6GSG | pdb_00006gsg

Crystal structure of Aspergillus oryzae catechol oxidase complexed with resorcinol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 
    0.212 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Unraveling Substrate Specificity and Catalytic Promiscuity of Aspergillus oryzae Catechol Oxidase.

Penttinen, L.Rutanen, C.Janis, J.Rouvinen, J.Hakulinen, N.

(2018) Chembiochem 19: 2348-2352

  • DOI: https://doi.org/10.1002/cbic.201800387
  • Primary Citation Related Structures: 
    6GSG

  • PubMed Abstract: 

    Catechol oxidases and tyrosinases are coupled binuclear copper enzymes that oxidize various o-diphenolic compounds to corresponding o-quinones. Tyrosinases have an additional monooxygenation ability to hydroxylate monophenol to o-diphenol. It is still not clear what causes the difference in the catalytic activities. We solved a complex structure of Aspergillus oryzae catechol oxidase with resorcinol bound into the active site. Catalytic activity of A. oryzae catechol oxidase was studied, for the first time, by high-resolution FT-ICR mass spectrometry to shed light on the reaction mechanism. The enzyme was also found to catalyze monooxygenation of small phenolics, which provides a novel perspective for the discussion of differences in the catalytic activity between tyrosinases and catechol oxidases. According to the results, two binding modes for resorcinol are suggested and a reaction mechanism for coupled binuclear copper enzymes is discussed.


  • Organizational Affiliation
    • Department of Chemistry, University of Eastern Finland, Yliopistokatu 7, 80130, Joensuu, Finland.

Macromolecule Content 

  • Total Structure Weight: 44.23 kDa 
  • Atom Count: 3,220 
  • Modeled Residue Count: 371 
  • Deposited Residue Count: 383 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Catechol oxidase383Aspergillus oryzae RIB40Mutation(s): 0 
Gene Names: AO090001000383
UniProt
Find proteins for Q2UNF9 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Explore Q2UNF9 
Go to UniProtKB:  Q2UNF9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2UNF9
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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
B
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G55220VL
GlyCosmos: G55220VL
GlyGen: G55220VL

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN

Query on MAN



Download:Ideal Coordinates CCD File
E [auth A]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
RCO

Query on RCO



Download:Ideal Coordinates CCD File
H [auth A]RESORCINOL
C6 H6 O2
GHMLBKRAJCXXBS-UHFFFAOYSA-N
CU

Query on CU



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
PEO

Query on PEO



Download:Ideal Coordinates CCD File
I [auth A]HYDROGEN PEROXIDE
H2 O2
MHAJPDPJQMAIIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free:  0.212 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.037α = 90
b = 114.037β = 90
c = 92.463γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Cootmodel building
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland256937
Academy of FinlandFinland292705

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-12-05
    Changes: Data collection, Database references
  • Version 1.2: 2018-12-12
    Changes: Data collection, Database references
  • Version 1.3: 2019-10-16
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-10-23
    Changes: Structure summary