1.13.11.24: quercetin 2,3-dioxygenase
This is an abbreviated version!
For detailed information about quercetin 2,3-dioxygenase, go to the full flat file.
Word Map on EC 1.13.11.24
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1.13.11.24
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flavonols
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dioxygenation
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bicupins
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o-heterocycle
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oxygenolysis
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synthesis
- 1.13.11.24
- flavonols
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dioxygenation
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bicupins
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o-heterocycle
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oxygenolysis
- synthesis
Reaction
Synonyms
2,3-QD, 2,3QD, 2,4-QD, Co-QDO, Co-QueD, Cu2+-containing 2,4-QD, cupin domain-containing protein, Fe-QDO, Fe-QueD, flavonol 2,4-dioxygenase, flavonol 2,4-oxygenase, manganese quercetin 2,3-dioxygenase, manganese quercetin dioxygenase, Mn-QDO, Mn-QueD, Ni-QueD, nickel quercetinase, pirin, QDO, QdoI, QueD, quercetin 2,4-dioxygenase, quercetin dioxygenase, quercetinase, type III extradiol dioxygenase, VdQase, YxaG
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General Information
General Information on EC 1.13.11.24 - quercetin 2,3-dioxygenase
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evolution
malfunction
metabolism
physiological function
additional information
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the ring-cleaving dioxygenase belongs to the cupin superfamily, characterized by a six-stranded beta-barrel fold and conserved amino acid motifs that provide the 3His or 2- or 3His-1Glu ligand environment of a divalent metal ion. The cupin domain comprises two conserved amino acid motifs with the consensus sequences G(X)5HXH(X)3-4E(X)6G (motif 1) and G(X)5-7PXG(X)2H(X)3N
evolution
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the ring-cleaving dioxygenase belongs to the cupin superfamily, characterized by a six-stranded beta-barrel fold and conserved amino acid motifs that provide the 3His or 2- or 3His-1Glu ligand environment of a divalent metal ion. The cupin domain comprises two conserved amino acid motifs with the consensus sequences G(X)5HXH(X)3-4E(X)6G (motif 1) and G(X)5-7PXG(X)2H(X)3N
evolution
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the ring-cleaving dioxygenase belongs to the cupin superfamily, characterized by a six-stranded beta-barrel fold and conserved amino acid motifs that provide the 3His or 2- or 3His-1Glu ligand environment of a divalent metal ion. The cupin domain comprises two conserved amino acid motifs with the consensus sequences G(X)5HXH(X)3-4E(X)6G (motif 1) and G(X)5-7PXG(X)2H(X)3N
evolution
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the ring-cleaving dioxygenase belongs to the cupin superfamily, characterized by a six-stranded beta-barrel fold and conserved amino acid motifs that provide the 3His or 2- or 3His-1Glu ligand environment of a divalent metal ion. The cupin domain comprises two conserved amino acid motifs with the consensus sequences G(X)5HXH(X)3-4E(X)6G (motif 1) and G(X)5-7PXG(X)2H(X)3N
evolution
quercetinases are metal-dependent dioxygenases of the cupin superfamily
evolution
Streptomyces sp. FLA / DSM 41951
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the ring-cleaving dioxygenase belongs to the cupin superfamily, characterized by a six-stranded beta-barrel fold and conserved amino acid motifs that provide the 3His or 2- or 3His-1Glu ligand environment of a divalent metal ion. The cupin domain comprises two conserved amino acid motifs with the consensus sequences G(X)5HXH(X)3-4E(X)6G (motif 1) and G(X)5-7PXG(X)2H(X)3N
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replacement of individual amino acids of the 3His/1Glu metal binding motif by alanine drastically reduces or abolishes quercetinase activity and affects its structural integrity. Only substitution of the glutamate ligand (E76) by histidine results in Ni- and Co-QueD variants that retain the native fold and show residual catalytic activity
malfunction
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the mutational removal of Glu73 causes a loss of enzyme activity
malfunction
the pathogenicity of VdQase knock-out mutants generated through Agrobacterium tumefasciens-mediated transformation is significantly reduced on susceptible potato cultivar Kennebec compared to wild-type isolates. Phenotype with a higher accumulation of flavonols in the stems of infected potatoes and a higher concentration of rutin in the leaves in response to the VdQase mutants as compared to wild-type isolates
malfunction
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the pathogenicity of VdQase knock-out mutants generated through Agrobacterium tumefasciens-mediated transformation is significantly reduced on susceptible potato cultivar Kennebec compared to wild-type isolates. Phenotype with a higher accumulation of flavonols in the stems of infected potatoes and a higher concentration of rutin in the leaves in response to the VdQase mutants as compared to wild-type isolates
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compounds TpMesMFla (TpMes = hydrotris(3-mesityl)pyrazolylborate, M = Mn, Fe, Co, Ni, Zn, Fla = 3-hydroxyflavonolate) as models for 2,4-quercetin dioxygenase. The structures differ in the degree of delocalization in the chelate ring formed through the binding of the two O donors of the flavonolate to the metal center, the resulting trend (Zn/Fe > Co > Mn > Ni) is, not in line with the one that found when investigating the redox properties of the complexes by cyclic voltammetry (Zn > Fe > Ni > Co > Mn). The complexes exhibit exceptionally well-behaved quasi-reversible redox transitions. After the O2 reaction, salicylic acid is one of the products
metabolism
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design of model ligands 2NCOO, 3 N, 3NCOO, 4 N (L2NCOOH: 2-((benzyl(pyridin-2-ylmethyl)amino)methyl)benzoic acid, L3N: N-benzyl-1-(pyridin-2-yl)-N-(pyridin-2-ylmethyl)methanamine, L3NCOOH: 2-{[bis(pyridin-2-ylmethyl)amino]methyl}benzoic acid, L4N: tris(pyridin-2-ylmethyl)amine) and their complexes [CoIILn(fla)] (n: 2NCOO (1), 3 N (2), 3NCOO (3), 4 N (4); fla: 3-flavonolate) as ES models of the Co(II)-containing quercetin 2,4-dioxygenase. [CoLn(fla)] exhibits higher single turnover O2 reactivity to produce products similar to the enzymatic reaction, and the decreasing order of reactivity is 3 > 4 > 1 > 2. The reaction rate constant k shows linear correlation with E1/2(CoIII/II) and Epa(fla-/fla radical)
metabolism
during oxidative ring-cleaving, electron transfer occurs from the quercetin to dioxygen via the nickel ion. Both the dioxygen and substrate are activated by binding to the nickel ion. The catalytic reaction includes the first attack of the Od atom on the quercetin to form the C-O bond, the movement of the coordinated Op atom, the formation of a five-membered heterocyclic ring, and the synergetic cleavage of the O-O bond and C-C bonds. The movement of the coordinated Op atom is the rate-limiting step
metabolism
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the nickel(II) flavonolate complex bearing a tridentate macrocyclic ligand, [NiII(Me3-TACN)(Fl)(NO3)](H2O) (Me3-TACN = 1,4,7-trimethyl-1,4,7-triazacyclononane, Fl = 3-hydroxyflavone) is a functional model for QueD. The complex shows two isomers with respect to the direction of a flavonolate ligand. Two isomers commonly are in the octahedral geometry with a bidentate of flavonolate and a monodentate of nitrate as well as a tridentate binding of the Me3-TACN ligand. The spin state is a triplet state, and the two singly occupied molecular orbitals (SOMOs) lie energetically lower than the highest (doubly) occupied molecular orbital (HOMO). The HOMO shows an electron density localized in the flavonolate ligand
metabolism
the reaction takes place via three major steps: attack of the superoxide on the C2 of the substrate pyrone ring to generate a Ni(II)-peroxide intermediate, formation of the second C-O bond between C4 and the peroxide to produce a peroxide bridge, and simultaneous cleavage of the C2-C3, C3-C4, and O1-O2 bonds with the formation of 2-protocatechuoylphloroglucinol carboxylic acid and carbon monoxide. The third step is rate-limiting, with a barrier of 17.4 kcal/mol. For the second C-O bond formation, an alternative pathway is that the peroxide attacks the C3 of the substrate pyrone ring, leading to the formation of a four-membered ring intermediate, which then undergoes concerted C2-C3 and O1-O2 bond cleavages to produce an alpha-keto acid. This pathway is associated with a barrier of 30.6 kcal/mol. When Glu74 is protonated, the 2,3-dioxygenolytic pathway, however, has a lower barrier (21.8 kcal/mol) than the 2,4-dioxygenolytic pathway
conversion of quercetin to 2-protocatechuoylphloroglucinol carboxylic acid is catalyzed by quercetinase, i.e. flavonol 2,4-dioxygenase. The the catalytic activity of wild-type QueD is likely mediated by a Ni2+ center
physiological function
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quercetin 2,3-dioxygenase (QDO) is an enzyme which accepts various transition metal ions as cofactors, and cleaves the heterocyclic ring of quercetin with consumption of dioxygen and release of carbon monoxide. QDO from Bacillus subtilis that binds Mn(II) displays an unprecedented nitroxygenase activity, whereby nitroxyl (HNO) is incorporated into quercetin cleavage products instead of dioxygen. The reaction proceeds with high regiospecificity, i.e. nitrogen and oxygen atoms of HNO are incorporated into specific fragments of the cleavage product. The reaction is an inherent property of the reactants, whereas the unique reactivity of Mn-QDO, as opposed to Co- or Fe-QDO that do not catalyze nitroxygenation. A nonenzymatic base-catalyzed reaction, which occurs in pH above 7.5, yields the same reaction products
physiological function
the enzyme is a cupin domain-containing protein with dioxygenase activity and quercetinase activity (VdQase) regulating Verticillium dahliaes pathogenicity in potato roots and contributing to counteraction against host defenses. Involvement of enzyme VdQase in the catabolism of quercetin and possibly other flavonols in planta. Involvement of VdQase in the interference with signaling, suggesting a role in pathogenicity. It is hypothesized that the by-product of dioxygenation 2-protocatechuoylphloroglucinolcarboxylic acid, after dissociating into phloroglucinol and protocatechuoyl moieties, becomes a starting point for benzoic acid and salicylic acid, thereby interfering with the jasmonate pathway and affecting the interaction outcome. These events may be key factors for Verticillium dahliaes in countering potato defenses and becoming notorious in the rhizosphere. Role of VdQase in rutin and quercetin utilization, overview
physiological function
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the enzyme is a cupin domain-containing protein with dioxygenase activity and quercetinase activity (VdQase) regulating Verticillium dahliaes pathogenicity in potato roots and contributing to counteraction against host defenses. Involvement of enzyme VdQase in the catabolism of quercetin and possibly other flavonols in planta. Involvement of VdQase in the interference with signaling, suggesting a role in pathogenicity. It is hypothesized that the by-product of dioxygenation 2-protocatechuoylphloroglucinolcarboxylic acid, after dissociating into phloroglucinol and protocatechuoyl moieties, becomes a starting point for benzoic acid and salicylic acid, thereby interfering with the jasmonate pathway and affecting the interaction outcome. These events may be key factors for Verticillium dahliaes in countering potato defenses and becoming notorious in the rhizosphere. Role of VdQase in rutin and quercetin utilization, overview
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enzyme-bound quercetin shields the FeII cofactor from interactions with the O2 mimic nitric oxide, tentatively suggesting that the reaction catalyzed by Bacillus (Fe-)quercetinase may proceed without direct interaction of dioxygen and metal ion, overview
additional information
Manual docking of the substrate quercetin into the active site showed that the different geometries of the copper site might be of catalytic importance
additional information
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Manual docking of the substrate quercetin into the active site showed that the different geometries of the copper site might be of catalytic importance
additional information
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synthesis of a series of flavonolate complexes as structural and functional models for the enzyme-substrate complexes of the active site of MII-containing quercetin 2,3-dioxygenase, structure analysis, overview
additional information
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synthetic routes to tris(imidazolyl)carboxylate ligands, {N,N-bis[(1-methyl-1H-imidazol-4-yl-kappaN3)methyl]glycinato-kappa2N,O}(dichloro)ferrate(1-), [3-(hydroxy-kappaO)-2-phenyl-4H-chromen-4-onato-kappaO4][bis(triphenylphosphane)]copper, (1Z,3Z)-N,N'-di(pyridin-2-yl)-1H-isoindole-1,3(2H)-diimine, chloro[(4-phenoxy-1,4,7-triazonan-1-yl-kappa3N1,N4,N7)acetato-kappaO]copper,2-{4-[hydroxy(di-1H-imidazol-4-yl)methyl]-1H-imidazol-2-yl}-2-methylpropanoic acid, and 2-(4-{bis[1-methyl-2-(propan-2-yl)-1H-imidazol-4-yl]methyl}-1-methyl-1H-imidazol-2-yl)-2-methylpropanoic acid, and representative metal complexes, which provide more accurate active site models for several classes of redox metalloenzymes, complex structures, detailed overview
additional information
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the mechanism which involves initial electron transfer from the divalent metal to O2, as proposed for the extradiol dioxygenases, requires that a MIII-superoxo state is thermodynamically accessible, overview
additional information
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for bacterial 2,4-QDs in which Co2+ or Ni2+ is employed as a cofactor, direct electron transfer from the activated Que to dioxygen (path C) may occur in analogy with cofactor-free dioxygenases. The subsequent radical coupling via intersystem crossing leads to an ESO2 complex, because Co2+ and Ni2+ are expected to be redox-inactive in this process
additional information
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residue Glu73 plays an important role in the catalytic reaction
additional information
Streptomyces sp. FLA / DSM 41951
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the mechanism which involves initial electron transfer from the divalent metal to O2, as proposed for the extradiol dioxygenases, requires that a MIII-superoxo state is thermodynamically accessible, overview
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