1vao Citations

Crystal structures and inhibitor binding in the octameric flavoenzyme vanillyl-alcohol oxidase: the shape of the active-site cavity controls substrate specificity.

Structure 5 907-20 (1997)
Related entries: 1ahv, 2vao, 1ahu, 1ahz

Cited: 67 times
EuropePMC logo PMID: 9261083

Abstract

Background

Lignin degradation leads to the formation of a broad spectrum of aromatic molecules that can be used by various fungal micro-organisms as their sole source of carbon. When grown on phenolic compounds, Penicillium simplicissimum induces the strong impression of a flavin-containing vanillyl-alcohol oxidase (VAO). The enzyme catalyses the oxidation of a vast array of substrates, ranging from aromatic amines to 4-alkyphenols. VAO is a member of a novel class of widely distributed oxidoreductases, which use flavin adenine dinucleotide (FAD) as a cofactor covalently bound to the protein. We have carried out the determination of the structure of VAO in order to shed light on the most interesting features of these novel oxidoreductases, such as the functional significance of covalent flavinylation and the mechanism of catalysis.

Results

The crystal structure of VAO has been determined in the native state and in complexes with four inhibitors. The enzyme is an octamer with 42 symmetry; the inhibitors bind in a hydrophobic, elongated cavity on the si side of the flavin molecule. Three residues, Tyr108, Tyr503 and Arg504 form an anion-binding subsite, which stabilises the phenolate form of the substrate. The structure of VAO complexed with the inhibitor 4-(1-heptenyl)phenol shows that the catalytic cavity is completely filled by the inhibitor, explaining why alkylphenols bearing aliphatic substituents longer than seven carbon atoms do not bind to the enzyme.

Conclusion

The shape of the active-site cavity controls substrate specificity by providing a 'size exclusion mechanism'. Inside the cavity, the substrate aromatic ring is positioned at an angle of 18 degrees to the flavin ring. This arrangement is ideally suited for a hydride transfer reaction, which is further facilitated by substrate deprotonation. Burying the substrate beneath the protein surface is a recurrent strategy, common to many flavoenzymes that effect substrate oxidation or reduction via hydride transfer.

Reviews - 1vao mentioned but not cited (1)

  1. Structural perspective on enzymatic halogenation. Blasiak LC, Drennan CL. Acc. Chem. Res. 42 147-155 (2009)

Articles - 1vao mentioned but not cited (1)

  1. Molecular characterization and expression of a novel alcohol oxidase from Aspergillus terreus MTCC6324. Chakraborty M, Goel M, Chinnadayyala SR, Dahiya UR, Ghosh SS, Goswami P. PLoS ONE 9 e95368 (2014)


Reviews citing this publication (14)

  1. Rational approaches to improving selectivity in drug design. Huggins DJ, Sherman W, Tidor B. J Med Chem 55 1424-1444 (2012)
  2. Redox biocatalysis and metabolism: molecular mechanisms and metabolic network analysis. Blank LM, Ebert BE, Buehler K, Bühler B. Antioxid Redox Signal 13 349-394 (2010)
  3. Cholesterol oxidase: biochemistry and structural features. Vrielink A, Ghisla S. FEBS J 276 6826-6843 (2009)
  4. The growing VAO flavoprotein family. Leferink NG, Heuts DP, Fraaije MW, van Berkel WJ. Arch Biochem Biophys 474 292-301 (2008)
  5. Enantiocomplementary enzymes: classification, molecular basis for their enantiopreference, and prospects for mirror-image biotransformations. Mugford PF, Wagner UG, Jiang Y, Faber K, Kazlauskas RJ. Angew Chem Int Ed Engl 47 8782-8793 (2008)
  6. To be or not to be an oxidase: challenging the oxygen reactivity of flavoenzymes. Mattevi A. Trends Biochem Sci 31 276-283 (2006)
  7. The ins and outs of ring-cleaving dioxygenases. Vaillancourt FH, Bolin JT, Eltis LD. Crit Rev Biochem Mol Biol 41 241-267 (2006)
  8. Investigation of intact protein complexes by mass spectrometry. Heck AJ, Van Den Heuvel RH. Mass Spectrom Rev 23 368-389 (2004)
  9. The covalent FAD of monoamine oxidase: structural and functional role and mechanism of the flavinylation reaction. Edmondson DE, Newton-Vinson P. Antioxid Redox Signal 3 789-806 (2001)
  10. Novel approaches to the biosynthesis of vanillin. Walton NJ, Narbad A, Faulds C, Williamson G. Curr Opin Biotechnol 11 490-496 (2000)
  11. The role of the [2Fe-2s] cluster centers in xanthine oxidoreductase. Nishino T, Okamoto K. J Inorg Biochem 82 43-49 (2000)
  12. A novel oxidoreductase family sharing a conserved FAD-binding domain. Fraaije MW, Van Berkel WJ, Benen JA, Visser J, Mattevi A. Trends Biochem Sci 23 206-207 (1998)
  13. Unification of protein families. Holm L. Curr Opin Struct Biol 8 372-379 (1998)
  14. Structure of D-amino acid oxidase: new insights from an old enzyme. Mattevi A, Vanoni MA, Curti B. Curr Opin Struct Biol 7 804-810 (1997)

Articles citing this publication (51)

  1. The effect of the source pressure on the abundance of ions of noncovalent protein assemblies in an electrospray ionization orthogonal time-of-flight instrument. Tahallah N, Pinkse M, Maier CS, Heck AJ. Rapid Commun Mass Spectrom 15 596-601 (2001)
  2. A 30-angstrom-long U-shaped catalytic tunnel in the crystal structure of polyamine oxidase. Binda C, Coda A, Angelini R, Federico R, Ascenzi P, Mattevi A. Structure 7 265-276 (1999)
  3. Crystal structure and mechanism of CO dehydrogenase, a molybdo iron-sulfur flavoprotein containing S-selanylcysteine. Dobbek H, Gremer L, Meyer O, Huber R. Proc Natl Acad Sci U S A 96 8884-8889 (1999)
  4. Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme. Trickey P, Wagner MA, Jorns MS, Mathews FS. Structure 7 331-345 (1999)
  5. Methionine 286 in transmembrane domain 3 of the GABAA receptor beta subunit controls a binding cavity for propofol and other alkylphenol general anesthetics. Krasowski MD, Nishikawa K, Nikolaeva N, Lin A, Harrison NL. Neuropharmacology 41 952-964 (2001)
  6. Crystal structures of the active and alloxanthine-inhibited forms of xanthine dehydrogenase from Rhodobacter capsulatus. Truglio JJ, Theis K, Leimkühler S, Rappa R, Rajagopalan KV, Kisker C. Structure 10 115-125 (2002)
  7. ThermoFAD, a Thermofluor-adapted flavin ad hoc detection system for protein folding and ligand binding. Forneris F, Orru R, Bonivento D, Chiarelli LR, Mattevi A. FEBS J 276 2833-2840 (2009)
  8. Detection of intact megaDalton protein assemblies of vanillyl-alcohol oxidase by mass spectrometry. van Berkel WJ, van den Heuvel RH, Versluis C, Heck AJ. Protein Sci 9 435-439 (2000)
  9. Structure of L-aspartate oxidase: implications for the succinate dehydrogenase/fumarate reductase oxidoreductase family. Mattevi A, Tedeschi G, Bacchella L, Coda A, Negri A, Ronchi S. Structure 7 745-756 (1999)
  10. Structural basis of inhibition of Mycobacterium tuberculosis DprE1 by benzothiazinone inhibitors. Batt SM, Jabeen T, Bhowruth V, Quill L, Lund PA, Eggeling L, Alderwick LJ, Fütterer K, Besra GS. Proc Natl Acad Sci U S A 109 11354-11359 (2012)
  11. The crystal structure of D-lactate dehydrogenase, a peripheral membrane respiratory enzyme. Dym O, Pratt EA, Ho C, Eisenberg D. Proc Natl Acad Sci U S A 97 9413-9418 (2000)
  12. Structures of the flavocytochrome p-cresol methylhydroxylase and its enzyme-substrate complex: gated substrate entry and proton relays support the proposed catalytic mechanism. Cunane LM, Chen ZW, Shamala N, Mathews FS, Cronin CN, McIntire WS. J Mol Biol 295 357-374 (2000)
  13. X-ray structure of 12-oxophytodienoate reductase 1 provides structural insight into substrate binding and specificity within the family of OYE. Breithaupt C, Strassner J, Breitinger U, Huber R, Macheroux P, Schaller A, Clausen T. Structure 9 419-429 (2001)
  14. Identification of the oxygen activation site in monomeric sarcosine oxidase: role of Lys265 in catalysis. Zhao G, Bruckner RC, Jorns MS. Biochemistry 47 9124-9135 (2008)
  15. The PHBH fold: not only flavoenzymes. Mattevi A. Biophys Chem 70 217-222 (1998)
  16. Aryl-alcohol oxidase protein sequence: a comparison with glucose oxidase and other FAD oxidoreductases. Varela E, Jesús Martínez M, Martínez AT. Biochim Biophys Acta 1481 202-208 (2000)
  17. Crystal structure of 6-hydroxy-D-nicotine oxidase from Arthrobacter nicotinovorans. Koetter JW, Schulz GE. J Mol Biol 352 418-428 (2005)
  18. Regio- and stereospecific conversion of 4-alkylphenols by the covalent flavoprotein vanillyl-alcohol oxidase. van den Heuvel RH, Fraaije MW, Laane C, van Berkel WJ. J Bacteriol 180 5646-5651 (1998)
  19. Structure and function of ∆1-tetrahydrocannabinolic acid (THCA) synthase, the enzyme controlling the psychoactivity of Cannabis sativa. Shoyama Y, Tamada T, Kurihara K, Takeuchi A, Taura F, Arai S, Blaber M, Shoyama Y, Morimoto S, Kuroki R. J Mol Biol 423 96-105 (2012)
  20. Discovery of a eugenol oxidase from Rhodococcus sp. strain RHA1. Jin J, Mazon H, van den Heuvel RH, Janssen DB, Fraaije MW. FEBS J 274 2311-2321 (2007)
  21. Covalent flavinylation of vanillyl-alcohol oxidase is an autocatalytic process. Jin J, Mazon H, van den Heuvel RH, Heck AJ, Janssen DB, Fraaije MW. FEBS J 275 5191-5200 (2008)
  22. Probing oxygen activation sites in two flavoprotein oxidases using chloride as an oxygen surrogate. Kommoju PR, Chen ZW, Bruckner RC, Mathews FS, Jorns MS. Biochemistry 50 5521-5534 (2011)
  23. Inversion of stereospecificity of vanillyl-alcohol oxidase. van Den Heuvel RH, Fraaije MW, Ferrer M, Mattevi A, van Berkel WJ. Proc Natl Acad Sci U S A 97 9455-9460 (2000)
  24. Elucidating the biosynthetic pathway for the polyketide-nonribosomal peptide collismycin A: mechanism for formation of the 2,2'-bipyridyl ring. Garcia I, Vior NM, Braña AF, González-Sabin J, Rohr J, Moris F, Méndez C, Salas JA. Chem Biol 19 399-413 (2012)
  25. Structural and kinetic analyses of the H121A mutant of cholesterol oxidase. Lim L, Molla G, Guinn N, Ghisla S, Pollegioni L, Vrielink A. Biochem J 400 13-22 (2006)
  26. Enantioselective hydroxylation of 4-alkylphenols by vanillyl alcohol oxidase Drijfhout FP, Fraaije MW, Jongejan H, van Berkel WJ, Franssen MC. Biotechnol Bioeng 59 171-177 (1998)
  27. Site-directed mutagenesis of selected residues at the active site of aryl-alcohol oxidase, an H2O2-producing ligninolytic enzyme. Ferreira P, Ruiz-Dueñas FJ, Martínez MJ, van Berkel WJ, Martínez AT. FEBS J 273 4878-4888 (2006)
  28. Farnesol oxidation in insects: evidence that the biosynthesis of insect juvenile hormone is mediated by a specific alcohol oxidase. Sperry AE, Sen SE. Insect Biochem Mol Biol 31 171-178 (2001)
  29. Rationally engineered flavin-dependent oxidase reveals steric control of dioxygen reduction. Zafred D, Steiner B, Teufelberger AR, Hromic A, Karplus PA, Schofield CJ, Wallner S, Macheroux P. FEBS J 282 3060-3074 (2015)
  30. Geometric restraint drives on- and off-pathway catalysis by the Escherichia coli menaquinol:fumarate reductase. Tomasiak TM, Archuleta TL, Andréll J, Luna-Chávez C, Davis TA, Sarwar M, Ham AJ, McDonald WH, Yankovskaya V, Stern HA, Johnston JN, Maklashina E, Cecchini G, Iverson TM. J Biol Chem 286 3047-3056 (2011)
  31. Asymmetric enzymatic hydration of hydroxystyrene derivatives. Wuensch C, Gross J, Steinkellner G, Gruber K, Glueck SM, Faber K. Angew Chem Int Ed Engl 52 2293-2297 (2013)
  32. The crystal structure and mechanism of an unusual oxidoreductase, GilR, involved in gilvocarcin V biosynthesis. Noinaj N, Bosserman MA, Schickli MA, Piszczek G, Kharel MK, Pahari P, Buchanan SK, Rohr J. J Biol Chem 286 23533-23543 (2011)
  33. Regioselective Enzymatic β-Carboxylation of para-Hydroxy- styrene Derivatives Catalyzed by Phenolic Acid Decarboxylases. Wuensch C, Pavkov-Keller T, Steinkellner G, Gross J, Fuchs M, Hromic A, Lyskowski A, Fauland K, Gruber K, Glueck SM, Faber K. Adv Synth Catal 357 1909-1918 (2015)
  34. Direction of the reactivity of vanillyl-alcohol oxidase with 4-alkylphenols. van den Heuvel RH, Fraaije MW, van Berkel WJ. FEBS Lett 481 109-112 (2000)
  35. Crystal Structure of Alcohol Oxidase from Pichia pastoris. Koch C, Neumann P, Valerius O, Feussner I, Ficner R. PLoS One 11 e0149846 (2016)
  36. Crystal structure and immunologic characterization of the major grass pollen allergen Phl p 4. Zafred D, Nandy A, Pump L, Kahlert H, Keller W. J Allergy Clin Immunol 132 696-703.e10 (2013)
  37. Searching distant homologs of the regulatory ACT domain in phenylalanine hydroxylase. Siltberg-Liberles J, Martinez A. Amino Acids 36 235-249 (2009)
  38. Structure and catalytic mechanism of 3-ketosteroid-Delta4-(5α)-dehydrogenase from Rhodococcus jostii RHA1 genome. van Oosterwijk N, Knol J, Dijkhuizen L, van der Geize R, Dijkstra BW. J Biol Chem 287 30975-30983 (2012)
  39. Common pitfalls in bioinformatics-based analyses: look before you leap. Peri S, Ibarrola N, Blagoev B, Mann M, Pandey A. Trends Genet 17 541-545 (2001)
  40. Precursor of ether phospholipids is synthesized by a flavoenzyme through covalent catalysis. Nenci S, Piano V, Rosati S, Aliverti A, Pandini V, Fraaije MW, Heck AJ, Edmondson DE, Mattevi A. Proc Natl Acad Sci U S A 109 18791-18796 (2012)
  41. Subcellular localization of vanillyl-alcohol oxidase in Penicillium simplicissimum. Fraaije MW, Sjollema KA, Veenhuis M, van Berkel WJ. FEBS Lett 422 65-68 (1998)
  42. A single loop is essential for the octamerization of vanillyl alcohol oxidase. Ewing TA, Gygli G, van Berkel WJ. FEBS J 283 2546-2559 (2016)
  43. Biocatalytic Properties and Structural Analysis of Eugenol Oxidase from Rhodococcus jostii RHA1: A Versatile Oxidative Biocatalyst. Nguyen QT, de Gonzalo G, Binda C, Rioz-Martínez A, Mattevi A, Fraaije MW. Chembiochem 17 1359-1366 (2016)
  44. First partial three-dimensional model of human monoamine oxidase A. Wouters J, Baudoux G. Proteins 32 97-110 (1998)
  45. Two tyrosine residues, Tyr-108 and Tyr-503, are responsible for the deprotonation of phenolic substrates in vanillyl-alcohol oxidase. Ewing TA, Nguyen QT, Allan RC, Gygli G, Romero E, Binda C, Fraaije MW, Mattevi A, van Berkel WJH. J Biol Chem 292 14668-14679 (2017)
  46. The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths. Gygli G, Lucas MF, Guallar V, van Berkel WJH. PLoS Comput Biol 13 e1005787 (2017)
  47. Form, symmetry and packing of biomacromolecules. I. Concepts and tutorial examples. Janner A. Acta Crystallogr A 66 301-311 (2010)
  48. Substrate Channel Flexibility in Pseudomonas aeruginosa MurB Accommodates Two Distinct Substrates. Chen MW, Lohkamp B, Schnell R, Lescar J, Schneider G. PLoS One 8 e66936 (2013)
  49. Unravelling the biosynthesis of pyriculol in the rice blast fungus Magnaporthe oryzae. Jacob S, Grötsch T, Foster AJ, Schüffler A, Rieger PH, Sandjo LP, Liermann JC, Opatz T, Thines E. Microbiology 163 541-553 (2017)
  50. Protein dynamics promote hydride tunnelling in substrate oxidation by aryl-alcohol oxidase. Carro J, Martínez-Júlvez M, Medina M, Martínez AT, Ferreira P. Phys Chem Chem Phys 19 28666-28675 (2017)
  51. A Xylenol Orange-Based Screening Assay for the Substrate Specificity of Flavin-Dependent para-Phenol Oxidases. Ewing TA, van Noord A, Paul CE, van Berkel WJH. Molecules 23 (2018)