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PDBsum entry 1gqg

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1gqg
Jmol
Contents
Protein chains
333 a.a. *
Ligands
DCD ×4
NAG ×13
NAG-NAG ×3
BMA ×2
Metals
_CU ×4
Waters ×1444
* Residue conservation analysis
PDB id:
1gqg
Name: Oxidoreductase
Title: Quercetin 2,3-dioxygenase in complex with the inhibitor diethyldithiocarbamate
Structure: Quercetin 2,3-dioxygenase. Chain: a, b, c, d. Engineered: yes
Source: Aspergillus japonicus. Organism_taxid: 34381. Expressed in: aspergillus awamori. Expression_system_taxid: 105351
Biol. unit: Dimer (from PDB file)
Resolution:
1.70Å     R-factor:   0.162     R-free:   0.183
Authors: R.A.Steiner,B.W.Dijkstra
Key ref:
R.A.Steiner et al. (2002). 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. Biochemistry, 41, 7955-7962. PubMed id: 12069585 DOI: 10.1021/bi0159736
Date:
23-Nov-01     Release date:   21-Jun-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q7SIC2  (QDOI_ASPJA) -  Quercetin 2,3-dioxygenase
Seq:
Struc:
350 a.a.
333 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.13.11.24  - Quercetin 2,3-dioxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Quercetin 2,3-Dioxygenase
      Reaction: Quercetin + O2 = 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate + CO + H+
Quercetin
Bound ligand (Het Group name = BMA)
matches with 43.48% similarity
+ O(2)
= 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate
+ CO
+ H(+)
      Cofactor: Fe cation or Cu cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     oxidoreductase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi0159736 Biochemistry 41:7955-7962 (2002)
PubMed id: 12069585  
 
 
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.
R.A.Steiner, I.M.Kooter, B.W.Dijkstra.
 
  ABSTRACT  
 
The crystal structures of the copper-dependent Aspergillus japonicus quercetin 2,3-dioxygenase (2,3QD) complexed with the inhibitors diethyldithiocarbamate (DDC) and kojic acid (KOJ) are reported at 1.70 and 2.15 A resolution, respectively. Both inhibitors asymmetrically chelate the metal center and assume a common orientation in the active site cleft. Their molecular plane blocks access to the inner portion of the cavity which is lined by the side chains of residues Met51, Thr53, Phe75, Phe114, and Met123 and which is believed to bind the flavonol B-ring of the natural substrate. The binding of the inhibitors brings order into the mixed coordination observed in the native enzyme. DDC and KOJ induce a single conformation of the Glu73 side chain, although in different ways. In the presence of DDC, Glu73 is detached from the copper ion with its carboxylate moiety pointing away from the active site cavity. In contrast, when KOJ is bound, Glu73 ligates the Cu ion through its O(epsilon)(1) atom with a monodentate geometry. Compared to the native coordinating conformation, this conformation is approximately 90 degrees rotated about the chi(3) angle. This latter Glu73 conformation is compatible with the presence of a bound substrate.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20711196 I.Miyazaki, S.Simizu, H.Okumura, S.Takagi, and H.Osada (2010).
A small-molecule inhibitor shows that pirin regulates migration of melanoma cells.
  Nat Chem Biol, 6, 667-673.
PDB code: 3acl
20419500 S.Tranchimand, P.Brouant, and G.Iacazio (2010).
The rutin catabolic pathway with special emphasis on quercetinase.
  Biodegradation, 21, 833-859.  
  16754979 I.Matera, M.Ferraroni, S.Bürger, A.Stolz, and F.Briganti (2006).
Preliminary crystallographic analysis of salicylate 1,2-dioxygenase from Pseudaminobacter salicylatoxidans.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 553-555.  
17119644 R.Bentley (2006).
From miso, saké and shoyu to cosmetics: a century of science for kojic acid.
  Nat Prod Rep, 23, 1046-1062.  
15778971 D.G.Covell, A.Wallqvist, R.Huang, N.Thanki, A.A.Rabow, and X.J.Lu (2005).
Linking tumor cell cytotoxicity to mechanism of drug action: an integrated analysis of gene expression, small-molecule screening and structural databases.
  Proteins, 59, 403-433.  
15951572 M.Adams, and Z.Jia (2005).
Structural and biochemical analysis reveal pirins to possess quercetinase activity.
  J Biol Chem, 280, 28675-28682.
PDB code: 1tq5
16114032 S.Raymond, A.Tocilj, E.Ajamian, Y.Li, M.N.Hung, A.Matte, and M.Cygler (2005).
Crystal structure of ureidoglycolate hydrolase (AllA) from Escherichia coli O157:H7.
  Proteins, 61, 454-459.
PDB code: 1yqc
14645093 M.Fittipaldi, R.A.Steiner, M.Matsushita, B.W.Dijkstra, E.J.Groenen, and M.Huber (2003).
Single-crystal EPR study at 95 GHz of the type 2 copper site of the inhibitor-bound quercetin 2,3-dioxygenase.
  Biophys J, 85, 4047-4054.  
12071961 I.M.Kooter, R.A.Steiner, B.W.Dijkstra, P.I.van Noort, M.R.Egmond, and M.Huber (2002).
EPR characterization of the mononuclear Cu-containing Aspergillus japonicus quercetin 2,3-dioxygenase reveals dramatic changes upon anaerobic binding of substrates.
  Eur J Biochem, 269, 2971-2979.  
12486225 R.A.Steiner, K.H.Kalk, and B.W.Dijkstra (2002).
Anaerobic enzyme.substrate structures provide insight into the reaction mechanism of the copper-dependent quercetin 2,3-dioxygenase.
  Proc Natl Acad Sci U S A, 99, 16625-16630.
PDB codes: 1h1i 1h1m
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.