DB code: D00843

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

CATH domain Related DB codes (homologues)
2.60.120.10 : Jelly Rolls S00145 S00155 D00842 T00255 M00216 T00101

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P42106 Quercetin 2,3-dioxygenase
Quercetinase
EC 1.13.11.24
Flavonol 2,4-dioxygenase
NP_391878.2 (Protein)
NC_000964.3 (DNA/RNA sequence)
PF07883 (Cupin_2)
[Graphical View]

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

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P42106 QDOI_BACSU Quercetin + O2 = 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate + CO + H+. Homodimer. Binds 2 Fe2+ ions per subunit.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00023 C00070 C00034 C00389 C00007 C04524 C00237 C00080
E.C.
Compound Iron Copper Manganese quercetin O2 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate CO H+
Type heavy metal heavy metal heavy metal aromatic ring (only carbon atom),carbohydrate others aromatic ring (only carbon atom),carbohydrate,carboxyl group others others
ChEBI 18248
82664
28694
30052
18291
35154
16243
15379
26689
27140
16068
17245
15378
PubChem 23925
23978
23930
5280343
977
440370
281
1038
1y3tA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Unbound Unbound Unbound Unbound Unbound Unbound
1y3tB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Unbound Unbound Unbound Unbound Unbound Unbound
2h0vA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Unbound Unbound Unbound Unbound Unbound Unbound
2h0vB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Unbound Unbound Unbound Unbound Unbound Unbound
1y3tA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Unbound Unbound Unbound Unbound Unbound Unbound
1y3tB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Unbound Unbound Unbound Unbound Unbound Unbound
2h0vA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Unbound Unbound Unbound Unbound Unbound Unbound
2h0vB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [3], [5], [6], [8], [9], [10]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1y3tA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 241 HIS 234;HIS 236;GLU 241;HIS 275(Iron-2 binding)
1y3tB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 241 HIS 234;HIS 236;GLU 241;HIS 275(Iron-2 binding)
2h0vA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 241 HIS 234;HIS 236;GLU 241;HIS 275(Iron-2 binding)
2h0vB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 241 HIS 234;HIS 236;GLU 241;HIS 275(Iron-2 binding)
1y3tA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 69 HIS 62;HIS 64;GLU 69;HIS 103(Iron-1 binding)
1y3tB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 69 HIS 62;HIS 64;GLU 69;HIS 103(Iron-1 binding)
2h0vA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 69 HIS 62;HIS 64;GLU 69;HIS 103(Iron-1 binding)
2h0vB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 69 HIS 62;HIS 64;GLU 69;HIS 103(Iron-1 binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
p.7961
[4]
Fig.5
[5]
Fig.4, p.16629-16630
[8]
p.196
[9]
Scheme 2, p.1012-1014
[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 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.

Created Updated
2010-04-22 2011-05-12