1JUH | pdb_00001juh

Crystal Structure of Quercetin 2,3-dioxygenase

PDB DOI: https://doi.org/10.2210/pdb1JUH/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aspergillus japonicus
Mutation(s): No

Deposited: 2001-08-24 Released: 2002-05-22
Deposition Author(s): Fusetti, F., Schroeter, K.H., Steiner, R.A., Dijkstra, B.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.189 (Depositor), 0.204 (DCC)
R-Value Work:
0.162 (Depositor), 0.179 (DCC)
R-Value Observed:
0.162 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of the copper-containing quercetin 2,3-dioxygenase from Aspergillus japonicus.

Fusetti, F., Schroter, K.H., Steiner, R.A., van Noort, P.I., Pijning, T., Rozeboom, H.J., Kalk, K.H., Egmond, M.R., Dijkstra, B.W.

(2002) Structure 10: 259-268

PubMed: 11839311 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(02)00704-9
Primary Citation Related Structures:
1JUH

PubMed Abstract:
Quercetin 2,3-dioxygenase is a copper-containing enzyme that catalyzes the insertion of molecular oxygen into polyphenolic flavonols. Dioxygenation catalyzed by iron-containing enzymes has been studied extensively, but dioxygenases employing other metal cofactors are poorly understood. We determined the crystal structure of quercetin 2,3-dioxygenase at 1.6 A resolution. The enzyme forms homodimers, which are stabilized by an N-linked heptasaccharide at the dimer interface. The mononuclear type 2 copper center displays two distinct geometries: a distorted tetrahedral coordination, formed by His66, His68, His112, and a water molecule, and a distorted trigonal bipyramidal environment, which additionally comprises Glu73. Manual docking of the substrate quercetin into the active site showed that the different geometries of the copper site might be of catalytic importance.

Organizational Affiliation

Laboratory of Biophysical Chemistry, Department of Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

Macromolecule Content

Total Structure Weight: 160.11 kDa
Atom Count: 12,719
Modeled Residue Count: 1,337
Deposited Residue Count: 1,400
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
quercetin 2,3-dioxygenase	A, B, C, D	350	Aspergillus japonicus	Mutation(s): 0 EC: 1.13.11.24
UniProt
Find proteins for Q7SIC2 (Aspergillus japonicus) Explore Q7SIC2 Go to UniProtKB: Q7SIC2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7SIC2
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	7		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G07617FP GlyCosmos: G07617FP GlyGen: G07617FP

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	4		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	4		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	2		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain YA [auth D] SDF format, chain Y [auth B] SDF format, chain XA [auth D] SDF format, chain X [auth B] SDF format, chain WA [auth D] SDF format, chain W [auth B] SDF format, chain L [auth A] SDF format, chain KA [auth C] SDF format, chain K [auth A] SDF format, chain JA [auth C] SDF format, chain J [auth A] SDF format, chain IA [auth C] SDF format, chain I [auth A] MOL2 format, chain YA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain I [auth A] mmCIF format, chain YA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain I [auth A]	I [auth A] IA [auth C] J [auth A] JA [auth C] K [auth A] I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], W [auth B], WA [auth D], X [auth B], XA [auth D], Y [auth B], YA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Interactions & Density Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain ZA [auth D] SDF format, chain Z [auth B] SDF format, chain M [auth A] SDF format, chain LA [auth C] MOL2 format, chain ZA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth C] mmCIF format, chain ZA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth C]	LA [auth C], M [auth A], Z [auth B], ZA [auth D]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain LA [auth C] Focus chain M [auth A] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain LA [auth C] Focus chain M [auth A] Focus chain Z [auth B] Focus chain ZA [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain VA [auth C] SDF format, chain V [auth A] SDF format, chain UA [auth C] SDF format, chain U [auth A] SDF format, chain TA [auth C] SDF format, chain T [auth A] SDF format, chain SA [auth C] SDF format, chain S [auth A] SDF format, chain RA [auth C] SDF format, chain R [auth A] SDF format, chain QA [auth C] SDF format, chain Q [auth A] SDF format, chain PA [auth C] SDF format, chain P [auth A] SDF format, chain OA [auth C] SDF format, chain O [auth A] SDF format, chain NA [auth C] SDF format, chain N [auth A] SDF format, chain MA [auth C] SDF format, chain HA [auth B] SDF format, chain GA [auth B] SDF format, chain FA [auth B] SDF format, chain EB [auth D] SDF format, chain EA [auth B] SDF format, chain DB [auth D] SDF format, chain DA [auth B] SDF format, chain CB [auth D] SDF format, chain CA [auth B] SDF format, chain BB [auth D] SDF format, chain BA [auth B] SDF format, chain AB [auth D] SDF format, chain AA [auth B] MOL2 format, chain VA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain AA [auth B] mmCIF format, chain VA [auth C] mmCIF format, chain V [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain EB [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain DB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain CB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain BB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain AA [auth B]	AA [auth B] AB [auth D] BA [auth B] BB [auth D] CA [auth B] AA [auth B], AB [auth D], BA [auth B], BB [auth D], CA [auth B], CB [auth D], DA [auth B], DB [auth D], EA [auth B], EB [auth D], FA [auth B], GA [auth B], HA [auth B], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth A], VA [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.189 (Depositor), 0.204 (DCC)
R-Value Work: 0.162 (Depositor), 0.179 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.55	α = 90
b = 55.78	β = 98.31
c = 123.68	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
DM	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2002-05-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-05-22
Type: Initial release
Version 1.1: 2008-04-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2018-10-03
Changes: Data collection
Version 1.4: 2020-01-22
Changes: Advisory, Database references, Derived calculations
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-11-20
Changes: Data collection, Database references, Structure summary