Crystal structure of recombinant pyranose 2-oxidase H167A mutant

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

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Structural basis for substrate binding and regioselective oxidation of monosaccharides at c3 by pyranose 2-oxidase.

Kujawa, M.Ebner, H.Leitner, C.Hallberg, B.M.Prongjit, M.Sucharitakul, J.Ludwig, R.Rudsander, U.Peterbauer, C.Chaiyen, P.Haltrich, D.Divne, C.

(2006) J Biol Chem 281: 35104-35115

  • DOI: https://doi.org/10.1074/jbc.M604718200
  • Primary Citation of Related Structures:  
    2IGK, 2IGM, 2IGN, 2IGO

  • PubMed Abstract: 

    Pyranose 2-oxidase (P2Ox) participates in fungal lignin degradation by producing the H2O2 needed for lignin-degrading peroxidases. The enzyme oxidizes cellulose- and hemicellulose-derived aldopyranoses at C2 preferentially, but also on C3, to the corresponding ketoaldoses. To investigate the structural determinants of catalysis, covalent flavinylation, substrate binding, and regioselectivity, wild-type and mutant P2Ox enzymes were produced and characterized biochemically and structurally. Removal of the histidyl-FAD linkage resulted in a catalytically competent enzyme containing tightly, but noncovalently bound FAD. This mutant (H167A) is characterized by a 5-fold lower kcat, and a 35-mV lower redox potential, although no significant structural changes were seen in its crystal structure. In previous structures of P2Ox, the substrate loop (residues 452-457) covering the active site has been either disordered or in a conformation incompatible with carbohydrate binding. We present here the crystal structure of H167A in complex with a slow substrate, 2-fluoro-2-deoxy-D-glucose. Based on the details of 2-fluoro-2-deoxy-D-glucose binding in position for oxidation at C3, we also outline a probable binding mode for D-glucose positioned for regioselective oxidation at C2. The tentative determinant for discriminating between the two binding modes is the position of the O6 hydroxyl group, which in the C2-oxidation mode can make favorable interactions with Asp452 in the substrate loop and, possibly, a nearby arginine residue (Arg472). We also substantiate our hypothesis with steady-state kinetics data for the alanine replacements of Asp452 and Arg472 as well as the double alanine 452/472 mutant.

  • Organizational Affiliation

    School of Biotechnology, Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyranose oxidase623Trametes ochraceaMutation(s): 1 
Gene Names: p2o
Find proteins for Q7ZA32 (Trametes ochracea)
Explore Q7ZA32 
Go to UniProtKB:  Q7ZA32
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7ZA32
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FAD

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
M [auth D]
O [auth C]
Q [auth E]
I [auth A],
K [auth B],
M [auth D],
O [auth C],
Q [auth E],
S [auth F],
U [auth H],
W [auth G]
C27 H33 N9 O15 P2
Query on MES

Download Ideal Coordinates CCD File 
J [auth A]
L [auth B]
N [auth D]
P [auth C]
R [auth E]
J [auth A],
L [auth B],
N [auth D],
P [auth C],
R [auth E],
T [auth F],
V [auth H],
X [auth G]
C6 H13 N O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.066α = 90
b = 102.996β = 106.43
c = 168.56γ = 90
Software Package:
Software NamePurpose
MAR345data collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2006-10-10 
  • Deposition Author(s): Divne, C.

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2014-11-12
    Changes: Structure summary
  • Version 1.4: 2017-10-18
    Changes: Advisory, Data collection, Refinement description
  • Version 1.5: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.6: 2024-02-21
    Changes: Data collection