D00843
type: Enzyme
cath: Jelly Rolls
ec: https://purl.uniprot.org/enzyme/1.13.11.24
uniprot: P42106
kegg enzyme: Quercetin 2,3-dioxygenase
kegg enzyme: Quercetinase
kegg enzyme: Flavonol 2,4-oxygenase
kegg cofactor: Iron
kegg cofactor: Copper
kegg cofactor: Manganese
kegg substrate: quercetin
kegg substrate: O2
kegg product: 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate
kegg product: CO
kegg product: H+
pdb: 1y3tA01
pdb: 1y3tB01
pdb: 2h0vA01
pdb: 2h0vB01
pdb: 1y3tA02
pdb: 1y3tB02
pdb: 2h0vA02
pdb: 2h0vB02
pdb bound state: Unbound
  compound: quercetin
  pdb: 1y3tA01
pdb bound state: Unbound
  compound: quercetin
  pdb: 1y3tB01
pdb bound state: Unbound
  compound: quercetin
  pdb: 2h0vA01
pdb bound state: Unbound
  compound: quercetin
  pdb: 2h0vB01
pdb bound state: Unbound
  compound: quercetin
  pdb: 1y3tA02
pdb bound state: Unbound
  compound: quercetin
  pdb: 1y3tB02
pdb bound state: Unbound
  compound: quercetin
  pdb: 2h0vA02
pdb bound state: Unbound
  compound: quercetin
  pdb: 2h0vB02
pdb bound state: Unbound
  compound: O2
  pdb: 1y3tA01
pdb bound state: Unbound
  compound: O2
  pdb: 1y3tB01
pdb bound state: Unbound
  compound: O2
  pdb: 2h0vA01
pdb bound state: Unbound
  compound: O2
  pdb: 2h0vB01
pdb bound state: Unbound
  compound: O2
  pdb: 1y3tA02
pdb bound state: Unbound
  compound: O2
  pdb: 1y3tB02
pdb bound state: Unbound
  compound: O2
  pdb: 2h0vA02
pdb bound state: Unbound
  compound: O2
  pdb: 2h0vB02
pdb bound state: Unbound
  compound: Copper
  pdb: 1y3tA01
pdb bound state: Unbound
  compound: Copper
  pdb: 1y3tB01
pdb bound state: Unbound
  compound: Copper
  pdb: 2h0vA01
pdb bound state: Unbound
  compound: Copper
  pdb: 2h0vB01
pdb bound state: Unbound
  compound: Copper
  pdb: 1y3tA02
pdb bound state: Unbound
  compound: Copper
  pdb: 1y3tB02
pdb bound state: Unbound
  compound: Copper
  pdb: 2h0vA02
pdb bound state: Unbound
  compound: Copper
  pdb: 2h0vB02
pdb bound state: Unbound
  compound: Manganese
  pdb: 1y3tA01
pdb bound state: Unbound
  compound: Manganese
  pdb: 1y3tB01
pdb bound state: Unbound
  compound: Manganese
  pdb: 2h0vA01
pdb bound state: Unbound
  compound: Manganese
  pdb: 2h0vB01
pdb bound state: Unbound
  compound: Manganese
  pdb: 1y3tA02
pdb bound state: Unbound
  compound: Manganese
  pdb: 1y3tB02
pdb bound state: Unbound
  compound: Manganese
  pdb: 2h0vA02
pdb bound state: Unbound
  compound: Manganese
  pdb: 2h0vB02
pdb bound state: Unbound
  compound: 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate
  pdb: 1y3tA01
pdb bound state: Unbound
  compound: 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate
  pdb: 1y3tB01
pdb bound state: Unbound
  compound: 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate
  pdb: 2h0vA01
pdb bound state: Unbound
  compound: 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate
  pdb: 2h0vB01
pdb bound state: Unbound
  compound: 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate
  pdb: 1y3tA02
pdb bound state: Unbound
  compound: 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate
  pdb: 1y3tB02
pdb bound state: Unbound
  compound: 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate
  pdb: 2h0vA02
pdb bound state: Unbound
  compound: 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate
  pdb: 2h0vB02
active site residues resources: 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.
active site residues resources: Crystal structure of the copper-containing quercetin 2,3-dioxygenase from Aspergillus japonicus.
active site residues resources: Bacillus subtilis YxaG is a novel Fe-containing quercetin 2,3-dioxygenase.
active site residues resources: Kinetic and spectroscopic studies on the quercetin 2,3-dioxygenase from Bacillus subtilis.
active site residues resources: Model systems for the CO-releasing flavonol 2,4-dioxygenase enzyme
active site residues resources: http://ezcatdb.cbrc.jp/EzCatDB/reference/D00843#11
references: Crystal structure of human homogentisate dioxygenase.
references: Germin is a manganese containing homohexamer with oxalate oxidase and superoxide dismutase activities.
references: 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.
references: 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.
references: Anaerobic enzyme.substrate structures provide insight into the reaction mechanism of the copper-dependent quercetin 2,3-dioxygenase.
references: Crystal structure of the copper-containing quercetin 2,3-dioxygenase from Aspergillus japonicus.
references: Bacillus subtilis YxaG is a novel Fe-containing quercetin 2,3-dioxygenase.
references: 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).
references: Kinetic and spectroscopic studies on the quercetin 2,3-dioxygenase from Bacillus subtilis.
references: Model systems for the CO-releasing flavonol 2,4-dioxygenase enzyme
comment: This enzyme from Bacillus is homologous to the counterpart enzyme from Aspergillus (fungi) (D00842 in EzCatDB), although it has been thought to use iron as a native cofactor unlike the homologous enzyme, which adopts copper as a cofactor (see [6]). However, according to the literature [7], [8] and [9], this enzyme may use manganese or copper as a cofactor. Thus, Cu2+, and Mn2+ were included as cofactor in this entry. Moreover, this enzyme is homologous to Oxalate oxidase 1 (EC=1.2.3.4, S00145 in EzCatDB) and homogentisate 1,2-dioxygenase (HGO), according to the literature [1] and [2]. This enzyme is composed of two similar domains with catalytic sites. However, it is not clear whether both the sites are used as catalytic site or only either of the site is used.

Jelly Rolls
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/2.60.120.10
catalytic domain: index.html

Iron
type: KeggCofactor
references: KEGG:C00023
compound type: heavy metal
references: CHEBI:18248
references: CHEBI:82664
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

Copper
type: KeggCofactor
references: KEGG:C00070
compound type: heavy metal
references: CHEBI:28694
references: CHEBI:30052
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

Manganese
type: KeggCofactor
references: KEGG:C00034
compound type: heavy metal
references: CHEBI:18291
references: CHEBI:35154
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

quercetin
type: KeggSubstrate
references: KEGG:C00389
compound type: aromatic ring (only carbon atom)
compound type: carbohydrate
references: CHEBI:16243
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

O2
type: KeggSubstrate
references: KEGG:C00007
compound type: others
references: CHEBI:15379
references: CHEBI:26689
references: CHEBI:27140
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate
type: KeggProduct
references: KEGG:C04524
compound type: aromatic ring (only carbon atom)
compound type: carbohydrate
compound type: carboxyl group
references: CHEBI:16068
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

CO
type: KeggProduct
references: KEGG:C00237
compound type: others
references: CHEBI:17245
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

H+
type: KeggProduct
references: KEGG:C00080
compound type: others
references: CHEBI:15378
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

1y3tA01
type: Pdb
references: 1y3t
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1y3t
catalytic residue: GLU 241
cofactor binding residue: HIS 234;HIS 236;GLU 241;HIS 275(Iron-2 binding)

1y3tB01
type: Pdb
references: 1y3t
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1y3t
catalytic residue: GLU 241
cofactor binding residue: HIS 234;HIS 236;GLU 241;HIS 275(Iron-2 binding)

2h0vA01
type: Pdb
references: 2h0v
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2h0v
catalytic residue: GLU 241
cofactor binding residue: HIS 234;HIS 236;GLU 241;HIS 275(Iron-2 binding)

2h0vB01
type: Pdb
references: 2h0v
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2h0v
catalytic residue: GLU 241
cofactor binding residue: HIS 234;HIS 236;GLU 241;HIS 275(Iron-2 binding)

1y3tA02
type: Pdb
references: 1y3t
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1y3t
catalytic residue: GLU 69
cofactor binding residue: HIS 62;HIS 64;GLU 69;HIS 103(Iron-1 binding)

1y3tB02
type: Pdb
references: 1y3t
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1y3t
catalytic residue: GLU 69
cofactor binding residue: HIS 62;HIS 64;GLU 69;HIS 103(Iron-1 binding)

2h0vA02
type: Pdb
references: 2h0v
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2h0v
catalytic residue: GLU 69
cofactor binding residue: HIS 62;HIS 64;GLU 69;HIS 103(Iron-1 binding)

2h0vB02
type: Pdb
references: 2h0v
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2h0v
catalytic residue: GLU 69
cofactor binding residue: HIS 62;HIS 64;GLU 69;HIS 103(Iron-1 binding)

Crystal structure of human homogentisate dioxygenase.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
references: http://www.ncbi.nlm.nih.gov/pubmed/10876237
journal: Nat Struct Biol
volume: 7
pages: 542-6
published year: 2000
authors:
  item: Titus GP
  item: Mueller HA
  item: Burgner J
  item: Rodriguez De Cordoba S
  item: Penalva MA
  item: Timm DE
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q93099

Germin is a manganese containing homohexamer with oxalate oxidase and superoxide dismutase activities.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
references: http://www.ncbi.nlm.nih.gov/pubmed/11062559
journal: Nat Struct Biol
volume: 7
pages: 1036-40
published year: 2000
authors:
  item: Woo EJ
  item: Dunwell JM
  item: Goodenough PW
  item: Marvier AC
  item: Pickersgill RW
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P45850

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.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH DIETHYLDITHIOCARBAMATE AND KOJIC ACID.
references: http://www.ncbi.nlm.nih.gov/pubmed/12069585
journal: Biochemistry
volume: 41
pages: 7955-62
published year: 2002
authors:
  item: Steiner RA
  item: Kooter IM
  item: Dijkstra BW
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q7SIC2

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.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12069586
journal: Biochemistry
volume: 41
pages: 7963-8
published year: 2002
authors:
  item: Steiner RA
  item: Meyer-Klaucke W
  item: Dijkstra BW

Anaerobic enzyme.substrate structures provide insight into the reaction mechanism of the copper-dependent quercetin 2,3-dioxygenase.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) IN COMPLEX WITH KAEMPFEROL AND QUERCETIN.
references: http://www.ncbi.nlm.nih.gov/pubmed/12486225
journal: Proc Natl Acad Sci U S A
volume: 99
pages: 16625-30
published year: 2002
authors:
  item: Steiner RA
  item: Kalk KH
  item: Dijkstra BW
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q7SIC2

Crystal structure of the copper-containing quercetin 2,3-dioxygenase from Aspergillus japonicus.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS), MUTAGENESIS OF GLU-73.
references: http://www.ncbi.nlm.nih.gov/pubmed/11839311
journal: Structure
volume: 10
pages: 259-68
published year: 2002
authors:
  item: Fusetti F
  item: Schroter KH
  item: Steiner RA
  item: van Noort PI
  item: Pijning T
  item: Rozeboom HJ
  item: Kalk KH
  item: Egmond MR
  item: Dijkstra BW
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q7SIC2

Bacillus subtilis YxaG is a novel Fe-containing quercetin 2,3-dioxygenase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/14741339
journal: FEBS Lett
volume: 557
pages: 45-8
published year: 2004
authors:
  item: Bowater L
  item: Fairhurst SA
  item: Just VJ
  item: Bornemann S

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).
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
references: http://www.ncbi.nlm.nih.gov/pubmed/15628860
journal: Biochemistry
volume: 44
pages: 193-201
published year: 2005
authors:
  item: Gopal B
  item: Madan LL
  item: Betz SF
  item: Kossiakoff AA
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P42106

Kinetic and spectroscopic studies on the quercetin 2,3-dioxygenase from Bacillus subtilis.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/16411777
journal: Biochemistry
volume: 45
pages: 1009-16
published year: 2006
authors:
  item: Schaab MR
  item: Barney BM
  item: Francisco WA

Model systems for the CO-releasing flavonol 2,4-dioxygenase enzyme
type: BibliographicResource
journal: Coord Chem Rev
volume: 254
pages: 781-793
published year: 2010
authors:
  item: Pap JS
  item: Kaizer J
  item: Speier G

ReferenceForCatalyticMechanism
reference index: 3
reference section: p.7961

ReferenceForCatalyticMechanism
reference index: 4
reference section: Fig.5

ReferenceForCatalyticMechanism
reference index: 5
reference section: Fig.4, p.16629-16630

ReferenceForCatalyticMechanism
reference index: 8
reference section: p.196

ReferenceForCatalyticMechanism
reference index: 9
reference section: Scheme 2, p.1012-1014

ReferenceForCatalyticMechanism
reference index: 10
reference section: Fig.3, p.782-784