Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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Two tyrosine residues, Tyr-108 and Tyr-503, are responsible for the deprotonation of phenolic substrates in vanillyl-alcohol oxidase
Ewing, Tom A. ; Nguyen, Quoc Thai ; Allan, Robert C. ; Gygli, Gudrun ; Romero, Elvira ; Binda, Claudia ; Fraaije, Marco W. ; Mattevi, Andrea ; Berkel, Willem J.H. Van - \ 2017
Journal of Biological Chemistry 292 (2017)35. - ISSN 0021-9258 - p. 14668 - 14679.
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: kobs1, which corresponds to its reaction with the deprotonated form of the substrate, and kobs2, which corresponds to its reaction with the protonated form of the substrate. In Y108F, Y503F, and Y108F/Y503F, the relative contribution of kobs2 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.
The VAO/PCMH flavoprotein family
Ewing, Tom A. ; Fraaije, Marco W. ; Mattevi, Andrea ; Berkel, Willem J.H. van - \ 2017
Archives of Biochemistry and Biophysics 632 (2017). - ISSN 0003-9861 - p. 104 - 117.
Enzyme mechanism - Flavoprotein - Oxidoreductase - Phylogeny - Protein family
The VAO/PCMH flavoprotein family consists of structurally homologous flavin-dependent enzymes that catalyze a wide range of chemical reactions. Family members share an architecture consisting of a conserved FAD-binding domain and a more variable substrate-binding domain, which enables varying interactions with a range of substrates while maintaining the same cofactor-binding fold. Here, we provide an overview of the current state of our knowledge on the members of the VAO/PCMH family. Based on a phylogenetic analysis, we divide the family into 11 subgroups. We discuss the properties of these subgroups, focusing on recent developments in terms of the discovery of new family members and mechanistic advances. We also highlight open questions that will provide challenges for future research.
3-hydroxybenzoate 6-hydroxylase from Rhodococcus jostii RHA1 contains a phosphatidylinositol cofactor
Montersino, Stefania ; Poele, Evelien te; Orru, Roberto ; Westphal, Adrie H. ; Barendregt, Arjan ; Heck, Albert J.R. ; Geize, Robert van der; Dijkhuizen, Lubbert ; Mattevi, Andrea ; Berkel, Willem J.H. van - \ 2017
Frontiers in Microbiology 8 (2017). - ISSN 1664-302X - 11 p.
Expression strain - Flavoprotein - Monooxygenase - Phospholipid - Rhodococcus

3-Hydroxybenzoate 6-hydroxylase (3HB6H, EC is a FAD-dependent monooxygenase involved in the catabolism of aromatic compounds in soil microorganisms. 3HB6H is unique among flavoprotein hydroxylases in that it harbors a phospholipid ligand. The purified protein obtained from expressing the gene encoding 3HB6H from Rhodococcus jostii RHA1 in the host Escherichia coli contains a mixture of phosphatidylglycerol and phosphatidylethanolamine, which are the major constituents of E. coli's cytoplasmic membrane. Here, we purified 3HB6H (RjHB6H) produced in the host R. jostii RHA#2 by employing a newly developed actinomycete expression system. Biochemical and biophysical analysis revealed that Rj3HB6H possesses similar catalytic and structural features as 3HB6H, but now contains phosphatidylinositol, which is a specific constituent of actinomycete membranes. Native mass spectrometry suggests that the lipid cofactor stabilizes monomer-monomer contact. Lipid analysis of 3HB6H from Pseudomonas alcaligenes NCIMB 9867 (Pa3HB6H) produced in E. coli supports the conclusion that 3HB6H enzymes have an intrinsic ability to bind phospholipids with different specificity, reflecting the membrane composition of their bacterial host.

Crystal structure of 3-hydroxybenzoate 6-hydroxylase uncovers lipid-assisted flavoprotein strategy for regioselective aromatic hydroxylation.
Montersino, S. ; Orru, R. ; Barendregt, A. ; Westphal, A.H. ; Duijn, E. van; Mattevi, A. ; Berkel, W.J.H. van - \ 2013
Journal of Biological Chemistry 288 (2013). - ISSN 0021-9258 - p. 26235 - 26245.
para-hydroxybenzoate hydroxylase - coenzyme-q biosynthesis - pseudomonas-fluorescens - genus rhodococcus - mass-spectrometry - escherichia-coli - data quality - substrate - enzyme - sequence
3-Hydroxybenzoate 6-hydroxylase (3HB6H) from Rhodococcus jostii RHA1 is a dimeric flavoprotein that catalyzes the NADH- and oxygen-dependent para-hydroxylation of 3-hydroxybenzoate to 2,5-dihydroxybenzoate. In this study, we report the crystal structure of 3HB6H as expressed in Escherichia coli. The overall fold of 3HB6H is similar to that of p-hydroxybenzoate hydroxylase and other flavoprotein aromatic hydroxylases. Unexpectedly, a lipid ligand is bound to each 3HB6H monomer. Mass spectral analysis identified the ligand as a mixture of phosphatidylglycerol and phosphatidylethanolamine. The fatty acid chains occupy hydrophobic channels that deeply penetrate into the interior of the substrate-binding domain of each subunit, whereas the hydrophilic part is exposed on the protein surface, connecting the dimerization domains via a few interactions. Most remarkably, the terminal part of a phospholipid acyl chain is directly involved in the substrate-binding site. Co-crystallized chloride ion and the crystal structure of the H213S variant with bound 3-hydroxybenzoate provide hints about oxygen activation and substrate hydroxylation. Essential roles are played by His-213 in catalysis and Tyr-105 in substrate binding. This phospholipid-assisted strategy to control regioselective aromatic hydroxylation is of relevance for optimization of flavin-dependent biocatalysts.
Structural basis of regioselective hydroxylation in 3 hydroxybenzoate hydroxylases
Montersino, S. ; Orru, R. ; Mattevi, A. ; Berkel, W.J.H. van - \ 2013
In: Flavins and Flavoproteins 2011: Proceedings 17th International Symposium on Flavins and Flavoproteins 2011, Berkeley, USA. - [S.l] : S.n. - p. 295 - 300.
Structural and biochemical characterization of 3-hydroxybenzoate 6-hydroxylase
Montersino, S. - \ 2012
Wageningen University. Promotor(en): Willem van Berkel, co-promotor(en): A. Mattevi. - [S.l.] : s.n. - ISBN 9789461732781 - 158
aspecifiek mono-oxygenase - moleculaire structuur - biochemie - unspecific monooxygenase - molecular conformation - biochemistry

The thesis deals with the characterization of a new flavoprotein hydroxylase 3 hydroxybenzoate 6-hydroxylase (3HB6H) from Rhodococcus jostii RHA1. 3HB6H is able to insert exclusively oxygen in para-position and the enzyme has been chosen to study the structural basis of such regioselectivity. As main result, functional mirror image active sites direct regioselective 3-hydroxybenzoate hydroxylation. Moreover, the nature and role of unprecedented phospholipid binding has been analyzed demonstrating a role in enzyme oligomerization and a possible protective role during catalysis. To conclude, the knowledge acquired improves our insight into the strategies of flavin-dependent regioselective hydroxylation and the results emerged in this thesis provide a foundation for further structural and kinetic studies on 3HB6H and related enzymes.

Insight into the regioselectivity of flavin-dependent aromatic hydroxylation
Montersino, S. ; Westphal, A.H. ; Orru, R. ; Bonvin, A. ; Mattevi, A. ; Berkel, W.J.H. van - \ 2011
Structure and function of 3-hydroxybenzoate 6-hydroxylase from Rhodococcus jostii RHA1.
Montersino, S. ; Orru, R. ; Mattevi, A. ; Berkel, W.J.H. van - \ 2011
Multiple pathways guide oxygen diffusion into flavoenzyme active sites
Baron, R. ; Riley, C. ; Chenprakhon, P. ; Thotsaporn, K. ; Winter, R.T. ; Alfieri, A. ; Forneris, F. ; Berkel, W.J.H. van; Chaiyen, P. ; Fraaije, M.W. ; Mattevi, A. ; McCammon, J.A. - \ 2009
Proceedings of the National Academy of Sciences of the United States of America 106 (2009)26. - ISSN 0027-8424 - p. 10603 - 10608.
x-ray crystallography - molecular-dynamics - streptomyces-coelicolor - cholesterol oxidase - alditol oxidase - protein - o-2 - enzyme - fluorescence - simulations
Dioxygen (O2) and other gas molecules have a fundamental role in a variety of enzymatic reactions. However, it is only poorly understood which O2 uptake mechanism enzymes employ to promote efficient catalysis and how general this is. We investigated O2 diffusion pathways into monooxygenase and oxidase flavoenzymes, using an integrated computational and experimental approach. Enhanced-statistics molecular dynamics simulations reveal spontaneous protein-guided O2 diffusion from the bulk solvent to preorganized protein cavities. The predicted protein-guided diffusion paths and the importance of key cavity residues for oxygen diffusion were verified by combining site-directed mutagenesis, rapid kinetics experiments, and high-resolution X-ray structures. This study indicates that monooxygenase and oxidase flavoenzymes employ multiple funnel-shaped diffusion pathways to absorb O2 from the solvent and direct it to the reacting C4a atom of the flavin cofactor. The difference in O2 reactivity among dehydrogenases, monooxygenases, and oxidases ultimately resides in the fine modulation of the local environment embedding the reactive locus of the flavin
Identification of a gatekeeper residue that prevents dehydrogenases from acting as oxidases
Leferink, N.G.H. ; Fraaije, M.W. ; Joosten, H.J. ; Schaap, P.J. ; Mattevi, A. ; Berkel, W.J.H. van - \ 2009
Journal of Biological Chemistry 284 (2009)7. - ISSN 0021-9258 - p. 4392 - 4397.
gamma-lactone dehydrogenase - monomeric sarcosine oxidase - vanillyl-alcohol oxidase - cholesterol oxidase - l-galactono-1,4-lactone dehydrogenase - streptomyces-coelicolor - substrate-specificity - oxygen reactivity - alditol oxidase - enzyme
The oxygen reactivity of flavoproteins is poorly understood. Here we show that a single Ala to Gly substitution in L-galactono-1,4-lactone dehydrogenase (GALDH) turns the enzyme into a catalytically competent oxidase. GALDH is an aldonolactone oxidoreductase with a vanillyl-alcohol oxidase (VAO) fold. We found that nearly all oxidases in the VAO family contain either a Gly or Pro at a structurally conserved position near the C4a locus of the isoalloxazine moiety of the flavin, whereas dehydrogenases prefer another residue at this position. Mutation of the corresponding residue in GALDH (Ala113Gly) resulted in a striking 400 fold increase in oxygen reactivity, while the cytochrome c reductase activity is retained. The activity of the A113G variant shows a linear dependence on oxygen concentration (kox = 3.5 x 10e5 M-1 s-1), similar to most other flavoprotein oxidases. The Ala113Gly replacement does not change the reduction potential of the flavin, but creates space for molecular oxygen to react with the reduced flavin. In the wild-type enzyme Ala113 acts as a gatekeeper, preventing oxygen to access the isoalloxazine nucleus. The presence of such an oxygen access gate seems to be a key factor for the prevention of oxidase activity within the VAO family, and is absent in members that act as oxidases.
Structural studies on flavin reductase PheA2 reveal binding of NAD in an unusual folded conformation and support novel mechanism of action
Heuvel, R.H.H. van den; Westphal, A.H. ; Heck, A.J.R. ; Walsh, M.A. ; Rovida, S. ; Berkel, W.J.H. van; Mattevi, A. - \ 2004
Journal of Biological Chemistry 279 (2004)13. - ISSN 0021-9258 - p. 12860 - 12867.
archaeon archaeoglobus-fulgidus - bacillus-thermoglucosidasius a7 - crystal-structure - escherichia-coli - nad(p)h-flavin oxidoreductase - bioluminescent bacterium - electrospray-ionization - phenol hydroxylase - mass-spectrometry - ferric reductase
The catabolism of toxic phenols in the thermophilic organism Bacillus thermoglucosidasius A7 is initiated by a two-component enzyme system. The smaller flavin reductase PheA2 component catalyzes the NADH-dependent reduction of free FAD according to a ping-pong bisubstrate-biproduct mechanism. The reduced FAD is then used by the larger oxygenase component PheA1 to hydroxylate phenols to the corresponding catechols. We have determined the x-ray structure of PheA2 containing a bound FAD cofactor (2.2 Angstrom), which is the first structure of a member of this flavin reductase family. We have also determined the x-ray structure of reduced holo-PheA2 in complex with oxidized NAD (2.1 Angstrom). PheA2 is a single domain homodimeric protein with each FAD-containing subunit being organized around a six-stranded beta-sheet and a capping alpha-helix. The tightly bound FAD prosthetic group (K-d=10 nM) binds near the dimer interface, and the re face of the FAD isoalloxazine ring is fully exposed to solvent. The addition of NADH to crystalline PheA2 reduced the flavin cofactor, and the NAD product was bound in a wide solvent-accessible groove adopting an unusual folded conformation with ring stacking. This is the first observation of an enzyme that is very likely to react with a folded compact pyridine nucleotide. The PheA2 crystallographic models strongly suggest that reactive exogenous FAD substrate binds in the NADH cleft after release of NAD product. Nanoflow electrospray mass spectrometry data indeed showed that PheA2 is able to bind one FAD cofactor and one FAD substrate. In conclusion, the structural data provide evidence that PheA2 contains a dual binding cleft for NADH and FAD substrate, which alternate during catalysis.
Phenol hydroxylase from Bacillus thermoglucosidasius A7: A novel two-enzyme system, 2nd Oxizymes meeting, Naples, Italy, June, 3-5, 2004 with a dual role for FAD
Berkel, W.J.H. van; Westphal, A.H. ; Kirchner, U. ; Müller, R. ; Heuvel, R.H.H. van den; Heck, A.J.R. ; Rovida, S. ; Mattevi, A. - \ 2004
Covalent flavinylation enhances the oxidative power of vanillyl-alcohol oxidase
Fraaije, M.W. ; Heuvel, R.H.H. van den; Mattevi, A. ; Berkel, W.J.H. van - \ 2003
Journal of Molecular Catalysis. B, Enzymatic 21 (2003)1-2. - ISSN 1381-1177 - p. 43 - 46.
p-cresol methylhydroxylase - site-directed mutagenesis - fad-binding - redox properties - mononucleotide - attachment
Vanillyl-alcohol oxidase (VAO) from Penicillium simplicissimum is an inducible flavoprotein that is active with a wide range of phenolic compounds. The enzyme is the prototype of a newly recognized family of structurally related oxidoreductases, whose members share a conserved FAD-binding domain. The flavin cofactor in VAO is covalently linked to His422 of the cap domain. Studies from His422 variants revealed that deletion of the histidyl-flavin bond does not result in any significant structural change. However, the covalent interaction increases the redox potential of the flavin, facilitating substrate oxidation. His61, located in the FAD-binding domain, is involved in the autocatalytic process of covalent flavinylation. This could be nicely demonstrated by creating the H61T mutant enzyme which binds the flavin in a non-covalently mode. Similar to the noncovalent His422 variants, H61T is 10-fold less active than wild-type VAO. From this and the similar crystal structures of apo and holo H61T it is concluded that the FAD binds to a preorganized binding site where His61 activates His422 for autocatalytic flavinylation. (C) 2002 Published by Elsevier Science B.V.
Enzymatic synthesis of natural vanillin
Berkel, W.J.H. van; Heuvel, R.H.H. van den; Berg, W.A.M. van den; Rovida, S. ; Mattevi, A. - \ 2003
In: Dutch-Japanese Workshop on Biocatalysis, Noordwijk [S.l] : S.n. - p. 37 - 37.
Enzymatic synthesis of natural vanillin
Heuvel, R.H.H. van den; Berg, W.A.M. van den; Rovida, S. ; Mattevi, A. ; Berkel, W.J.H. van - \ 2003
In: 6th International Symposium on Biocatalysis and Biotransformations [S.l] : S.n. - p. 449 - 449.
Production of natural vanillin by laboratory-evolved vanillyl-alcohol oxidase
Heuvel, R.H.H. van den; Berg, W.A.M. van den; Rovida, S. ; Mattevi, A. ; Berkel, W.J.H. van - \ 2002
In: Applied Biocatalysis : 7th annual meeting of the working party Biotransformations, Zurich, 2002. - [S.l.] : [s.n.], 2002
Covalent flavinylation enhances the oxidative power of vanillyl-alcohol oxidase
Fraaije, M.W. ; Mattevi, A. ; Heuvel, R.H.H. van den; Berkel, W.J.H. van - \ 2001
In: Applied Biocatalysis 1980-2020 : The future impact of modelling proteins and thermodynamics, Trondheim, 2001. - [S.l.] : [s.n.], 2001
Vanillyl-alcohol oxidase, a tasteful biocatalyst
Heuvel, R.H.H. van den; Fraaije, M.W. ; Mattevi, A. ; Laane, C. ; Berkel, W.J.H. van - \ 2001
Journal of Molecular Catalysis. B, Enzymatic 11 (2001). - ISSN 1381-1177 - p. 185 - 188.
The covalent flavoenzyme vanillyl-alcohol oxidase (VAO) is a versatile biocatalyst. It converts a wide range of phenolic compounds by catalysing oxidation, deamination, demethylation, dehydrogenation and hydroxylation reactions. The production of natural vanillin, 4-hydroxybenzaldehyde, coniferyl alcohol and enantiomeric pure phenol derivatives is of interest for biotechnological applications. The hydroxylation of 4-alkylphenols is highly stereospecific for the (R)-isomer, whereas dehydrogenation of these substrates is specific for the cis- or trans-isomer. On the basis of crystallographic data, we suggest that the stereospecificity is related to the active site residue Asp170. Another important feature of VAO is the covalent flavin attachment. Studies from site-directed mutants suggest that the covalent flavin-protein interaction improves the catalytic performance as well as the long-term stability of VAO
Inverted stereospecificity of vanillyl-alcohol oxidase
Heuvel, R.H.H. van den; Fraaije, M.W. ; Mattevi, A. ; Berkel, W.J.H. van - \ 2000
In: INPEC-2000, Groningen, 2000
Asp170 is crucial for the redox properties of vanillyl-alcohol oxidase
Heuvel, R.H.H. van den; Fraaije, M.W. ; Mattevi, A. ; Berkel, W.J.H. van - \ 2000
Journal of Biological Chemistry 275 (2000). - ISSN 0021-9258 - p. 14799 - 14808.
Vanillyl-alcohol oxidase is a flavoprotein containing a covalent flavin that catalyzes the oxidation of 4-(methoxymethyl)phenol to 4-hydroxybenzaldehyde. The reaction proceeds through the formation of a p-quinone methide intermediate, after which, water addition takes place. Asp-170, located near the N5-atom of the flavin, has been proposed to act as an active site base. To test this hypothesis, we have addressed the properties of D170E, D170S, D170A, and D170N variants. Spectral and fluorescence analysis, together with the crystal structure of D170S, suggests that the Asp-170 replacements do not induce major structural changes. However, in D170A and D170N, 50 and 100°respectively, of the flavin is non-covalently bound. Kinetic characterization of the vanillyl-alcohol oxidase variants revealed that Asp-170 is required for catalysis. D170E is 50-fold less active, and the other Asp-170 variants are about 103-fold less active than wild type enzyme. Impaired catalysis of the Asp-170 variants is caused by slow flavin reduction. Furthermore, the mutant proteins have lost the capability of forming a stable complex between reduced enzyme and the p-quinone methide intermediate. The redox midpoint potentials in D170E ( 6 mV) and D170S (-91 mV) are considerably decreased compared with wild type vanillyl-alcohol oxidase ( 55 mV). This supports the idea that Asp-170 interacts with the protonated N5-atom of the reduced cofactor, thus increasing the FAD redox potential. Taken together, we conclude that Asp-170 is involved in the process of autocatalytic flavinylation and is crucial for efficient redox catalysis.
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