"threo"-3-phenylserine formula_0 glycine + benzaldehyde
This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is L-threo-3-phenylserine benzaldehyde-lyase (glycine-forming). This enzyme is also called L-threo-3-phenylserine benzaldehyde-lyase. It employs one cofactor, pyridoxal phosphate.
Structural studies.
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code 1V72.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14284666
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14284673
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Phosphatidylserine decarboxylase
|
The enzyme phosphatidylserine decarboxylase (EC 4.1.1.65) catalyzes the chemical reaction
phosphatidyl-L-serine formula_0 phosphatidylethanolamine + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is phosphatidyl-L-serine carboxy-lyase (phosphatidylethanolamine-forming). Other names in common use include PS decarboxylase, and phosphatidyl-L-serine carboxy-lyase. This enzyme participates in glycine, serine and threonine metabolism, and glycerophospholipid metabolism. It has two cofactors: pyridoxal phosphate, and Pyruvate.
References.
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https://en.wikipedia.org/wiki?curid=14284673
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14284685
|
Phosphoketolase
|
The enzyme phosphoketolase(EC 4.1.2.9) catalyzes the chemical reactions
D-xylulose 5-phosphate + phosphate formula_0 acetyl phosphate + D-glyceraldehyde 3-phosphate + H2O (EC 4.1.2.9)
D-fructose 6-phosphate + phosphate formula_0 acetyl phosphate + D-erythrose 4-phosphate + H2O (EC 4.1.2.22)
D-sedoheptulose 7-phosphate + phosphate formula_0 acetyl phosphate + D-ribose 5-phosphate + H2O
Phosphoketolase is considered a promiscuous enzyme because it was demonstrated to use 3 different sugar phosphates as substrates. In a recent genetic study, more than 150 putative phosphoketolase genes exhibiting varying catalytic properties were found in 650 analyzed bacterial genomes.
This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. It participates in 3 metabolic pathways: pentose phosphate pathway, methane metabolism, and carbon fixation. It employs one cofactor, thiamin diphosphate. Phosphoketolase was previously used for biotechnological purposes as it enables the construction of synthetic pathways that allow complete carbon conservation without the generation of reducing power.
References.
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[
{
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https://en.wikipedia.org/wiki?curid=14284685
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14284696
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Phosphonopyruvate decarboxylase
|
The enzyme phosphonopyruvate decarboxylase (EC 4.1.1.82) catalyzes the chemical reaction
3-phosphonopyruvate formula_0 2-phosphonoacetaldehyde + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is 3-phosphonopyruvate carboxy-lyase (2-phosphonoacetaldehyde-forming). This enzyme is also called 3-phosphonopyruvate carboxy-lyase. This enzyme participates in aminophosphonate metabolism.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14284696
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14284712
|
Phosphopantothenoylcysteine decarboxylase
|
The enzyme phosphopantothenoylcysteine decarboxylase (EC 4.1.1.36) catalyzes the chemical reaction
N-[(R)-4'-phosphopantothenoyl]-L-cysteine formula_0 pantotheine 4'-phosphate + CO2
This enzyme belongs to the family of lyases, to be specific the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is N-[(R)-4'-phosphopantothenoyl]-L-cysteine carboxy-lyase (pantotheine-4'-phosphate-forming). This enzyme participates in coenzyme A (CoA) biosynthesis from pantothenic acid.
Structural studies.
As of late 2007, 3 structures have been solved for this class of enzymes, with PDB accession codes 1MVL, 1MVN, and 1QZU.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14284712
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14284725
|
Propioin synthase
|
The enzyme propioin synthase (EC 4.1.2.35) catalyzes the chemical reaction
4-hydroxy-3-hexanone formula_0 2 propanal
This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is 4-hydroxy-3-hexanone propanal-lyase (propanal-forming). Other names in common use include 4-hydroxy-3-hexanone aldolase, and 4-hydroxy-3-hexanone propanal-lyase.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14284725
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14284745
|
Protocatechuate decarboxylase
|
Class of enzymes
The enzyme protocatechuate decarboxylase (EC 4.1.1.63) catalyzes the chemical reaction
3,4-dihydroxybenzoate formula_0 catechol + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is 3,4-dihydroxybenzoate carboxy-lyase (catechol-forming). Other names in common use include 3,4-dihydroxybenzoate decarboxylase, and protocatechuate carboxy-lyase. This enzyme participates in benzoate degradation via hydroxylation.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
}
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https://en.wikipedia.org/wiki?curid=14284745
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14284761
|
Rhamnulose-1-phosphate aldolase
|
The enzyme rhamnulose-1-phosphate aldolase (EC 4.1.2.19) catalyzes the chemical reaction
-rhamnulose 1-phosphate formula_0 glycerone phosphate + ("S")-lactaldehyde
This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is L-rhamnulose-1-phosphate (S)-lactaldehyde-lyase (glycerone-phosphate-forming). Other names in common use include rhamnulose phosphate aldolase, L-rhamnulose 1-phosphate aldolase, L-rhamnulose-phosphate aldolase, and L-rhamnulose-1-phosphate lactaldehyde-lyase. This enzyme participates in pentose and glucuronate interconversions and fructose and mannose metabolism.
Structural studies.
As of late 2007, two structures have been solved for this class of enzymes, with PDB accession codes 1GT7 and 1OJR.
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=14284761
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14284784
|
Sphinganine-1-phosphate aldolase
|
The enzyme sphinganine-1-phosphate aldolase (EC 4.1.2.27) catalyzes the chemical reaction
sphinganine 1-phosphate formula_0 phosphoethanolamine + palmitaldehyde
This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is sphinganine-1-phosphate palmitaldehyde-lyase (phosphoethanolamine-forming). Other names in common use include dihydrosphingosine 1-phosphate aldolase, sphinganine-1-phosphate alkanal-lyase, sphinganine-1-phosphate lyase, and sphinganine-1-phosphate palmitaldehyde-lyase. This enzyme participates in sphingolipid metabolism. It employs one cofactor, pyridoxal phosphate.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14284784
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14284795
|
Stipitatonate decarboxylase
|
The enzyme stipitatonate decarboxylase (EC 4.1.1.60) catalyzes the chemical reaction
stipitatonate formula_0 stipitatate + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is stipitatonate carboxy-lyase (decyclizing, stipitatate-forming). This enzyme is also called stipitatonate carboxy-lyase (decyclizing).
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
}
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https://en.wikipedia.org/wiki?curid=14284795
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14284808
|
Sulfinoalanine decarboxylase
|
The enzyme sulfinoalanine decarboxylase (EC 4.1.1.29) catalyzes the chemical reaction
3-sulfino-L-alanine formula_0 hypotaurine + CO2
Hence, this enzyme has one substrate, 3-sulfino-L-alanine (also known as Cysteine sulfinic acid), and two products, hypotaurine and CO2.
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is 3-sulfino-L-alanine carboxy-lyase (hypotaurine-forming). Other names in common use include cysteine-sulfinate decarboxylase, L-cysteinesulfinic acid decarboxylase, cysteine-sulfinate decarboxylase, CADCase/CSADCase, CSAD, cysteic decarboxylase, cysteinesulfinic acid decarboxylase, cysteinesulfinate decarboxylase, sulfoalanine decarboxylase, and 3-sulfino-L-alanine carboxy-lyase. This enzyme participates in taurine metabolism. It employs one cofactor, pyridoxal phosphate.
Structural studies.
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code 2JIS.
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=14284808
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14284823
|
Sulfopyruvate decarboxylase
|
The enzyme sulfopyruvate decarboxylase (EC 4.1.1.79) catalyzes the chemical reaction
3-sulfopyruvate formula_0 2-sulfoacetaldehyde + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is 3-sulfopyruvate carboxy-lyase (2-sulfoacetaldehyde-forming). This enzyme is also called sulfopyruvate carboxy-lyase.
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=14284823
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14284834
|
Tagatose-bisphosphate aldolase
|
The enzyme tagatose-bisphosphate aldolase (EC 4.1.2.40) catalyzes the chemical reaction
-tagatose 1,6-bisphosphate formula_0 glycerone phosphate + glyceraldehyde 3-phosphate
This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is D-tagatose 1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase (glycerone-phosphate-forming). This enzyme is also called D-tagatose-1,6-bisphosphate triosephosphate lyase. 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 1GVF.
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=14284834
|
14284849
|
Tartrate decarboxylase
|
The enzyme tartrate decarboxylase (EC 4.1.1.73) catalyzes the chemical reaction
("R,R")-tartrate formula_0 -glycerate + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is (R,R)-tartrate carboxy-lyase (D-glycerate-forming). This enzyme is also called (R,R)-tartrate carboxy-lyase.
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=14284849
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14284864
|
Tartronate-semialdehyde synthase
|
The enzyme tartronate-semialdehyde synthase (EC 4.1.1.47) catalyzes the chemical reaction
2 glyoxylate formula_0 tartronate semialdehyde + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is glyoxylate carboxy-lyase (dimerizing tartronate-semialdehyde-forming). Other names in common use include tartronate semialdehyde carboxylase, glyoxylate carbo-ligase, glyoxylic carbo-ligase, hydroxymalonic semialdehyde carboxylase, tartronic semialdehyde carboxylase, glyoxalate carboligase, and glyoxylate carboxy-lyase (dimerizing). This enzyme participates in glyoxylate and dicarboxylate metabolism. It has 2 cofactors: FAD, and Thiamin diphosphate.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14284864
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14284878
|
Threonine aldolase
|
The enzyme threonine aldolase (EC 4.1.2.5) is an enzyme that catalyzes the chemical reaction
L-threonine formula_0 glycine + acetaldehyde
This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is L-threonine acetaldehyde-lyase (glycine-forming). This enzyme is also called L-threonine acetaldehyde-lyase. This enzyme participates in glycine, serine and threonine metabolism. It employs one cofactor, pyridoxal phosphate.
Structural studies.
As of late 2007, 5 structures have been solved for this class of enzymes, with PDB accession codes 1JG8, 1LW4, 1LW5, 1M6S, and 1SVV.
Presence in human and mouse.
The enzyme is synthesized and functional in mice.
Humans also have the remnants of the gene, coding this enzyme (GLY1), however it is damaged by past mutations and inactive. Human gene contains two single nucleotide deletions causing frameshifts and premature stop codons. Also, the encoded protein would not be active anyway due mutations in other highly conserved regions. Human gene is no longer transcribed into RNA.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
}
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https://en.wikipedia.org/wiki?curid=14284878
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14284894
|
Threonine-phosphate decarboxylase
|
The enzyme threonine-phosphate decarboxylase (EC 4.1.1.81) catalyzes the chemical reaction
L-threonine O-3-phosphate formula_0 (R)-1-aminopropan-2-yl phosphate + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is L-threonine-O-3-phosphate carboxy-lyase [(R)-1-aminopropan-2-yl-phosphate-forming]. Other names in common use include L-threonine-O-3-phosphate decarboxylase, CobD and L-threonine-O-3-phosphate carboxy-lyase. This enzyme is part of the biosynthetic pathway to cobalamin (vitamin B12) in anaerobic bacteria such as "Salmonella typhimurium" and "Bacillus megaterium". In the next step, (R)-1-aminopropan-2-ol is attached to adenosylcobyric acid, forming adenosylcobinamide phosphate.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14284894
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14284914
|
Trimethylamine-oxide aldolase
|
The enzyme trimethylamine-oxide aldolase (EC 4.1.2.32) catalyzes the chemical reaction
trimethylamine "N"-oxide formula_0 dimethylamine + formaldehyde
This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is trimethylamine-N-oxide formaldehyde-lyase (dimethylamine-forming). Other names in common use include trimethylamine N-oxide formaldehyde-lyase, trimethylamine N-oxide aldolase, trimethylamine N-oxide demethylase, and trimethylamine-N-oxide formaldehyde-lyase. This enzyme participates in methane 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=14284914
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14284932
|
Tryptophanase
|
Enzyme that converts tryptophan into indole
The enzyme tryptophanase (EC 4.1.99.1) catalyzes the chemical reaction
-tryptophan + H2O formula_0 indole + pyruvate + NH3
This enzyme belongs to the family of lyases, specifically in the "catch-all" class of carbon-carbon lyases. The systematic name of this enzyme class is -tryptophan indole-lyase (deaminating; pyruvate-forming). Other names in common use include -tryptophanase, and -tryptophan indole-lyase (deaminating). This enzyme participates in tryptophan metabolism and nitrogen metabolism. It has 2 cofactors: pyridoxal phosphate, and potassium.
Structural studies.
As of late 2007, 3 structures have been solved for this class of enzymes, with PDB accession codes 1AX4, 2C44, and 2OQX.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14284932
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14284942
|
Tyrosine decarboxylase
|
Enzyme
The enzyme tyrosine decarboxylase (EC 4.1.1.25) catalyzes the chemical reaction
L-tyrosine formula_0 tyramine + CO2
Hence, this enzyme has one substrate, L-tyrosine, and two products, tyramine and carbon dioxide.
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is L-tyrosine carboxy-lyase (tyramine-forming). Other names in common use include L-tyrosine decarboxylase, L-(−)-tyrosine apodecarboxylase, and L-tyrosine carboxy-lyase. This enzyme participates in tyrosine metabolism and alkaloid biosynthesis. It employs one cofactor, pyridoxal phosphate.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14284942
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14284951
|
Tyrosine phenol-lyase
|
The enzyme tyrosine phenol-lyase (EC 4.1.99.2) catalyzes the chemical reaction
-tyrosine + H2O formula_0 phenol + pyruvate + NH3
This enzyme belongs to the family of lyases, specifically in the "catch-all" class of carbon-carbon lyases. The systematic name of this enzyme class is -tyrosine phenol-lyase (deaminating; pyruvate-forming). Other names in common use include beta-tyrosinase, and -tyrosine phenol-lyase (deaminating). This enzyme participates in tyrosine metabolism and nitrogen metabolism. It employs one cofactor, pyridoxal phosphate.
Structural studies.
As of late 2007, five structures have been solved for this class of enzyme, with PDB accession codes 1C7G, 1TPL, 2EZ1, 2EZ2, and 2TPL.
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=14284951
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14284961
|
UDP-galacturonate decarboxylase
|
The enzyme UDP-galacturonate decarboxylase (EC 4.1.1.67) catalyzes the chemical reaction
UDP-D-galacturonate formula_0 UDP-L-arabinose + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is UDP-D-galacturonate carboxy-lyase (UDP-L-arabinose-forming). Other names in common use include UDP-galacturonic acid decarboxylase, UDPGalUA carboxy lyase, and UDP-D-galacturonate carboxy-lyase. This enzyme participates in nucleotide sugars 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=14284961
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14284972
|
UDP-glucuronate decarboxylase
|
Class of enzymes
The enzyme UDP-glucuronate decarboxylase (EC 4.1.1.35) catalyzes the chemical reaction
UDP-D-glucuronate formula_0 UDP-D-xylose + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is UDP-D-glucuronate carboxy-lyase (UDP-D-xylose-forming). Other names in common use include uridine-diphosphoglucuronate decarboxylase, and UDP-D-glucuronate carboxy-lyase. This enzyme participates in starch and sucrose metabolism and nucleotide sugars metabolism. It employs one cofactor, NAD+.
Structural studies.
As of late 2007, two structures have been solved for this class of enzymes, with PDB accession codes 2B69 and 2BLL.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14284972
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14284991
|
Uracil-5-carboxylate decarboxylase
|
Class of enzymes
The enzyme uracil-5-carboxylate decarboxylase (EC 4.1.1.66) catalyzes the chemical reaction
uracil 5-carboxylate formula_0 uracil + CO2
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is uracil-5-carboxylate carboxy-lyase (uracil-forming). Other names in common use include uracil-5-carboxylic acid decarboxylase, and uracil-5-carboxylate carboxy-lyase.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14284991
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14285005
|
Valine decarboxylase
|
In enzymology, a valine decarboxylase (EC 4.1.1.14) is an enzyme that catalyzes the chemical reaction
L-valine formula_0 2-methylpropanamine + CO2
Hence, this enzyme has one substrate, L-valine, and two products, 2-methylpropanamine and CO2.
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is L-valine carboxy-lyase (2-methylpropanamine-forming). Other names in common use include leucine decarboxylase and L-valine carboxy-lyase. It employs one cofactor, pyridoxal phosphate.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14285005
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14285018
|
Vanillin synthase
|
In enzymology, a vanillin synthase (EC 4.1.2.41) is an enzyme that catalyzes the chemical reaction
3-hydroxy-3-(4-hydroxy-3-methoxyphenyl)propanoyl-CoA formula_0 vanillin + acetyl-CoA
Hence, this enzyme has one substrate, 3-hydroxy-3-(4-hydroxy-3-methoxyphenyl)propanoyl-CoA, and two products, vanillin and acetyl-CoA.
This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is 3-hydroxy-3-(4-hydroxy-3-methoxyphenyl)propanoyl-CoA vanillin-lyase (acetyl-CoA-forming). Other names in common use include 3-hydroxy-3-(4-hydroxy-3-methoxyphenyl)propionyl-CoA:vanillin lyase, and (acetyl-CoA-forming).
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14285018
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14285398
|
2,3-dihydroxybenzoate—serine ligase
|
Class of enzymes
In enzymology, an enterobactin synthase (2,3-dihydroxybenzoate—serine ligase, EC 6.3.2.14) is an enzyme that catalyzes the chemical reaction
ATP + 2,3-dihydroxybenzoate + L-serine formula_0 products of ATP breakdown + N-(2,3-dihydroxybenzoyl)-L-serine
The 3 substrates of this enzyme are ATP, 2,3-dihydroxybenzoate, and L-serine, whereas its two products are products of ATP breakdown and N-(2,3-dihydroxybenzoyl)-L-serine.
This enzyme belongs to the family of ligases, specifically those forming carbon-nitrogen bonds as acid-D-amino-acid ligases (peptide synthases). The systematic name of this enzyme class is 2,3-dihydroxybenzoate:L-serine ligase. Other names in common use include N-(2,3-dihydroxybenzoyl)-serine synthetase, and 2,3-dihydroxybenzoylserine synthetase.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14285398
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14285406
|
2-furoate—CoA ligase
|
Class of enzymes
In enzymology, a 2-furoate—CoA ligase (EC 6.2.1.31) is an enzyme that catalyzes the chemical reaction
ATP + 2-furoate + CoA formula_0 AMP + diphosphate + 2-furoyl-CoA
The 3 substrates of this enzyme are ATP, 2-furoate, and CoA, whereas its 3 products are AMP, diphosphate, and 2-furoyl-CoA.
This enzyme belongs to the family of ligases, specifically those forming carbon-sulfur bonds as acid-thiol ligases. The systematic name of this enzyme class is 2-furoate:CoA ligase (AMP-forming). This enzyme is also called 2-furoyl coenzyme A synthetase.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14285406
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14285419
|
2-oxoglutarate carboxylase
|
Class of enzymes
In enzymology, a 2-oxoglutarate carboxylase (EC 6.4.1.7) is an enzyme that catalyzes the chemical reaction
ATP + 2-oxoglutarate + HCO3- formula_0 ADP + phosphate + oxalosuccinate
The 3 substrates of this enzyme are ATP, 2-oxoglutarate, and HCO3-, whereas its 3 products are ADP, phosphate, and oxalosuccinate.
This enzyme belongs to the family of ligases, specifically those forming carbon-carbon bonds. The systematic name of this enzyme class is . Other names in common use include oxalosuccinate synthetase, carboxylating factor for ICDH (incorrect), CFI, and OGC.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14285419
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14285432
|
3-alpha,7-alpha-dihydroxy-5-beta-cholestanate—CoA ligase
|
Class of enzymes
In enzymology, a 3α,7α-dihydroxy-5β-cholestanate—CoA ligase (EC 6.2.1.28) is an enzyme that catalyzes the chemical reaction
ATP + (25R)-3alpha,7alpha-dihydroxy-5beta-cholestan-26-oate + CoA formula_0 AMP + diphosphate + (25R)-3alpha,7alpha-dihydroxy-5beta-cholestanoyl-CoA
The 3 substrates of this enzyme are ATP, (25R)-3alpha,7alpha-dihydroxy-5beta-cholestan-26-oate, and CoA, whereas its 3 products are AMP, diphosphate, and (25R)-3alpha,7alpha-dihydroxy-5beta-cholestanoyl-CoA.
This enzyme belongs to the family of ligases, specifically those forming carbon-sulfur bonds as acid-thiol ligases. The systematic name of this enzyme class is (25R)-3alpha,7alpha-dihydroxy-5beta-cholestan-26-oate:CoA ligase (AMP-forming). Other names in common use include 3alpha,7alpha-dihydroxy-5beta-cholestanoyl coenzyme A synthetase, DHCA-CoA ligase, and 3alpha,7alpha-dihydroxy-5beta-cholestanate:CoA ligase (AMP-forming). This enzyme participates in bile acid biosynthesis.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
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https://en.wikipedia.org/wiki?curid=14285432
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14285439
|
4-chlorobenzoate—CoA ligase
|
Class of enzymes
In enzymology, a 4-chlorobenzoate—CoA ligase (EC 6.2.1.33) is an enzyme that catalyzes the chemical reaction
4-chlorobenzoate + CoA + ATP formula_0 4-chlorobenzoyl-CoA + AMP + diphosphate
The 3 substrates of this enzyme are 4-chlorobenzoate, CoA, and ATP, whereas its 3 products are 4-chlorobenzoyl-CoA, AMP, and diphosphate.
This enzyme belongs to the family of ligases, specifically those forming carbon-sulfur bonds as acid-thiol ligases. The systematic name of this enzyme class is 4-chlorobenzoate:CoA ligase. This enzyme participates in 2,4-dichlorobenzoate degradation. It employs one cofactor, magnesium.
Structural studies.
As of late 2007, two structures have been solved for this class of enzymes, with PDB accession codes 1T5D and 1T5H.
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=14285439
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14285448
|
4-Coumarate-CoA ligase
|
InterPro Family
In enzymology, a 4-coumarate—CoA ligase (EC 6.2.1.12) is an enzyme that catalyzes the chemical reaction
ATP + 4-coumarate + CoA formula_0 AMP + diphosphate + 4-coumaroyl-CoA
The 3 substrates of this enzyme are ATP, 4-coumarate, and CoA, whereas its 3 products are AMP, diphosphate, and 4-coumaroyl-CoA.
This enzyme belongs to the family of ligases, to be specific those forming carbon-sulfur bonds as acid-thiol ligases. The systematic name of this enzyme class is 4-coumarate:CoA ligase (AMP-forming). Other names in common use include 4-coumaroyl-CoA synthetase, p-coumaroyl CoA ligase, p-coumaryl coenzyme A synthetase, p-coumaryl-CoA synthetase, p-coumaryl-CoA ligase, feruloyl CoA ligase, hydroxycinnamoyl CoA synthetase, 4-coumarate:coenzyme A ligase, caffeoyl coenzyme A synthetase, p-hydroxycinnamoyl coenzyme A synthetase, feruloyl coenzyme A synthetase, sinapoyl coenzyme A synthetase, 4-coumaryl-CoA synthetase, hydroxycinnamate:CoA ligase, p-coumaryl-CoA ligase, p-hydroxycinnamic acid:CoA ligase, and 4CL. This enzyme participates in phenylpropanoid biosynthesis.
References.
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[
{
"math_id": 0,
"text": "\\rightleftharpoons"
}
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https://en.wikipedia.org/wiki?curid=14285448
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14285455
|
4-hydroxybenzoate—CoA ligase
|
Class of enzymes
In enzymology, a 4-hydroxybenzoate—CoA ligase (EC 6.2.1.27) is an enzyme that catalyzes the chemical reaction
ATP + 4-hydroxybenzoate + CoA formula_0 AMP + diphosphate + 4-hydroxybenzoyl-CoA
The 3 substrates of this enzyme are ATP, 4-hydroxybenzoate, and CoA, whereas its 3 products are AMP, diphosphate, and 4-hydroxybenzoyl-CoA.
This enzyme belongs to the family of ligases, specifically those forming carbon-sulfur bonds as acid-thiol ligases. The systematic name of this enzyme class is 4-hydroxybenzoate:CoA ligase (AMP-forming). Other names in common use include 4-hydroxybenzoate-CoA synthetase, 4-hydroxybenzoate-coenzyme A ligase (AMP-forming), 4-hydroxybenzoyl coenzyme A synthetase, and 4-hydroxybenzoyl-CoA ligase. This enzyme participates in benzoate degradation via coa ligation.
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=14285455
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14285459
|
4-methyleneglutamate—ammonia ligase
|
Class of enzymes
In enzymology, a 4-methyleneglutamate—ammonia ligase (EC 6.3.1.7) is an enzyme that catalyzes the chemical reaction
ATP + 4-methylene-L-glutamate + NH3 formula_0 AMP + diphosphate + 4-methylene-L-glutamine
The 3 substrates of this enzyme are ATP, 4-methylene-L-glutamate, and NH3, whereas its 3 products are AMP, diphosphate, and 4-methylene-L-glutamine.
This enzyme belongs to the family of ligases, specifically those forming carbon-nitrogen bonds as acid-D-ammonia (or amine) ligases (amide synthases). The systematic name of this enzyme class is 4-methylene-L-glutamate:ammonia ligase (AMP-forming). This enzyme is also called 4-methyleneglutamine synthetase. This enzyme participates in c5-branched dibasic acid 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=14285459
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14285465
|
5-(carboxyamino)imidazole ribonucleotide synthase
|
Class of enzymes
In enzymology, a 5-(carboxyamino)imidazole ribonucleotide synthase (EC 6.3.4.18) is an enzyme that catalyzes the chemical reaction
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3− formula_0 ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
The 3 substrates of this enzyme are ATP, 5-amino-1-(5-phospho-D-ribosyl)imidazole ("AIR"), and HCO3−, whereas its 3 products are ADP, phosphate, and 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole.
This enzyme belongs to the family of ligases, specifically those forming generic carbon-nitrogen bonds. The systematic name of this enzyme class is 5-amino-1-(5-phospho-D-ribosyl)imidazole:carbon-dioxide ligase (ADP-forming).
References.
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[
{
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https://en.wikipedia.org/wiki?curid=14285465
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14285470
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5-formyltetrahydrofolate cyclo-ligase
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Class of enzymes
In enzymology, a 5-formyltetrahydrofolate cyclo-ligase (EC 6.3.3.2) is an enzyme that catalyzes the chemical reaction
ATP + 5-formyltetrahydrofolate (folinic acid) formula_0 ADP + phosphate + 5,10-methenyltetrahydrofolate
Thus, the two substrates of this enzyme are ATP and 5-formyltetrahydrofolate, whereas its 3 products are ADP, phosphate, and 5,10-methenyltetrahydrofolate.
This enzyme belongs to the family of ligases, specifically the cyclo-ligases, which form carbon-nitrogen bonds. The systematic name of this enzyme class is 5-formyltetrahydrofolate cyclo-ligase (ADP-forming). Other names in common use include 5,10-methenyltetrahydrofolate synthetase (MTHFS), formyltetrahydrofolic cyclodehydrase, and 5-formyltetrahydrofolate cyclodehydrase. This enzyme participates in one carbon pool by folate.
Structural studies.
As of late 2007, 5 structures have been solved for this class of enzymes, with PDB accession codes 1SBQ, 1SOU, 1U3F, 1U3G, and 2JCB.
Role in pathology.
Mutations of the MTHFS gene cause the disease 5,10-methenyltetrahydrofolate synthetase deficiency.
References.
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[
{
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https://en.wikipedia.org/wiki?curid=14285470
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14285474
|
6-carboxyhexanoate—CoA ligase
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InterPro Family
In enzymology, a 6-carboxyhexanoate—CoA ligase (EC 6.2.1.14) is an enzyme that catalyzes the chemical reaction
ATP + 6-carboxyhexanoate + CoA formula_0 AMP + diphosphate + 6-carboxyhexanoyl-CoA
The 3 substrates of this enzyme are ATP, 6-carboxyhexanoate, and CoA, whereas its 3 products are AMP, diphosphate, and 6-carboxyhexanoyl-CoA.
This enzyme belongs to the family of ligases, specifically those forming carbon-sulfur bonds as acid-thiol ligases. The systematic name of this enzyme class is 6-carboxyhexanoate:CoA ligase (AMP-forming). Other names in common use include 6-carboxyhexanoyl-CoA synthetase, and pimelyl-CoA synthetase. This enzyme participates in biotin metabolism.
References.
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[
{
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https://en.wikipedia.org/wiki?curid=14285474
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14285481
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Acetate—CoA ligase (ADP-forming)
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Class of enzymes
In enzymology, an acetate—CoA ligase (ADP-forming) (EC 6.2.1.13) is an enzyme that catalyzes the chemical reaction
ATP + acetate + CoA formula_0 ADP + phosphate + acetyl-CoA
The 3 substrates of this enzyme are ATP, acetate, and CoA, whereas its 3 products are ADP, phosphate, and acetyl-CoA.
This enzyme belongs to the family of ligases, specifically those forming carbon-sulfur bonds as acid-thiol ligases. The systematic name of this enzyme class is acetate:CoA ligase (ADP-forming). Other names in common use include acetyl-CoA synthetase (ADP-forming), acetyl coenzyme A synthetase (adenosine diphosphate-forming), and acetate thiokinase. This enzyme participates in pyruvate metabolism and propanoate metabolism.
References.
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[
{
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https://en.wikipedia.org/wiki?curid=14285481
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14285492
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Acetoacetate—CoA ligase
|
Class of enzymes
In enzymology, an acetoacetate—CoA ligase (EC 6.2.1.16) is an enzyme that catalyzes the chemical reaction
ATP + acetoacetate + CoA formula_0 AMP + diphosphate + acetoacetyl-CoA
The 3 substrates of this enzyme are ATP, acetoacetate, and CoA, whereas its 3 products are AMP, diphosphate, and acetoacetyl-CoA.
This enzyme belongs to the family of ligases, specifically those forming carbon-sulfur bonds as acid-thiol ligases. The systematic name of this enzyme class is acetoacetate:CoA ligase (AMP-forming). This enzyme is also called acetoacetyl-CoA synthetase. This enzyme participates in butanoate metabolism.
References.
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[
{
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https://en.wikipedia.org/wiki?curid=14285492
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14285499
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Acetone carboxylase
|
Class of enzymes
In enzymology, an acetone carboxylase (EC 6.4.1.6) is an enzyme that catalyzes the chemical reaction
acetone + CO2 + ATP + 2 H2O formula_0 acetoacetate + AMP + 2 phosphate
The 4 substrates of this enzyme are acetone, CO2, ATP, and H2O, whereas its 3 products are acetoacetate, AMP, and phosphate.
This enzyme belongs to the family of ligases, specifically those forming carbon-carbon bonds. The systematic name of this enzyme class is acetone:carbon-dioxide ligase (AMP-forming).
References.
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[
{
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https://en.wikipedia.org/wiki?curid=14285499
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14285504
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Acid—CoA ligase (GDP-forming)
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Class of enzymes
In enzymology, an acid—CoA ligase (GDP-forming) (EC 6.2.1.10) is an enzyme that catalyzes the chemical reaction
GTP + an acid + CoA formula_0 GDP + phosphate + acyl-CoA
The 3 substrates of this enzyme are GTP, acid, and CoA, whereas its 3 products are GDP, phosphate, and acyl-CoA.
This enzyme belongs to the family of ligases, specifically those forming carbon-sulfur bonds as acid-thiol ligases. The systematic name of this enzyme class is acid:CoA ligase (GDP-forming). Other names in common use include acyl-CoA synthetase (GDP-forming), and acyl coenzyme A synthetase (guanosine diphosphate forming).
References.
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[
{
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https://en.wikipedia.org/wiki?curid=14285504
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14285509
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Adenosylcobyric acid synthase (glutamine-hydrolysing)
|
In enzymology, an adenosylcobyric acid synthase (glutamine-hydrolysing) (EC 6.3.5.10) is an enzyme that catalyzes the chemical reaction
4 ATP + adenosylcobyrinic acid "a,c"-diamide + 4 -glutamine + 4 H2O formula_0 4 ADP + 4 phosphate + adenosylcobyric acid + 4 -glutamate
The four substrates of this enzyme are ATP, adenosylcobyrinic acid a,c-diamide, L-glutamine, and H2O; its four products are ADP, phosphate, adenosylcobyric acid, and L-glutamate.
This enzyme belongs to the family of ligases, specifically those forming carbon-nitrogen bonds carbon-nitrogen ligases with glutamine as amido-N-donor (Glutamine amidotransferases). The systematic name of this enzyme class is adenosylcobyrinic-acid-a,c-diamide:L-glutamine amido-ligase (ADP-forming). This enzyme is part of the biosynthetic pathway to cobalamin (vitamin B12) in bacteria.
References.
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[
{
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https://en.wikipedia.org/wiki?curid=14285509
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14285518
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Aerobactin synthase
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Class of enzymes
In enzymology, an aerobactin synthase (EC 6.3.2.39) is an enzyme that catalyzes the chemical reaction
4 ATP + citrate + 2 N6-acetyl-N6-hydroxy-L-lysine + 2 H2O formula_0 4 ADP + 4 phosphate + aerobactin
The 4 substrates of this enzyme are ATP, citrate, N6-acetyl-N6-hydroxy-L-lysine, and H2O, whereas its 3 products are ADP, phosphate, and aerobactin.
This enzyme belongs to the family of ligases, specifically those forming carbon-nitrogen bonds as acid-D-amino-acid ligases (peptide synthases). The systematic name of this enzyme class is citrate:N6-acetyl-N6-hydroxy-L-lysine ligase (ADP-forming). This enzyme is also called citrate:6-N-acetyl-6-N-hydroxy-L-lysine ligase (ADP-forming). This enzyme participates in lysine degradation.
References.
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[
{
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https://en.wikipedia.org/wiki?curid=14285518
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14285525
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Alanine—tRNA ligase
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In enzymology, an alanine—tRNA ligase (EC 6.1.1.7) is an enzyme that catalyzes the chemical reaction
ATP + L-alanine + tRNAAla formula_0 AMP + diphosphate + L-alanyl-tRNAAla
The 3 substrates of this enzyme are ATP, L-alanine, and tRNA(Ala), whereas its 3 products are AMP, diphosphate, and L-alanyl-tRNA(Ala).
This enzyme belongs to the family of ligases, to be specific those forming carbon-oxygen bonds in aminoacyl-tRNA and related compounds. The systematic name of this enzyme class is L-alanine:tRNAAla ligase (AMP-forming). Other names in common use include alanyl-tRNA synthetase, alanyl-transfer ribonucleate synthetase, alanyl-transfer RNA synthetase, alanyl-transfer ribonucleic acid synthetase, alanine-transfer RNA ligase, alanine transfer RNA synthetase, alanine tRNA synthetase, alanine translase, alanyl-transfer ribonucleate synthase, AlaRS, and Ala-tRNA synthetase. This enzyme participates in alanine and aspartate metabolism and aminoacyl-trna biosynthesis.
Structural studies.
As of late 2007, 7 structures have been solved for this class of enzymes, with PDB accession codes 1RIQ, 1V4P, 1YFR, 1YFS, 1YFT, 1YGB, and 2E1B.
References.
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[
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https://en.wikipedia.org/wiki?curid=14285525
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14285532
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Aminodeoxychorismate synthase
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In enzymology, an aminodeoxychorismate synthase (EC 2.6.1.85) is an enzyme that catalyzes the chemical reaction
chorismate + L-glutamine formula_0 4-amino-4-deoxychorismate + L-glutamate
Thus, the two substrates of this enzyme are chorismate and L-glutamine, whereas its two products are 4-amino-4-deoxychorismate and L-glutamate.
It is part of a pathway for the biosynthesis of "para"-aminobenzoic acid (PABA); a precursor for the production of folates. Folates are family of cofactors that are essential for living organisms. Folate cofactors are used in several one-carbon transfer reactions required during the synthesis of essential metabolites, including methionine and thymidylate.
Aminodeoxychorismate synthase (PabB), a 51 kDa protein in "E. coli", is encoded by the gene "pabB". 4-amino-4-deoxychorismate, the product of PabB, can be converted to "para"-aminobenzoic acid by the enzyme 4-amino-4-deoxychorismate lyase (PabC).
Nonmenclature.
This enzyme belongs to the class of transferases. This means that aminodeoxychorismate synthase catalyzes the transfer of one functional group from a molecule to another. Specifically, aminodeoxychorismate synthase is a transaminase that transfers an amino group to a keto acid. The systematic name is Chorismate:L-glutamine aminotransferase. Formerly aminodeoxychorismate synthase was referred to as PABA synthase; however this name is no longer recommended as it is understood that the formation of PABA requires the action of a further enzyme (4-amino-4-deoxychorismate lyase).
Common names that the enzyme goes by are:
Reaction.
In certain microbial species such as "Escherichia coli, "aminodeoxychorismate synthase is a heterodimeric complex composed of two proteins, glutamine amidotransferase (PabA) and 4-amino-4-deoxychorismate synthase (PabB). In other species such as plants or lower eukaryotes an enzyme comprising a single polypeptide performs both reactions.
In "Escherichia coli", the reaction is a two step process. Glutamine amidotransferase (PabA) and 4-amino-4-deoxychorismate synthase (PabB) form a heterodimeric complex that catalyzes the synthesis of 4-amino-4-deoxychorismate. The first step occurs with PabA abstracting ammonia from glutamine. The second step occurs when PabB reacts both substrates (chorismate and ammonia) to synthesize 4-amino-4-deoxychorismate.
In plants such as "Arabidopsis thaliana", aminodeoxychorismate synthase is a monomeric enzyme that carries out both steps of the reaction.
Structure.
Aminodeoxychorismate synthase (PabB) is either a heterodimeric or monomeric enzyme depending on what organism it is from. The enzyme has 452-residues and consists of both alpha and beta folds that is very similar to some types of anthranilate synthase. The core of PabB consists of two domains that form a beta sandwich. Also, it has helices and loops around the outside of its core. The chorismate binding site on PabB consists of amino acids residues that make up beta sheet core and the two key alpha helices.
Certain aminodeoxychorismate synthase enzymes contain an additional binding site for tryptophan, thought to be a non-functional vestigial binding site. It is believed that aminodeoxychorismate synthase may have evolved from anthranilate synthase (TrpE) - an enzyme that catalyses the production of an intermediate on the path to tryptophan.
Homologues.
Enzymes with similar structures to aminodeoxychorismate synthase are:
A common feature among this list of enzymes is that they all utilize chorismate as a substrate.
Anti-folate drug target.
Aminodeoxychorismate synthase is targeted by the antibiotics "atrop"-abyssomycin C and 6-fluoroshikimic acid. By inhibiting the production of an intermediate on the pathway to PABA, folate levels are depleted. Without sufficient folate, DNA and protein synthesis are severely impaired.
References.
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https://en.wikipedia.org/wiki?curid=14285532
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14285542
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Anthranilate—CoA ligase
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In enzymology, an anthranilate—CoA ligase (EC 6.2.1.32) is an enzyme that catalyzes the chemical reaction
ATP + anthranilate + CoA formula_0 AMP + diphosphate + anthranilyl-CoA
The 3 substrates of this enzyme are ATP, anthranilate, and CoA, whereas its 3 products are AMP, diphosphate, and anthranilyl-CoA.
This enzyme belongs to the family of ligases, specifically those forming carbon-sulfur bonds as acid-thiol ligases. The systematic name of this enzyme class is anthranilate:CoA ligase (AMP-forming). Other names in common use include anthraniloyl coenzyme A synthetase, 2-aminobenzoate-CoA ligase, 2-aminobenzoate-coenzyme A ligase, and 2-aminobenzoate coenzyme A ligase. This enzyme participates in 3 metabolic pathways: carbazole degradation, benzoate degradation via coa ligation, and acridone alkaloid biosynthesis.
References.
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https://en.wikipedia.org/wiki?curid=14285542
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14285550
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Arachidonate—CoA ligase
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In enzymology, an arachidonate—CoA ligase (EC 6.2.1.15) is an enzyme that catalyzes the chemical reaction
ATP + arachidonate + CoA formula_0 AMP + diphosphate + arachidonoyl-CoA
The 3 substrates of this enzyme are ATP, arachidonate, and CoA, whereas its 3 products are AMP, diphosphate, and arachidonoyl-CoA.
This enzyme belongs to the family of ligases, specifically those forming carbon-sulfur bonds as acid-thiol ligases. The systematic name of this enzyme class is arachidonate:CoA ligase (AMP-forming). This enzyme is also called arachidonoyl-CoA synthetase.
References.
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https://en.wikipedia.org/wiki?curid=14285550
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14285556
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Arginine—tRNA ligase
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In enzymology, an arginine—tRNA ligase (EC 6.1.1.19) is an enzyme that catalyzes the chemical reaction
ATP + L-arginine + tRNAArg formula_0 AMP + diphosphate + L-arginyl-tRNAArg
The 3 substrates of this enzyme are ATP, L-arginine, and tRNA(Arg), whereas its 3 products are AMP, diphosphate, and L-arginyl-tRNA(Arg).
This enzyme belongs to the family of ligases, to be specific those forming carbon-oxygen bonds in aminoacyl-tRNA and related compounds. The systematic name of this enzyme class is L-arginine:tRNAArg ligase (AMP-forming). Other names in common use include arginyl-tRNA synthetase, arginyl-transfer ribonucleate synthetase, arginyl-transfer RNA synthetase, arginyl transfer ribonucleic acid synthetase, arginine-tRNA synthetase, and arginine translase. This enzyme participates in arginine and proline metabolism and aminoacyl-trna biosynthesis.
It contains a conserved domain at the N terminus called arginyl tRNA synthetase N terminal domain or additional domain 1 (Add-1). This domain is about 140 residues long and it has been suggested that it is involved in tRNA recognition.
Structural studies.
As of late 2007, 4 structures have been solved for this class of enzymes, with PDB accession codes 1BS2, 1F7U, 1F7V, and 1IQ0.
References.
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https://en.wikipedia.org/wiki?curid=14285556
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14285564
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Asparagine—tRNA ligase
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In enzymology, an asparagine-tRNA ligase (EC 6.1.1.22) is an enzyme that catalyzes the chemical reaction
ATP + L-asparagine + tRNAAsn formula_0 AMP + diphosphate + L-asparaginyl-tRNAAsn
The 3 substrates of this enzyme are ATP, L-asparagine, and tRNA(Asn), whereas its 3 products are AMP, diphosphate, and L-asparaginyl-tRNA(Asn).
This enzyme belongs to the family of ligases, to be specific those forming carbon-oxygen bonds in aminoacyl-tRNA and related compounds. The systematic name of this enzyme class is L-asparagine:tRNAAsn ligase (AMP-forming). Other names in common use include asparaginyl-tRNA synthetase, asparaginyl-transfer ribonucleate synthetase, asparaginyl transfer RNA synthetase, asparaginyl transfer ribonucleic acid synthetase, asparagyl-transfer RNA synthetase, and asparagine translase. This enzyme participates in alanine and aspartate metabolism and aminoacyl-trna biosynthesis.
Structural studies.
As of late 2007, 3 structures have been solved for this class of enzymes, with PDB accession codes 1X54, 1X55, and 1X56.
References.
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https://en.wikipedia.org/wiki?curid=14285564
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14285632
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Asparaginyl-tRNA synthase (glutamine-hydrolysing)
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In enzymology, an asparaginyl-tRNA synthase (glutamine-hydrolysing) (EC 6.3.5.6) is an enzyme that catalyzes the chemical reaction
ATP + aspartyl-tRNAAsn + -glutamine formula_0 ADP + phosphate + asparaginyl-tRNAAsn + -glutamate
The 3 substrates of this enzyme are ATP, aspartyl-tRNA(Asn), and L-glutamine, whereas its 4 products are ADP, phosphate, asparaginyl-tRNA(Asn), and L-glutamate.
This enzyme belongs to the family of ligases, specifically those forming carbon-nitrogen bonds carbon-nitrogen ligases with glutamine as amido-N-donor. The systematic name of this enzyme class is aspartyl-tRNAAsn:L-glutamine amido-ligase (ADP-forming). This enzyme participates in glutamate metabolism and alanine and aspartate metabolism.
References.
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https://en.wikipedia.org/wiki?curid=14285632
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14285645
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Aspartate—ammonia ligase
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Enzyme
In enzymology, an aspartate—ammonia ligase (EC 6.3.1.1) is an enzyme that catalyzes the chemical reaction
ATP + L-aspartate + NH3 formula_0 AMP + diphosphate + L-asparagine
The 3 substrates of this enzyme are ATP, L-aspartate, and NH3, whereas its 3 products are AMP, diphosphate, and L-asparagine.
This enzyme belongs to the family of ligases, specifically those forming carbon-nitrogen bonds as acid-D-ammonia (or amine) ligases (amide synthases). The systematic name of this enzyme class is L-aspartate:ammonia ligase (AMP-forming). Other names in common use include asparagine synthetase, and L-asparagine synthetase. This enzyme participates in 3 metabolic pathways: alanine and aspartate metabolism, cyanoamino acid metabolism, and nitrogen metabolism.
Structural studies.
As of late 2007, two structures have been solved for this class of enzymes, with PDB accession codes 11AS and 12AS.
References.
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https://en.wikipedia.org/wiki?curid=14285645
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14285656
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Aspartate—ammonia ligase (ADP-forming)
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Class of enzymes
In enzymology, an aspartate—ammonia ligase (ADP-forming) (EC 6.3.1.4) is an enzyme that catalyzes the chemical reaction
ATP + L-aspartate + NH3 formula_0 ADP + phosphate + L-asparagine
The 3 substrates of this enzyme are ATP, L-aspartate, and NH3, whereas its 3 products are ADP, phosphate, and L-asparagine.
This enzyme belongs to the family of ligases, specifically those forming carbon-nitrogen bonds as acid-D-ammonia (or amine) ligases (amide synthases). The systematic name of this enzyme class is L-aspartate:ammonia ligase (ADP-forming). Other names in common use include asparagine synthetase (ADP-forming), and asparagine synthetase (adenosine diphosphate-forming). This enzyme participates in nitrogen metabolism.
References.
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[
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https://en.wikipedia.org/wiki?curid=14285656
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14285666
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Aspartate—tRNA(Asn) ligase
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Aspartate—tRNAAsn ligase (EC 6.1.1.23, "nondiscriminating aspartyl-tRNA synthetase") is an enzyme with systematic name "L-aspartate:tRNAAsx ligase (AMP-forming)". This enzyme catalyses the following chemical reaction
ATP + L-aspartate + tRNAAsx formula_0 AMP + diphosphate + aspartyl-tRNAAsx
The 3 substrates of this enzyme are ATP, L-asparagine, and tRNAAsx, whereas its 3 products are AMP, diphosphate, and asparaginyl-tRNAAsx.
When this enzyme acts on tRNAAsp, it catalyses the same reaction as EC 6.1.1.12, aspartate---tRNA ligase. It has, however, diminished discrimination, so that it can also form aspartyl-tRNAAsn. This relaxation of specificity has been found to result from the absence of a loop in the tRNA that specifically recognizes the third position of the anticodon [1]. This accounts for the ability of this enzyme in, for example, Thermus thermophilus, to recognize both tRNAAsp (GUC anticodon) and tRNAAsn (GUU anticodon). The aspartyl-tRNAAsn is not used in protein synthesis until it is converted by EC 6.3.5.6, asparaginyl-tRNA synthase (glutamine-hydrolysing), into asparaginyl-tRNAAsn.
This enzyme belongs to the family of ligases, to be specific those forming carbon-oxygen bonds in aminoacyl-tRNA and related compounds. The systematic name of this enzyme class is L-asparaginyl:tRNAAsx ligase (AMP-forming). This enzyme is also called nondiscriminating asparaginyl-tRNA synthetase. This enzyme participates in alanine and asparagine metabolism.
References.
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[
{
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https://en.wikipedia.org/wiki?curid=14285666
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14285677
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Aspartate—tRNA ligase
|
In enzymology, an aspartate—tRNA ligase (EC 6.1.1.12) is an enzyme that catalyzes the chemical reaction
ATP + L-aspartate + tRNAAsp formula_0 AMP + diphosphate + L-aspartyl-tRNAAsp
The 3 substrates of this enzyme are ATP, L-aspartate, and tRNA(Asp), whereas its 3 products are AMP, diphosphate, and L-aspartyl-tRNA(Asp).
This enzyme belongs to the family of ligases, to be specific those forming carbon-oxygen bonds in aminoacyl-tRNA and related compounds. The systematic name of this enzyme class is L-aspartate:tRNAAsp ligase (AMP-forming). Other names in common use include aspartyl-tRNA synthetase, aspartyl ribonucleic synthetase, aspartyl-transfer RNA synthetase, aspartic acid translase, aspartyl-transfer ribonucleic acid synthetase, and aspartyl ribonucleate synthetase. This enzyme participates in alanine and aspartate metabolism and aminoacyl-trna biosynthesis.
Structural studies.
As of late 2007, 10 structures have been solved for this class of enzymes, with PDB accession codes 1ASY, 1ASZ, 1B8A, 1C0A, 1EFW, 1EOV, 1EQR, 1G51, 1IL2, and 1L0W.
References.
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[
{
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https://en.wikipedia.org/wiki?curid=14285677
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14285683
|
Benzoate—CoA ligase
|
Class of enzymes
In enzymology, a benzoate—CoA ligase (EC 6.2.1.25) is an enzyme that catalyzes the chemical reaction
ATP + benzoate + CoA formula_0 AMP + diphosphate + benzoyl-CoA
The 3 substrates of this enzyme are ATP, benzoate, and CoA, whereas its 3 products are AMP, diphosphate, and benzoyl-CoA.
This enzyme belongs to the family of ligases, specifically those forming carbon-sulfur bonds as acid-thiol ligases. The systematic name of this enzyme class is benzoate:CoA ligase (AMP-forming). Other names in common use include benzoate-coenzyme A ligase, benzoyl-coenzyme A synthetase, and benzoyl CoA synthetase (AMP forming). This enzyme participates in benzoate degradation via coa ligation.
Structural studies.
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code 2V7B.
References.
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[
{
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https://en.wikipedia.org/wiki?curid=14285683
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14285694
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Biotin—(acetyl-CoA-carboxylase) ligase
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Enzyme
In enzymology, a biotin—[acetyl-CoA-carboxylase] ligase (EC 6.3.4.15) is an enzyme that catalyzes the chemical reaction
ATP + biotin + apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)] formula_0 AMP + diphosphate + [acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
The 3 substrates of this enzyme are ATP, biotin, and apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)], whereas its 3 products are AMP, diphosphate, and acetyl-CoA:carbon-dioxide ligase (ADP-forming).
This enzyme belongs to the family of ligases, specifically those forming generic carbon-nitrogen bonds.
This enzyme participates in biotin metabolism. This protein may use the morpheein model of allosteric regulation.
Nomenclature.
The systematic name of this enzyme class is biotin:apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)] ligase (AMP-forming). Other names in common use include:
References.
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Further reading.
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14285702
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Biotin carboxylase
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Class of enzymes
In enzymology, a biotin carboxylase (EC 6.3.4.14) is an enzyme that catalyzes the chemical reaction
ATP + biotin-carboxyl-carrier protein + CO2 formula_0 ADP + phosphate + carboxybiotin-carboxyl-carrier protein
The three substrates of this enzyme are ATP, biotin-carboxyl-carrier protein (BCCP), and CO2, whereas its three products are ADP, phosphate, and carboxybiotin-carboxyl-carrier protein.
The systematic name of this enzyme class is biotin-carboxyl-carrier-protein:carbon-dioxide ligase (ADP-forming). This enzyme is also called biotin carboxylase (component of acetyl CoA carboxylase). This enzyme participates in fatty acid biosynthesis. This enzyme participates in fatty acid biosynthesis by providing one of the catalytic functions of the Acetyl-CoA carboxylase complex. As previously mentioned, after the carboxybiotin product is formed, the carboxyltransferase unit of the complex will transfer the activated carboxy group from BCCP to Acetyl-CoA, forming a malonate analog known as malonyl-CoA. Malonyl-CoA serves as the primary carbon donor in fatty acid biosynthesis, followed by a series of reduction and dehydration reactions to remove the acyl group.
Reaction pathway.
Biotin carboxylases are a conserved enzyme present within biotin-dependent carboxylase complexes such as acetyl-CoA carboxylase. How biotin carboxylase functions is, within the relevant carboxylase complex, there is a biotin carboxyl-carrier protein which is covalently linked to biotin via a Lys-residue. Both biotin carboxylase activity as well as the BCCP within the carboxylase complex are highly conserved among this enzyme class. The main source of variation for carboxylases arises from the carboxyltransferase component, as the molecule to which the carboxyl group is transferred (from biotin) dictates the necessary specificity component to catalyze this transfer.
The structure of biotin carboxylase heavily influences the reaction pathway the enzyme catalyzes, so discussion of this reaction pathway must also touch on how the substrates and intermediates are stabilized within the active site. Bicarbonate (HCO3−) is held within the active site of biotin carboxylase by hydrogen bonding with biotin as well as a bidentate ion pair interaction of the negatively charged oxygen's with Arg292 iminium ion. It is hypothesized that the Glu296 residue of B.C. acts as a base, deprotonating bicarbonate molecule, thus facilitating nucleophilic attack of the carbonyl-oxygen on the terminal phosphate molecule of ATP. This initial reaction of the pathway can happen because the ATP is also held tightly within the active site pocket via non-covalent coordination of ATP with magnesium ions.
After this nucleophilic attack, the carbonate molecule is degraded to CO2 via electron pushing, producing a PO43- ion which then acts as a base and deprotonates the amide of the ureido ring within biotin. An enolate-like intermediate is formed, producing a negative charge on the oxygen, which is stabilized by the iminium ion of Arg338. The enolate then executes a nucleophilic attack on CO2 (which is being held in place through H-bonding with Glu296 residue), ultimately leading to the product of this enzymatic pathway: carboxybiotin. After this reaction occurs, the carboxyltransferase enzyme present within the complex acts upon the carboxybiotin to transfer the carboxyl group to the target acceptor molecule i.e. acetyl Co-A, propionyl Co-A etc.
Structural studies.
As of late 2007[ [update]], 5 structures have been solved for this class of enzymes, with PDB accession codes 1BNC, 1DV1, 1DV2, 2GPS, and 2GPW.
The crystal structure has been determined for the biotin carboxylase (acetyl-CoA carboxylase) of "Escherichia coli", but the eukaryotic B.C. is difficult to obtain info on as it is catalytically inactive in solution. "E. coli" biotin carboxylase is composed of two homogenous dimers made up of 3 domains: A, B, and C. It is believed that the B domain of each monomer is essential to the function of this enzyme, as there is extreme flexibility of this domain seen in the crystal structure. Upon binding of the ATP substrate, a conformational change occurs where the B domain essentially closes over the active site. While this change is thought to bring ATP within close enough proximity for the reaction to occur, the active site was still solvent exposed. Because of this anomaly in the crystal structure, it is believed that the attachment of biotin to BCCP aids in this reaction pathway, essentially covering biotin within the active site, as evidence shows free biotin is not as great of a substrate for this enzyme when compared to biotin-BCCP. A C-terminal conserved domain within this enzyme contains most of the active site residues. The Glu296 and Arg338 are highly conserved residues among this subclass of enzymes, and work to stabilize the reaction intermediates and keep them within the active site pocket until the carboxylation is complete.
This enzyme is vital to life and has maintained its function across a variety of organisms. While the structure itself may be divergent based on the biotin carboxylase function and which complex it is present in, the enzyme still works to serve the same function. Fatty acid synthesis provides sterols and other lipids essential to biochemical pathways, and the necessity for this enzyme function is confirmed by the highly conserved active site amino acid sequence.
References.
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14285711
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Biotin—CoA ligase
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In enzymology, a biotin—CoA ligase (EC 6.2.1.11) is an enzyme that catalyzes the chemical reaction
ATP + biotin + CoA formula_0 AMP + diphosphate + biotinyl-CoA
The 3 substrates of this enzyme are ATP, biotin, and CoA, whereas its 3 products are AMP, diphosphate, and biotinyl-CoA.
This enzyme belongs to the family of ligases, specifically those forming carbon-sulfur bonds as acid-thiol ligases. The systematic name of this enzyme class is biotin:CoA ligase (AMP-forming). Other names in common use include biotinyl-CoA synthetase, biotin CoA synthetase, and biotinyl coenzyme A synthetase. This enzyme participates in biotin metabolism.
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14285718
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Biotin—(methylcrotonoyl-CoA-carboxylase) ligase
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In enzymology, a biotin-[methylcrotonoyl-CoA-carboxylase] ligase (EC 6.3.4.11) is an enzyme that catalyzes the chemical reaction
ATP + biotin + apo-[3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)] formula_0 AMP + diphosphate + [3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)]
The 3 substrates of this enzyme are ATP, biotin, and ], whereas its 3 products are AMP, diphosphate, and .
This enzyme belongs to the family of ligases, specifically those forming generic carbon-nitrogen bonds. The systematic name of this enzyme class is biotin:apo-[3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)] ligase (AMP-forming). Other names in common use include biotin-[methylcrotonoyl-CoA-carboxylase] synthetase, biotin-beta-methylcrotonyl coenzyme A carboxylase synthetase, beta-methylcrotonyl coenzyme A holocarboxylase synthetase, and holocarboxylase-synthetase. This enzyme participates in biotin metabolism.
References.
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14285730
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Biotin—(methylmalonyl-CoA-carboxytransferase) ligase
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In enzymology, a biotin—[methylmalonyl-CoA-carboxytransferase] ligase (EC 6.3.4.9) is an enzyme that catalyzes the chemical reaction
ATP + biotin + apo-[methylmalonyl-CoA:pyruvate carboxytransferase] formula_0 AMP + diphosphate + [methylmalonyl-CoA:pyruvate carboxytransferase]
The 3 substrates of this enzyme are ATP, biotin, and ], whereas its 3 products are AMP, diphosphate, and .
This enzyme belongs to the family of ligases, specifically those forming generic carbon-nitrogen bonds. The systematic name of this enzyme class is biotin:apo[methylmalonyl-CoA:pyruvate carboxytransferase] ligase (AMP-forming). This enzyme participates in biotin metabolism.
References.
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14285749
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Butyrate—CoA ligase
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Butyrate—CoA ligase, also known as xenobiotic/medium-chain fatty acid-ligase (XM-ligase), is an enzyme (EC 6.2.1.2) that catalyzes the chemical reaction:
ATP + a carboxylic acid + CoA formula_0 AMP + diphosphate + an acyl-CoA
The 3 substrates of this enzyme are ATP, carboxylic acid, and CoA, whereas its 3 products are AMP, diphosphate, and acyl-CoA.
This enzyme belongs to the family of ligases, specifically those forming carbon-sulfur bonds as acid-thiol ligases. This enzyme participates in the glycine conjugation of xenobiotics and butanoate metabolism.
Nomenclature.
The systematic name of this enzyme class is butanoate:CoA ligase (AMP-forming). Other names in common use include:
References.
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14285758
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(carboxyethyl)arginine beta-lactam-synthase
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Class of enzymes
In enzymology, a (carboxyethyl)arginine β-lactam-synthase (EC 6.3.3.4) is an enzyme that catalyzes the chemical reaction
ATP + -"N"2-(2-carboxyethyl)arginine formula_0 AMP + diphosphate + deoxyamidinoproclavaminate
Thus, the two substrates of this enzyme are ATP and L-N2-(2-carboxyethyl)arginine, whereas its 3 products are AMP, diphosphate, and deoxyamidinoproclavaminate.
This enzyme belongs to the family of ligases, specifically the cyclo-ligases, which form carbon-nitrogen bonds. The systematic name of this enzyme class is L-N2-(2-carboxyethyl)arginine cyclo-ligase (AMP-forming). This enzyme is also called L-2-N-(2-carboxyethyl)arginine cyclo-ligase (AMP-forming). This enzyme participates in clavulanic acid biosynthesis.
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14285764
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Carnosine synthase
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Class of enzymes
Carnosine synthase (EC 6.3.2.11) is an enzyme that catalyzes the chemical reaction
ATP + L-histidine + beta-alanine formula_0 ADP + phosphate + carnosine
The 3 substrates of this enzyme are ATP, L-histidine, and beta-alanine, whereas its 3 products are ADP (previously thought to form AMP), diphosphate, and carnosine.
This enzyme belongs to the family of ligases, specifically those forming carbon-nitrogen bonds as acid-D-amino-acid ligases (peptide synthases). The systematic name of this enzyme class is 'L-histidine:beta-alanine ligase (AMP-forming)' (incorrect on AMP-forming). Other names in common use include 'carnosine synthetase', 'carnosine-anserine synthetase', 'homocarnosine synthetase', and 'carnosine-homocarnosine synthetase'.
Gene.
The gene encoding this enzyme has been identified by Jakub Drozak and coworkers in 2010. The gene encoding the Carnosine synthase is ATPGD1, a member of the “ATP-grasp family” of ligases. Because of its involvement in the formation of carnosine, this gene is now also named 'CARNS1'.
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14285771
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Citrate—CoA ligase
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Enzyme
In enzymology, a citrate—CoA ligase (EC 6.2.1.18) is an enzyme that catalyzes the chemical reaction
ATP + citrate + CoA formula_0 ADP + phosphate + (3S)-citryl-CoA
The 3 substrates of this enzyme are ATP, citrate, and CoA, whereas its 3 products are ADP, phosphate, and (3S)-citryl-CoA.
This enzyme belongs to the family of ligases, specifically those forming carbon-sulfur bonds as acid-thiol ligases. The systematic name of this enzyme class is citrate:CoA ligase (ADP-forming). Other names in common use include citryl-CoA synthetase, citrate:CoA ligase, and citrate thiokinase. This enzyme participates in citric acid cycle.
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14285776
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(citrate (pro-3S)-lyase) ligase
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Class of enzymes
In enzymology, a [citrate ("pro"-3"S")-lyase] ligase (EC 6.2.1.22) is an enzyme that catalyzes the chemical reaction
ATP + acetate + citrate (pro-3S)-lyase(thiol form) formula_0 AMP + diphosphate + citrate (pro-3S)-lyase(acetyl form)
The 3 substrates of this enzyme are ATP, acetate, and citrate (pro-3S)-lyase(thiol form), whereas its 3 products are AMP, diphosphate, and citrate (pro-3S)-lyase(acetyl form).
This enzyme belongs to the family of ligases, specifically those forming carbon-sulfur bonds as acid-thiol ligases. The systematic name of this enzyme class is acetate:citrate (pro-3S)-lyase(thiol-form) ligase (AMP-forming). Other names in common use include citrate lyase ligase, citrate lyase synthetase, acetate: SH-acyl-carrier-protein enzyme ligase (AMP), acetate:HS-citrate lyase ligase, and acetate:citrate-(pro-3S)-lyase(thiol-form) ligase (AMP-forming). This enzyme participates in two-component system - general.
References.
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14285783
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Cobalt chelatase
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Enzyme
Cobalt chelatase (EC 6.6.1.2) is an enzyme that catalyzes the chemical reaction
ATP + hydrogenobyrinic acid a,c-diamide + Co2+ + H2O formula_0 ADP + phosphate + cob(II)yrinic acid a,c-diamide + H+
The four substrates of this enzyme are ATP, hydrogenobyrinic acid a,c-diamide, Co2+, and H2O; its four products are ADP, phosphate, cob(II)yrinic acid a,c-diamide, and H+.
The aerobic cobalt chelatase (aerobic cobalamin biosynthesis pathway) consists of three subunits, CobT, CobN (InterPro: "IPR003672") and CobS (InterPro: "IPR006537").
The macrocycle of vitamin B12 can be complexed with metal via the ATP-dependent reactions in the aerobic pathway (e.g., in "Pseudomonas denitrificans") or via ATP-independent reactions of sirohydrochlorin in the anaerobic pathway (e.g., in "Salmonella typhimurium"). The corresponding cobalt chelatases are not homologous. However, aerobic cobalt chelatase subunits CobN and CobS are homologous to Mg-chelatase subunits BchH and BchI, respectively. CobT, too, has been found to be remotely related to the third subunit of Mg-chelatase, BchD (involved in bacteriochlorophyll synthesis, e.g., in Rhodobacter capsulatus).
This enzyme belongs to the family of ligases, specifically those forming nitrogen-D-metal bonds in coordination complexes. The systematic name of this enzyme class is hydrogenobyrinic-acid-a,c-diamide:cobalt cobalt-ligase (ADP-forming). Other names in common use include hydrogenobyrinic acid a,c-diamide cobaltochelatase, CobNST, and CobNCobST. This enzyme is part of the biosynthetic pathway to cobalamin (vitamin B12) in aerobic bacteria.
References.
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Further reading.
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14285794
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Cysteine—tRNA ligase
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In enzymology, a cysteine—tRNA ligase (EC 6.1.1.16) is an enzyme that catalyzes the chemical reaction
ATP + L-cysteine + tRNACys formula_0 AMP + diphosphate + L-cysteinyl-tRNACys
The 3 substrates of this enzyme are ATP, L-cysteine, and tRNA(Cys), whereas its 3 products are AMP, diphosphate, and L-cysteinyl-tRNA(Cys).
This enzyme belongs to the family of ligases, to be specific those forming carbon-oxygen bonds in aminoacyl-tRNA and related compounds. The systematic name of this enzyme class is L-cysteine:tRNACys ligase (AMP-forming). Other names in common use include cysteinyl-tRNA synthetase, cysteinyl-transferRNA synthetase, cysteinyl-transfer ribonucleate synthetase, and cysteine translase. This enzyme participates in cysteine metabolism and aminoacyl-trna biosynthesis.
Structural studies.
As of late 2007, 3 structures have been solved for this class of enzymes, with PDB accession codes 1LI5, 1LI7, and 1U0B.
References.
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14285800
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D-alanine—alanyl-poly(glycerolphosphate) ligase
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Class of enzymes
In enzymology, a -alanine—alanyl-poly(glycerolphosphate) ligase (EC 6.3.2.16) is an enzyme that catalyzes the chemical reaction
ATP + D-alanine + alanyl-poly(glycerolphosphate) formula_0 ADP + phosphate + D-alanyl-alanyl-poly(glycerolphosphate)
The 3 substrates of this enzyme are ATP, D-alanine, and alanyl-poly(glycerolphosphate), whereas its 3 products are ADP, phosphate, and D-alanyl-alanyl-poly(glycerolphosphate).
This enzyme belongs to the family of ligases, specifically those forming carbon-nitrogen bonds as acid-D-amino-acid ligases (peptide synthases). The systematic name of this enzyme class is D-alanine:alanyl-poly(glycerolphosphate) ligase (ADP-forming). Other names in common use include D-alanyl-alanyl-poly(glycerolphosphate) synthetase, D-alanine:membrane-acceptor ligase, D-alanylalanylpoly(phosphoglycerol) synthetase, D-alanyl-poly(phosphoglycerol) synthetase, and D-alanine-membrane acceptor-ligase. This enzyme participates in d-alanine metabolism.
References.
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