4MIG

Pyranose 2-oxidase from Phanerochaete chrysosporium, recombinant wild type


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal structures of Phanerochaete chrysosporium pyranose 2-oxidase suggest that the N-terminus acts as a propeptide that assists in homotetramer assembly.

Hassan, N.Tan, T.C.Spadiut, O.Pisanelli, I.Fusco, L.Haltrich, D.Peterbauer, C.K.Divne, C.

(2013) FEBS Open Bio 3: 496-504

  • DOI: https://doi.org/10.1016/j.fob.2013.10.010
  • Primary Citation of Related Structures:  
    4MIF, 4MIG, 4MIH

  • PubMed Abstract: 

    The flavin-dependent homotetrameric enzyme pyranose 2-oxidase (P2O) is found mostly, but not exclusively, in lignocellulose-degrading fungi where it catalyzes the oxidation of β-d-glucose to the corresponding 2-keto sugar concomitantly with hydrogen peroxide formation during lignin solubilization. Here, we present crystal structures of P2O from the efficient lignocellulolytic basidiomycete Phanerochaete chrysosporium. Structures were determined of wild-type PcP2O from the natural fungal source, and two variants of recombinant full-length PcP2O, both in complex with the slow substrate 3-deoxy-3-fluoro-β-d-glucose. The active sites in PcP2O and P2O from Trametes multicolor (TmP2O) are highly conserved with identical substrate binding. Our structural analysis suggests that the 17 °C higher melting temperature of PcP2O compared to TmP2O is due to an increased number of intersubunit salt bridges. The structure of recombinant PcP2O expressed with its natural N-terminal sequence, including a proposed propeptide segment, reveals that the first five residues of the propeptide intercalate at the interface between A and B subunits to form stabilizing, mainly hydrophobic, interactions. In the structure of mature PcP2O purified from the natural source, the propeptide segment in subunit A has been replaced by a nearby loop in the B subunit. We propose that the propeptide in subunit A stabilizes the A/B interface of essential dimers in the homotetramer and that, upon maturation, it is replaced by the loop in the B subunit to form the mature subunit interface. This would imply that the propeptide segment of PcP2O acts as an intramolecular chaperone for oligomerization at the A/B interface of the essential dimer.


  • Organizational Affiliation

    KTH Royal Institute of Technology, School of Biotechnology, Albanova University Center, Roslagstullsbacken 21, S-10691 Stockholm Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyranose 2-oxidase
A, B, C, D
648Phanerodontia chrysosporiumMutation(s): 0 
Gene Names: p2op2oxpox
EC: 1.1.3.10
UniProt
Find proteins for Q6QWR1 (Phanerodontia chrysosporium)
Explore Q6QWR1 
Go to UniProtKB:  Q6QWR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6QWR1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FDA
Query on FDA

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
M [auth C],
P [auth D]
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
C27 H35 N9 O15 P2
YPZRHBJKEMOYQH-UYBVJOGSSA-N
G3F
Query on G3F

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
N [auth C],
Q [auth D]
3-deoxy-3-fluoro-beta-D-glucopyranose
C6 H11 F O5
BUMRBAMACDBPKO-AIECOIEWSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
L [auth B]
O [auth C]
G [auth A],
H [auth A],
I [auth A],
L [auth B],
O [auth C],
R [auth D],
S [auth D],
T [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.544α = 90
b = 166.448β = 106.41
c = 91.844γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
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: 2013-12-11
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Data collection, Refinement description
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Structure summary