4J3R | pdb_00004j3r

Crystal structure of catechol oxidase from Aspergillus oryzae, soaked in 4-tert-butylcatechol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.222 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

The crystal structure of an extracellular catechol oxidase from the ascomycete fungus Aspergillus oryzae.

Hakulinen, N.Gasparetti, C.Kaljunen, H.Kruus, K.Rouvinen, J.

(2013) J Biol Inorg Chem 18: 917-929

  • DOI: https://doi.org/10.1007/s00775-013-1038-9
  • Primary Citation Related Structures: 
    4J3P, 4J3Q, 4J3R

  • PubMed Abstract: 

    Catechol oxidases (EC 1.10.3.1) catalyse the oxidation of o-diphenols to their corresponding o-quinones. These oxidases contain two copper ions (CuA and CuB) within the so-called coupled type 3 copper site as found in tyrosinases (EC 1.14.18.1) and haemocyanins. The crystal structures of a limited number of bacterial and fungal tyrosinases and plant catechol oxidases have been solved. In this study, we present the first crystal structure of a fungal catechol oxidase from Aspergillus oryzae (AoCO4) at 2.5-Å resolution. AoCO4 belongs to the newly discovered family of short-tyrosinases, which are distinct from other tyrosinases and catechol oxidases because of their lack of the conserved C-terminal domain and differences in the histidine pattern for CuA. The sequence identity of AoCO4 with other structurally known enzymes is low (less than 30 %), and the crystal structure of AoCO4 diverges from that of enzymes belonging to the conventional tyrosinase family in several ways, particularly around the central α-helical core region. A diatomic oxygen moiety was identified as a bridging molecule between the two copper ions CuA and CuB separated by a distance of 4.2-4.3 Å. The UV/vis absorption spectrum of AoCO4 exhibits a distinct maximum of absorbance at 350 nm, which has been reported to be typical of the oxy form of type 3 copper enzymes.


  • Organizational Affiliation
    • Department of Chemistry, University of Eastern Finland, Joensuu Campus, PO Box 111, 80101, Joensuu, Finland, nina.hakulinen@uef.fi.

Macromolecule Content 

  • Total Structure Weight: 43.71 kDa 
  • Atom Count: 3,123 
  • Modeled Residue Count: 372 
  • Deposited Residue Count: 383 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
catechol oxidase383Aspergillus oryzaeMutation(s): 0 
Gene Names: 5990879
EC: 1.10.3.1
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: 5
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

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],
H [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
I [auth A]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
J [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CU

Query on CU



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

Query on OXY



Download:Ideal Coordinates CCD File
E [auth A]OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.222 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.07α = 90
b = 119.07β = 90
c = 84.29γ = 120
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-27
    Type: Initial release
  • Version 1.1: 2013-12-04
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-09
    Changes: Structure summary