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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1gqg
Original Entry
Quercetin 2,3-dioxygenase
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Overview of all sites for 1gqg
Homologues of 1gqg
Entries for UniProt/Swiss-Prot: Q7SIC2
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PDB entry: 1gqg
PDBsum entry: 1gqg
UniProt/Swiss-Prot: Q7SIC2
IntEnz entry:
Literature Report:
Quercetin 2,3-dioxygenase is a copper-dependent enzyme that catalyses the reaction of dioxygen with quercin (3,5,7,3',4'-pentahydroxy flavone). Dioxygenases are enzymes that catalyses the incorporation of both atoms of molecular oxygen into organic substrates, most notably during the degradation of aromatic compounds. They typically use a metal ion to circumvent the spin barrier that prevents the direct reaction of the triplet ground state of dioxygen with singlet-state organic compounds. In most of the well-studied dioxygenases, the metal used is iron; quercetin 2,3-dioxygenase is the only known member of this family to use copper.
Quercetin 2,3-dioxygenase uses a Cu(II) ion to avoid problems of spin associated with reactions involving dioxygen. In the first step, the C3 hydroxyl of the substrate coordinates the Cu(II) and transfers its proton to Glu 73. Dioxygen must now bind to this complex. The ground state [Cu(II)-substrate] binds dioxygen quite poorly, and the low-lying excited state [Cu(I)-substrate(radical)] is the acceptor instead. Recent theoretical calculations suggest that dioxygen binds to the Cu(I) of this state rather than to the substrate radical. The resulting dioxygen adduct (with three unpaired spins) is now well set up for attack by the peroxy radical on the C2 radical of the substrate, with formation of a C2-O bond.

Next, the peroxide oxygen attached to the copper forms a second C-O bond with C4, concurrent with breaking of the C4 carbonyl pi bond and bond formation between the C4 carbonyl oxygen and the copper. Glu 73 provides electrostatic stabilisation by shifting its hydrogen bond donation from the C3 substrate oxygen to the C4 substrate oxygen.

The bridging peroxide O-O bond is now cleaved, with simultaneous cleavage of the C3-C2 and C3-C4 bonds to release C3 as carbon monoxide and form a new ketone at C2 and carboxylate (still coordinated to copper) at C4. Finally, the proton stored on Glu 73 is transferred to the C4 carboxylate, and the product then leaves.

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Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLUA 73 73Sidechain
ElectrostaticTransition state
Accepts proton from C3 hydroxyl of substrate. Acts as a hydrogen bond donor to the C3 and later the C4 substrate oxygens.
Evidence from paper Evidence concerns Evidence type
PubMed ID 15360243 Current protein Computer modelling
PubMed ID 12069585 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 12069585 Current protein Mutagenesis of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
CUA1352 0
ElectrostaticTransition state
Electron donor/acceptorSubstrate
Coordinates the substrate C3 hydroxyl group and allows deprotonation of this group by Glu 73. Allows formation of a radical complex that can react with dioxygen. Accepts spin from dioxygen to avoid the need for any spin-orbit-induced spin transition. Later coordinates the C4 carbonyl oxygen as C4 is attacked by a peroxide oxygen.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12069585 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 12069585 Current protein Ligand is essential for catalysis
PubMed ID 15360243 Current protein Computer modelling
Functional analysis of the copper-dependent quercetin 2,3-dioxygenase. 1. Ligand-induced coordination changes probed by X-ray crystallography: inhibition, ordering effect, and mechanistic insights.
R. A. Steiner and I. M. Kooter and B. W. Dijkstra
Biochemistry 41, (25) 7955-62, (2002).
Hybrid DFT study of the mechanism of quercetin 2,3-dioxygenase.
P. E. Siegbahn
Inorg Chem 43, (19) 5944-53, (2004).
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