4PVK

Phl p 4 I153V N158H variant, a glucose oxidase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 


Literature

Rationally engineered flavin-dependent oxidase reveals steric control of dioxygen reduction.

Zafred, D., Steiner, B., Teufelberger, A.R., Hromic, A., Karplus, P.A., Schofield, C.J., Wallner, S., Macheroux, P.

(2015) FEBS J 282: 3060-3074

  • DOI: 10.1111/febs.13212
  • Primary Citation of Related Structures:  
    4PVE, 4PVH, 4PVJ, 4PVK, 4PWB, 4PWC, 4PZF

  • PubMed Abstract: 

    • The ability of flavoenzymes to reduce dioxygen varies greatly, and is controlled by the protein environment, which may cause either a rapid reaction (oxidases) or a sluggish reaction (dehydrogenases). Previously, a 'gatekeeper' amino acid residue was identified that controls the reactivity to dioxygen in proteins from the vanillyl alcohol oxidase superfamily of flavoenzymes ...

    The ability of flavoenzymes to reduce dioxygen varies greatly, and is controlled by the protein environment, which may cause either a rapid reaction (oxidases) or a sluggish reaction (dehydrogenases). Previously, a 'gatekeeper' amino acid residue was identified that controls the reactivity to dioxygen in proteins from the vanillyl alcohol oxidase superfamily of flavoenzymes. We have identified an alternative gatekeeper residue that similarly controls dioxygen reactivity in the grass pollen allergen Phl p 4, a member of this superfamily that has glucose dehydrogenase activity and the highest redox potential measured in a flavoenzyme. A substitution at the alternative gatekeeper site (I153V) transformed the enzyme into an efficient oxidase by increasing dioxygen reactivity by a factor of 60,000. An inverse exchange (V169I) in the structurally related berberine bridge enzyme (BBE) decreased its dioxygen reactivity by a factor of 500. Structural and biochemical characterization of these and additional variants showed that our model enzymes possess a cavity that binds an anion and resembles the 'oxyanion hole' in the proximity of the flavin ring. We showed also that steric control of access to this site is the most important parameter affecting dioxygen reactivity in BBE-like enzymes. Analysis of flavin-dependent oxidases from other superfamilies revealed similar structural features, suggesting that dioxygen reactivity may be governed by a common mechanistic principle.

    Organizational Affiliation: 

    Institute of Biochemistry, Graz University of Technology, Austria.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pollen allergen Phl p 4.0202A500Phleum pratenseMutation(s): 4 
Gene Names: phlp4
UniProt
Find proteins for B2ZWE9 (Phleum pratense)
Explore B2ZWE9 
Go to UniProtKB:  B2ZWE9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2ZWE9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
MLI
Query on MLI
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]		MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.37α = 90
b = 117.37β = 90
c = 201γ = 120
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2015-03-04
    Changes: Database references
  • Version 1.2: 2015-03-25
    Changes: Database references
  • Version 1.3: 2015-04-01
    Changes: Structure summary
  • Version 1.4: 2015-04-22
    Changes: Other
  • Version 1.5: 2015-09-02
    Changes: Database references