2F6C

Reaction geometry and thermostability of pyranose 2-oxidase from the white-rot fungus Peniophora sp., Thermostability mutant E542K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Reaction Geometry and Thermostable Variant of Pyranose 2-Oxidase from the White-Rot Fungus Peniophora sp.

Bannwarth, M.Heckmann-Pohl, D.Bastian, S.Giffhorn, F.Schulz, G.E.

(2006) Biochemistry 45: 6587-6595

  • DOI: 10.1021/bi052465d
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pyranose 2-oxidase catalyzes the oxidation of a number of carbohydrates using dioxygen; glucose, for example, is oxidized at carbon 2. The structure of pyranose 2-oxidase with the reaction product 2-keto-beta-d-glucose bound in the active center is r ...

    Pyranose 2-oxidase catalyzes the oxidation of a number of carbohydrates using dioxygen; glucose, for example, is oxidized at carbon 2. The structure of pyranose 2-oxidase with the reaction product 2-keto-beta-d-glucose bound in the active center is reported in a new crystal form at 1.41 A resolution. The binding structure suggests that the alpha-anomer cannot be processed. The binding mode of the oxidized product was used to model other sugars accepted by the enzyme and to explain its specificity and catalytic rates. The reported structure at pH 6.0 shows a drastic conformational change in the loop of residues 454-461 (loop 454-461) at the active center compared to that of a closely homologous enzyme analyzed at pH 4.5 with a bound acetate inhibitor. In our structures, the loop is highly mobile and shifts to make way for the sugar to pass into the active center. Presumably, loop 454-461 functions as a gatekeeper. Apart from the wild-type enzyme, a thermostable variant was analyzed at 1.84 A resolution. In this variant, Glu542 is exchanged for a lysine. The observed stabilization could be a result of the mutated residue changing an ionic contact at a comparatively weak interface of the tetramer.


    Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyranose 2-oxidase
A
595Peniophora sp. (strain SG)Mutation(s): 1 
Gene Names: p2ox (poxSG)
EC: 1.1.3.10
Find proteins for Q8J136 (Peniophora sp. (strain SG))
Go to UniProtKB:  Q8J136
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.150 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 101.931α = 90.00
b = 101.931β = 90.00
c = 118.602γ = 90.00
Software Package:
Software NamePurpose
EPMRphasing
APRVdata scaling
MAR345data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description