5MXJ

Structure of the Y108F mutant of vanillyl alcohol oxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Two tyrosine residues, Tyr-108 and Tyr-503, are responsible for the deprotonation of phenolic substrates in vanillyl-alcohol oxidase.

Ewing, T.A.Nguyen, Q.T.Allan, R.C.Gygli, G.Romero, E.Binda, C.Fraaije, M.W.Mattevi, A.van Berkel, W.J.H.

(2017) J Biol Chem 292: 14668-14679

  • DOI: 10.1074/jbc.M117.778449
  • Primary Citation of Related Structures:  
    5MXJ, 5MXU

  • PubMed Abstract: 
  • A number of oxidoreductases from the VAO/ para -cresol methylhydroxylase flavoprotein family catalyze the oxidation of para -substituted phenols. One of the best-studied is vanillyl-alcohol oxidase (VAO) from the fungus Penicillium simplicissimum For oxidation of phenols by VAO to occur, they must first be bound in the active site of the enzyme in their phenolate anion form ...

    A number of oxidoreductases from the VAO/ para -cresol methylhydroxylase flavoprotein family catalyze the oxidation of para -substituted phenols. One of the best-studied is vanillyl-alcohol oxidase (VAO) from the fungus Penicillium simplicissimum For oxidation of phenols by VAO to occur, they must first be bound in the active site of the enzyme in their phenolate anion form. The crystal structure of VAO reveals that two tyrosine residues, Tyr-108 and Tyr-503, are positioned to facilitate this deprotonation. To investigate their role in catalysis, we created three VAO variants, Y108F, Y503F, and Y108F/Y503F, and studied their biochemical properties. Steady-state kinetics indicated that the presence of at least one of the tyrosine residues is essential for efficient catalysis by VAO. Stopped-flow kinetics revealed that the reduction of VAO by chavicol or vanillyl alcohol occurs at two different rates: k obs1 , which corresponds to its reaction with the deprotonated form of the substrate, and k obs2 , which corresponds to its reaction with the protonated form of the substrate. In Y108F, Y503F, and Y108F/Y503F, the relative contribution of k obs2 to the reduction is larger than in wild-type VAO, suggesting deprotonation is impaired in these variants. Binding studies disclosed that the competitive inhibitor isoeugenol is predominantly in its deprotonated form when bound to wild-type VAO, but predominantly in its protonated form when bound to the variants. These results indicate that Tyr-108 and Tyr-503 are responsible for the activation of substrates in VAO, providing new insights into the catalytic mechanism of VAO and related enzymes that oxidize para -substituted phenols.


    Organizational Affiliation

    From the Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands, willem.vanberkel@wur.nl.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vanillyl-alcohol oxidaseA, B560Penicillium simplicissimumMutation(s): 1 
Gene Names: VAOA
EC: 1.1.3.38
UniProt
Find proteins for P56216 (Penicillium simplicissimum)
Explore P56216 
Go to UniProtKB:  P56216
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56216
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B],
G [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.184 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.9α = 90
b = 137.9β = 90
c = 132.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European UnionNetherlandsINDOX project (FP7-KBBE-2013-7-613549)
European Community s Seventh Framework ProgrammeItalyBioStruct-X (Grants 7551 and 10205)

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Database references
  • Version 1.2: 2018-01-31
    Changes: Structure summary