EzCatDB: D00842
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DB codeD00842
CATH domainDomain 12.60.120.10 : Jelly RollsCatalytic domain
Domain 22.60.120.10 : Jelly Rolls
E.C.1.13.11.24
CSA1gqg

CATH domainRelated DB codes (homologues)
2.60.120.10 : Jelly RollsS00145,S00155,D00843,T00255,M00216,T00101

Enzyme Name
UniProtKBKEGG

Q7SIC2
Protein nameQuercetin 2,3-dioxygenaseQuercetin 2,3-dioxygenase
Quercetinase
Flavonol 2,4-oxygenase
SynonymsEC 1.13.11.24
2,3QD
Quercetinase
Flavonol 2,4-dioxygenase


UniProtKB:Accession NumberQ7SIC2
Entry nameQDOI_ASPJA
ActivityQuercetin + O2 = 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate + CO + H+.
SubunitHomodimer.
Subcellular location
CofactorBinds 1 copper ion per subunit.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00070C00389C00007C04524C00237C00080
CompoundCopperquercetinO22-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoateCOH+
Typeheavy metalaromatic ring (only carbon atom),carbohydrateothersaromatic ring (only carbon atom),carbohydrate,carboxyl groupothersothers
ChEBI28694
30052
16243
15379
26689
27140
16068
17245
15378
PubChem23978
5280343
977
440370
281
1038
              
1gqgA01Bound:_CUUnboundUnboundUnboundUnbound 
1gqgB01Bound:_CUUnboundUnboundUnboundUnbound 
1gqgC01Bound:_CUUnboundUnboundUnboundUnbound 
1gqgD01Bound:_CUUnboundUnboundUnboundUnbound 
1gqhA02Bound:_CUAnalogue:KOJUnboundUnboundUnbound 
1gqhB02Bound:_CUAnalogue:KOJUnboundUnboundUnbound 
1gqhC02Bound:_CUAnalogue:KOJUnboundUnboundUnbound 
1gqhD02Bound:_CUAnalogue:KOJUnboundUnboundUnbound 
1h1iA01Bound:_CUBound:QUEUnboundUnboundUnbound 
1h1iB01Bound:_CUBound:QUEUnboundUnboundUnbound 
1h1iC01Bound:_CUBound:QUEUnboundUnboundUnbound 
1h1iD01Bound:_CUBound:QUEUnboundUnboundUnbound 
1h1mA02Bound:_CUAnalogue:KMPUnboundUnboundUnbound 
1h1mB02Bound:_CUAnalogue:KMPUnboundUnboundUnbound 
1h1mC02Bound:_CUAnalogue:KMPUnboundUnboundUnbound 
1h1mD02Bound:_CUAnalogue:KMPUnboundUnboundUnbound 
1juhA01Bound:_CUUnboundUnboundUnboundUnbound 
1juhB01Bound:_CUUnboundUnboundUnboundUnbound 
1juhC01Bound:_CUUnboundUnboundUnboundUnbound 
1juhD01Bound:_CUUnboundUnboundUnboundUnbound 
1gqgA02UnboundUnboundUnboundUnboundUnbound 
1gqgB02UnboundUnboundUnboundUnboundUnbound 
1gqgC02UnboundUnboundUnboundUnboundUnbound 
1gqgD02UnboundUnboundUnboundUnboundUnbound 
1gqhA01UnboundUnboundUnboundUnboundUnbound 
1gqhB01UnboundUnboundUnboundUnboundUnbound 
1gqhC01UnboundUnboundUnboundUnboundUnbound 
1gqhD01UnboundUnboundUnboundUnboundUnbound 
1h1iA02UnboundUnboundUnboundUnboundUnbound 
1h1iB02UnboundUnboundUnboundUnboundUnbound 
1h1iC02UnboundUnboundUnboundUnboundUnbound 
1h1iD02UnboundUnboundUnboundUnboundUnbound 
1h1mA01UnboundUnboundUnboundUnboundUnbound 
1h1mB01UnboundUnboundUnboundUnboundUnbound 
1h1mC01UnboundUnboundUnboundUnboundUnbound 
1h1mD01UnboundUnboundUnboundUnboundUnbound 
1juhA02UnboundUnboundUnboundUnboundUnbound 
1juhB02UnboundUnboundUnboundUnboundUnbound 
1juhC02UnboundUnboundUnboundUnboundUnbound 
1juhD02UnboundUnboundUnboundUnboundUnbound 

Active-site residues
resource
literature [1], [3], [5], [6], [10]
pdbCatalytic residuesCofactor-binding residues
          
1gqgA01GLU 73(Copper binding)
HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1gqgB01GLU 73(Copper binding)
HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1gqgC01GLU 73(Copper binding)
HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1gqgD01GLU 73(Copper binding)
HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1gqhA02GLU 73(Copper binding)
HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1gqhB02GLU 73(Copper binding)
HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1gqhC02GLU 73(Copper binding)
HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1gqhD02GLU 73(Copper binding)
HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1h1iA01GLU 73(Copper binding)
HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1h1iB01GLU 73(Copper binding)
HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1h1iC01GLU 73(Copper binding)
HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1h1iD01GLU 73(Copper binding)
HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1h1mA02GLU 73(Copper binding)
HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1h1mB02GLU 73(Copper binding)
HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1h1mC02GLU 73(Copper binding)
HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1h1mD02GLU 73(Copper binding)
HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1juhA01GLU 73(Copper binding)
HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1juhB01GLU 73(Copper binding)
HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1juhC01GLU 73(Copper binding)
HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1juhD01GLU 73(Copper binding)
HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1gqgA02                      
 
1gqgB02                      
 
1gqgC02                      
 
1gqgD02                      
 
1gqhA01                      
 
1gqhB01                      
 
1gqhC01                      
 
1gqhD01                      
 
1h1iA02                      
 
1h1iB02                      
 
1h1iC02                      
 
1h1iD02                      
 
1h1mA01                      
 
1h1mB01                      
 
1h1mC01                      
 
1h1mD01                      
 
1juhA02                      
 
1juhB02                      
 
1juhC02                      
 
1juhD02                      
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]p.7961
[4]Fig.5, p.7976
[5]Fig.4, p.16629-16630
[6]p.264-265
[10]Fig.3, p.782-784

references
[1]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
PubMed ID10876237
JournalNat Struct Biol
Year2000
Volume7
Pages542-6
AuthorsTitus GP, Mueller HA, Burgner J, Rodriguez De Cordoba S, Penalva MA, Timm DE
TitleCrystal structure of human homogentisate dioxygenase.
Related PDB1ey2,1eyb
Related UniProtKBQ93099
[2]
CommentsX-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
PubMed ID11062559
JournalNat Struct Biol
Year2000
Volume7
Pages1036-40
AuthorsWoo EJ, Dunwell JM, Goodenough PW, Marvier AC, Pickersgill RW
TitleGermin is a manganese containing homohexamer with oxalate oxidase and superoxide dismutase activities.
Related PDB1fi2
Related UniProtKBP45850
[3]
CommentsX-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH DIETHYLDITHIOCARBAMATE AND KOJIC ACID.
PubMed ID12069585
JournalBiochemistry
Year2002
Volume41
Pages7955-62
AuthorsSteiner RA, Kooter IM, Dijkstra BW
TitleFunctional 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.
Related PDB1gqg,1gqh
Related UniProtKBQ7SIC2
[4]
PubMed ID12069586
JournalBiochemistry
Year2002
Volume41
Pages7963-8
AuthorsSteiner RA, Meyer-Klaucke W, Dijkstra BW
TitleFunctional analysis of the copper-dependent quercetin 2,3-dioxygenase. 2. X-ray absorption studies of native enzyme and anaerobic complexes with the substrates quercetin and myricetin.
[5]
CommentsX-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) IN COMPLEX WITH KAEMPFEROL AND QUERCETIN.
PubMed ID12486225
JournalProc Natl Acad Sci U S A
Year2002
Volume99
Pages16625-30
AuthorsSteiner RA, Kalk KH, Dijkstra BW
TitleAnaerobic enzyme.substrate structures provide insight into the reaction mechanism of the copper-dependent quercetin 2,3-dioxygenase.
Related PDB1h1i,1h1m
Related UniProtKBQ7SIC2
[6]
CommentsX-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS), MUTAGENESIS OF GLU-73.
PubMed ID11839311
JournalStructure
Year2002
Volume10
Pages259-68
AuthorsFusetti F, Schroter KH, Steiner RA, van Noort PI, Pijning T, Rozeboom HJ, Kalk KH, Egmond MR, Dijkstra BW
TitleCrystal structure of the copper-containing quercetin 2,3-dioxygenase from Aspergillus japonicus.
Related PDB1juh
Related UniProtKBQ7SIC2
[7]
PubMed ID14741339
JournalFEBS Lett
Year2004
Volume557
Pages45-8
AuthorsBowater L, Fairhurst SA, Just VJ, Bornemann S
TitleBacillus subtilis YxaG is a novel Fe-containing quercetin 2,3-dioxygenase.
[8]
CommentsX-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
PubMed ID15628860
JournalBiochemistry
Year2005
Volume44
Pages193-201
AuthorsGopal B, Madan LL, Betz SF, Kossiakoff AA
TitleThe crystal structure of a quercetin 2,3-dioxygenase from Bacillus subtilis suggests modulation of enzyme activity by a change in the metal ion at the active site(s).
Related PDB1y3t
Related UniProtKBP42106
[9]
PubMed ID16411777
JournalBiochemistry
Year2006
Volume45
Pages1009-16
AuthorsSchaab MR, Barney BM, Francisco WA
TitleKinetic and spectroscopic studies on the quercetin 2,3-dioxygenase from Bacillus subtilis.
[10]
JournalCoord Chem Rev
Year2010
Volume254
Pages781-793
AuthorsPap JS, Kaizer J, Speier G
TitleModel systems for the CO-releasing flavonol 2,4-dioxygenase enzyme

comments
This enzyme belongs to the cupin superfamily.
This enzymes, Quercetin 2,3-dioxygenase (EC=1.13.11.24), is high similarity to Oxalate oxidase 1 (EC=1.2.3.4, S00145 in EzCatDB, literature [2]) and a counterpart enzyme from Bacillus (D00843 in EzCatDB).
According to the literature [3],[5] and [10], there are two alternative cordination forms fot the copper ion in this enzyme: (1) the cooper is ligated by three histidine residues and a water in a distorted tetrahedral geometry. (2) the copper is ligated by a glutamate residue along with the histidine residues and the water in a trigonal bipyramidal geometry. In substrate binding, the water can be replaced by the hydroxyl oxygen (O3 atom) of the substrate, quercetin.
Moreover, the glutamate residue (Glu73 in 1gqg) acts as a general base to deprotonate the O3 atom, leading to the radical formation at the C2 atom. This activation seems to allow it react with the triplet dioxygen (see [5] and [10]).

createdupdated
2010-04-222011-05-18
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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