DB code: D00842

CATH domain 2.60.120.10 : Jelly Rolls Catalytic domain
2.60.120.10 : Jelly Rolls
E.C. 1.13.11.24
CSA 1gqg
M-CSA 1gqg
MACiE

CATH domain Related DB codes (homologues)
2.60.120.10 : Jelly Rolls S00145 S00155 D00843 T00255 M00216 T00101

Uniprot Enzyme Name
UniprotKB Protein name Synonyms
Q7SIC2 Quercetin 2,3-dioxygenase
EC 1.13.11.24
2,3QD
Quercetinase
Flavonol 2,4-dioxygenase

KEGG enzyme name
Quercetin 2,3-dioxygenase
Quercetinase
Flavonol 2,4-oxygenase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q7SIC2 QDOI_ASPJA Quercetin + O2 = 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate + CO + H+. Homodimer. Binds 1 copper ion per subunit.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00070 C00389 C00007 C04524 C00237 C00080
E.C.
Compound Copper quercetin O2 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate CO H+
Type heavy metal aromatic ring (only carbon atom),carbohydrate others aromatic ring (only carbon atom),carbohydrate,carboxyl group others others
ChEBI 28694
30052
16243
15379
26689
27140
16068
17245
15378
PubChem 23978
5280343
977
440370
281
1038
1gqgA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CU Unbound Unbound Unbound Unbound
1gqgB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CU Unbound Unbound Unbound Unbound
1gqgC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CU Unbound Unbound Unbound Unbound
1gqgD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CU Unbound Unbound Unbound Unbound
1gqhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CU Analogue:KOJ Unbound Unbound Unbound
1gqhB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CU Analogue:KOJ Unbound Unbound Unbound
1gqhC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CU Analogue:KOJ Unbound Unbound Unbound
1gqhD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CU Analogue:KOJ Unbound Unbound Unbound
1h1iA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CU Bound:QUE Unbound Unbound Unbound
1h1iB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CU Bound:QUE Unbound Unbound Unbound
1h1iC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CU Bound:QUE Unbound Unbound Unbound
1h1iD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CU Bound:QUE Unbound Unbound Unbound
1h1mA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CU Analogue:KMP Unbound Unbound Unbound
1h1mB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CU Analogue:KMP Unbound Unbound Unbound
1h1mC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CU Analogue:KMP Unbound Unbound Unbound
1h1mD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CU Analogue:KMP Unbound Unbound Unbound
1juhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CU Unbound Unbound Unbound Unbound
1juhB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CU Unbound Unbound Unbound Unbound
1juhC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CU Unbound Unbound Unbound Unbound
1juhD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_CU Unbound Unbound Unbound Unbound
1gqgA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1gqgB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1gqgC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1gqgD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1gqhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1gqhB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1gqhC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1gqhD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1h1iA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1h1iB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1h1iC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1h1iD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1h1mA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1h1mB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1h1mC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1h1mD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1juhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1juhB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1juhC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1juhD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [1], [3], [5], [6], [10]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1gqgA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73(Copper binding) HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1gqgB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73(Copper binding) HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1gqgC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73(Copper binding) HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1gqgD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73(Copper binding) HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1gqhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73(Copper binding) HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1gqhB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73(Copper binding) HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1gqhC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73(Copper binding) HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1gqhD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73(Copper binding) HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1h1iA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73(Copper binding) HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1h1iB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73(Copper binding) HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1h1iC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73(Copper binding) HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1h1iD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73(Copper binding) HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1h1mA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73(Copper binding) HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1h1mB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73(Copper binding) HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1h1mC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73(Copper binding) HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1h1mD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73(Copper binding) HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1juhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73(Copper binding) HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1juhB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73(Copper binding) HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1juhC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73(Copper binding) HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1juhD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 73(Copper binding) HIS 66;HIS 68;GLU 73;HIS 112(Copper binding)
1gqgA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1gqgB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1gqgC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1gqgD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1gqhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1gqhB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1gqhC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1gqhD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1h1iA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1h1iB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1h1iC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1h1iD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1h1mA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1h1mB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1h1mC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1h1mD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1juhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1juhB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1juhC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1juhD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. 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]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID
PubMed ID 10876237
Journal Nat Struct Biol
Year 2000
Volume 7
Pages 542-6
Authors Titus GP, Mueller HA, Burgner J, Rodriguez De Cordoba S, Penalva MA, Timm DE
Title Crystal structure of human homogentisate dioxygenase.
Related PDB 1ey2 1eyb
Related UniProtKB Q93099
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
Medline ID
PubMed ID 11062559
Journal Nat Struct Biol
Year 2000
Volume 7
Pages 1036-40
Authors Woo EJ, Dunwell JM, Goodenough PW, Marvier AC, Pickersgill RW
Title Germin is a manganese containing homohexamer with oxalate oxidase and superoxide dismutase activities.
Related PDB 1fi2
Related UniProtKB P45850
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH DIETHYLDITHIOCARBAMATE AND KOJIC ACID.
Medline ID
PubMed ID 12069585
Journal Biochemistry
Year 2002
Volume 41
Pages 7955-62
Authors Steiner RA, Kooter IM, Dijkstra BW
Title 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.
Related PDB 1gqg 1gqh
Related UniProtKB Q7SIC2
[4]
Resource
Comments
Medline ID
PubMed ID 12069586
Journal Biochemistry
Year 2002
Volume 41
Pages 7963-8
Authors Steiner RA, Meyer-Klaucke W, Dijkstra BW
Title Functional 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.
Related PDB
Related UniProtKB
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) IN COMPLEX WITH KAEMPFEROL AND QUERCETIN.
Medline ID
PubMed ID 12486225
Journal Proc Natl Acad Sci U S A
Year 2002
Volume 99
Pages 16625-30
Authors Steiner RA, Kalk KH, Dijkstra BW
Title Anaerobic enzyme.substrate structures provide insight into the reaction mechanism of the copper-dependent quercetin 2,3-dioxygenase.
Related PDB 1h1i 1h1m
Related UniProtKB Q7SIC2
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS), MUTAGENESIS OF GLU-73.
Medline ID
PubMed ID 11839311
Journal Structure
Year 2002
Volume 10
Pages 259-68
Authors Fusetti F, Schroter KH, Steiner RA, van Noort PI, Pijning T, Rozeboom HJ, Kalk KH, Egmond MR, Dijkstra BW
Title Crystal structure of the copper-containing quercetin 2,3-dioxygenase from Aspergillus japonicus.
Related PDB 1juh
Related UniProtKB Q7SIC2
[7]
Resource
Comments
Medline ID
PubMed ID 14741339
Journal FEBS Lett
Year 2004
Volume 557
Pages 45-8
Authors Bowater L, Fairhurst SA, Just VJ, Bornemann S
Title Bacillus subtilis YxaG is a novel Fe-containing quercetin 2,3-dioxygenase.
Related PDB
Related UniProtKB
[8]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
Medline ID
PubMed ID 15628860
Journal Biochemistry
Year 2005
Volume 44
Pages 193-201
Authors Gopal B, Madan LL, Betz SF, Kossiakoff AA
Title The 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 PDB 1y3t
Related UniProtKB P42106
[9]
Resource
Comments
Medline ID
PubMed ID 16411777
Journal Biochemistry
Year 2006
Volume 45
Pages 1009-16
Authors Schaab MR, Barney BM, Francisco WA
Title Kinetic and spectroscopic studies on the quercetin 2,3-dioxygenase from Bacillus subtilis.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID
Journal Coord Chem Rev
Year 2010
Volume 254
Pages 781-793
Authors Pap JS, Kaizer J, Speier G
Title Model systems for the CO-releasing flavonol 2,4-dioxygenase enzyme
Related PDB
Related UniProtKB

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]).

Created Updated
2010-04-22 2011-05-18