EzCatDB: D00843
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DB codeD00843
CATH domainDomain 12.60.120.10 : Jelly RollsCatalytic domain
Domain 22.60.120.10 : Jelly RollsCatalytic domain
E.C.1.13.11.24

CATH domainRelated DB codes (homologues)
2.60.120.10 : Jelly RollsS00145,S00155,D00842,T00255,M00216,T00101

Enzyme Name
UniProtKBKEGG

P42106
Protein nameQuercetin 2,3-dioxygenaseQuercetin 2,3-dioxygenase
Quercetinase
Flavonol 2,4-oxygenase
SynonymsQuercetinase
EC 1.13.11.24
Flavonol 2,4-dioxygenase
RefSeqNP_391878.2 (Protein)
NC_000964.3 (DNA/RNA sequence)
PfamPF07883 (Cupin_2)
[Graphical view]


UniProtKB:Accession NumberP42106
Entry nameQDOI_BACSU
ActivityQuercetin + O2 = 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate + CO + H+.
SubunitHomodimer.
Subcellular location
CofactorBinds 2 Fe2+ ions per subunit.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00023C00070C00034C00389C00007C04524C00237C00080
CompoundIronCopperManganesequercetinO22-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoateCOH+
Typeheavy metalheavy metalheavy metalaromatic ring (only carbon atom),carbohydrateothersaromatic ring (only carbon atom),carbohydrate,carboxyl groupothersothers
ChEBI18248
82664
28694
30052
18291
35154
16243
27140
26689
15379
16068
17245
15378
PubChem23925
23978
23930
5280343
977
440370
281
1038
                
1y3tA01Bound:_FEUnboundUnboundUnboundUnboundUnboundUnbound 
1y3tB01Bound:_FEUnboundUnboundUnboundUnboundUnboundUnbound 
2h0vA01Bound:_FEUnboundUnboundUnboundUnboundUnboundUnbound 
2h0vB01Bound:_FEUnboundUnboundUnboundUnboundUnboundUnbound 
1y3tA02Bound:_FEUnboundUnboundUnboundUnboundUnboundUnbound 
1y3tB02Bound:_FEUnboundUnboundUnboundUnboundUnboundUnbound 
2h0vA02Bound:_FEUnboundUnboundUnboundUnboundUnboundUnbound 
2h0vB02Bound:_FEUnboundUnboundUnboundUnboundUnboundUnbound 

Active-site residues
resource
literature [3], [5], [6], [8], [9], [10]
pdbCatalytic residuesCofactor-binding residues
          
1y3tA01GLU 241
HIS 234;HIS 236;GLU 241;HIS 275(Iron-2 binding)
1y3tB01GLU 241
HIS 234;HIS 236;GLU 241;HIS 275(Iron-2 binding)
2h0vA01GLU 241
HIS 234;HIS 236;GLU 241;HIS 275(Iron-2 binding)
2h0vB01GLU 241
HIS 234;HIS 236;GLU 241;HIS 275(Iron-2 binding)
1y3tA02GLU  69
HIS  62;HIS  64;GLU  69;HIS 103(Iron-1 binding)
1y3tB02GLU  69
HIS  62;HIS  64;GLU  69;HIS 103(Iron-1 binding)
2h0vA02GLU  69
HIS  62;HIS  64;GLU  69;HIS 103(Iron-1 binding)
2h0vB02GLU  69
HIS  62;HIS  64;GLU  69;HIS 103(Iron-1 binding)

References for Catalytic Mechanism
ReferencesSectionsNo. 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]
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 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.

createdupdated
2010-04-222011-05-12


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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