Planta

, Volume 236, Issue 3, pp 781–793

Structural basis for modification of flavonol and naphthol glucoconjugates by Nicotiana tabacum malonyltransferase (NtMaT1)

  • Babu A. Manjasetty
  • Xiao-Hong Yu
  • Santosh Panjikar
  • Goro Taguchi
  • Mark R. Chance
  • Chang-Jun Liu
Original Article

Abstract

Plant HXXXD acyltransferase-catalyzed malonylation is an important modification reaction in elaborating the structural diversity of flavonoids and anthocyanins, and a universal adaptive mechanism to detoxify xenobiotics. Nicotiana tabacum malonyltransferase 1 (NtMaT1) is a member of anthocyanin acyltransferase subfamily that uses malonyl-CoA (MLC) as donor catalyzing transacylation in a range of flavonoid and naphthol glucosides. To gain insights into the molecular basis underlying its catalytic mechanism and versatile substrate specificity, we resolved the X-ray crystal structure of NtMaT1 to 3.1 Å resolution. The structure comprises two α/β mixed subdomains, as typically found in the HXXXD acyltransferases. The partial electron density map of malonyl-CoA allowed us to reliably dock the entire molecule into the solvent channel and subsequently define the binding sites for both donor and acceptor substrates. MLC bound to the NtMaT1 occupies one end of the long solvent channel between two subdomains. On superimposing and comparing the structure of NtMaT1 with that of an enzyme from anthocyanin acyltransferase subfamily from red chrysanthemum (Dm3Mat3) revealed large architectural variation in the binding sites, both for the acyl donor and for the acceptor, although their overall protein folds are structurally conserved. Consequently, the shape and the interactions of malonyl-CoA with the binding sites’ amino acid residues differ substantially. These major local architectural disparities point to the independent, divergent evolution of plant HXXXD acyltransferases in different species. The structural flexibility of the enzyme and the amendable binding pattern of the substrates provide a basis for the evolution of the distinct, versatile substrate specificity of plant HXXXD acyltransferases.

Keywords

HXXXD acyltransferase BAHD Nicotiana tabacum malonyltransferase Flavonol Xenobiotics Crystal structure 

References

  1. Altman A, Hasegawa PM (2011) Plant biotechnology and agriculture: prospects for the 21st century. Academic Press, UKGoogle Scholar
  2. Buglino J, Onwueme KC, Ferreras JA et al (2004) Crystal structure of PapA5, a phthiocerol dimycocerosyl transferase from Mycobacterium tuberculosis. J Biol Chem 279:30634–30642PubMedCrossRefGoogle Scholar
  3. Collaborative Computational Project Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50:760–763CrossRefGoogle Scholar
  4. Cowtan K (2000) General quadratic functions in real and reciprocal space and their application to likelihood phasing. Acta Crystallogr D Biol Crystallogr 56:1612–1621PubMedCrossRefGoogle Scholar
  5. Cowtan K (2006) The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr D Biol Crystallogr 62:1002–1011PubMedCrossRefGoogle Scholar
  6. D’Auria JC (2006) Acyltransferases in plants: a good time to be BAHD. Curr Opin Plant Biol 9:331–340PubMedCrossRefGoogle Scholar
  7. Day JA, Saunders EM (2004) Glycosidation of chlorophenols by Lemna minor. Environ Toxicol Chem 23:613–620PubMedCrossRefGoogle Scholar
  8. DeLano W (2003) The PyMOL molecular graphics system. Version 1.3, Schrödinger, LLCGoogle Scholar
  9. Dhaubhadel S, Farhangkhoee M, Chapman R (2008) Identification and characterization of isoflavonoid specific glycosyltransferase and malonyltransferase from soybean seeds. J Exp Bot 59:981–994PubMedCrossRefGoogle Scholar
  10. Dixon RA (2004) Phytoestrogens. Annu Rev Plant Biol 55:225–261PubMedCrossRefGoogle Scholar
  11. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126–2132PubMedCrossRefGoogle Scholar
  12. Ferrer JL, Austin MB, Stewart C Jr, Noel JP (2008) Structure and function of enzymes involved in the biosynthesis of phenylpropanoids. Plant Physiol Biochem 46:356–370PubMedCrossRefGoogle Scholar
  13. Fraenkel GS (1959) The raison d’Etre of secondary plant substances. Science 129:1466–1470PubMedCrossRefGoogle Scholar
  14. Fujiwara H, Tanaka Y, Yonekura-Sakakibara K et al (1998) cDNA cloning, gene expression and subcellular localization of anthocyanin 5-aromatic acyltransferase from Gentiana triflora. Plant J 16:421–431PubMedCrossRefGoogle Scholar
  15. Garvey GS, McCormick SP, Rayment I (2008) Structural and functional characterization of the TRI101 trichothecene 3-O-acetyltransferase from Fusarium sporotrichioides and Fusarium graminearum: kinetic insights to combating Fusarium head blight. J Biol Chem 283:1660–1669PubMedCrossRefGoogle Scholar
  16. Garvey GS, McCormick SP, Alexander NJ, Rayment I (2009) Structural and functional characterization of TRI3 trichothecene 15-O-acetyltransferase from Fusarium sporotrichioides. Protein Sci 18:747–761PubMedGoogle Scholar
  17. Gerasimenko I, Ma X, Sheludko Y et al (2004) Purification and partial amino acid sequences of the enzyme vinorine synthase involved in a crucial step of ajmaline biosynthesis. Bioorg Med Chem 12:2781–2786PubMedCrossRefGoogle Scholar
  18. Gibrat JF, Madej T, Bryant SH (1996) Surprising similarities in structure comparison. Curr Opin Struct Biol 6:377–385PubMedCrossRefGoogle Scholar
  19. Gould K, Davies KM, Winefield C (2009) Anthocyanins: biosynthesis, functions, and applications. SpringerGoogle Scholar
  20. Harborne JB, Williams CA (2000) Advances in flavonoid research since 1992. Phytochemistry 55:481–504PubMedCrossRefGoogle Scholar
  21. Heller W, Forkmann G (1994) In: Harborne JB (ed) The flavonoids. Chapman & Hall, London, pp 499–535Google Scholar
  22. Hendrickson WA, Horton JR, LeMaster DM (1990) Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J 9:1665–1672PubMedGoogle Scholar
  23. Jez JM et al (2000) Structural control of polyketide formation in plant-specific polyketide synthesis. Chem Biol 7:919–930PubMedCrossRefGoogle Scholar
  24. Jogl G, Tong L (2003) Crystal structure of carnitine acetyltransferase and implications for the catalytic mechanism and fatty acid transport. Cell 112:113–122PubMedCrossRefGoogle Scholar
  25. Jogl G, Hsiao Y-S, Tong L (2004) Structure and function of carnitine acyltransferases. Ann N Y Acad Sci 1033:17–29PubMedCrossRefGoogle Scholar
  26. Krissinel E (2010) Crystal contacts as nature’s docking solutions. J Comput Chem 31:133–143PubMedCrossRefGoogle Scholar
  27. Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372:774–797PubMedCrossRefGoogle Scholar
  28. Lamy S, Blanchette M, Michaud-Levesque J et al (2006) Delphinidin, a dietary anthocyanidin, inhibits vascular endothelial growth factor receptor-2 phosphorylation. Carcinogenesis 27:989–996PubMedCrossRefGoogle Scholar
  29. Lamy S, Beaulieu E, Labbé D et al (2008) Delphinidin, a dietary anthocyanidin, inhibits platelet-derived growth factor ligand/receptor (PDGF/PDGFR) signaling. Carcinogenesis 29:1033–1041PubMedCrossRefGoogle Scholar
  30. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291CrossRefGoogle Scholar
  31. Liu C-J, Deavours BE, Richard SB et al (2006) Structural basis for dual functionality of isoflavonoid O-methyltransferases in the evolution of plant defense responses. Plant Cell 18:3656–3669PubMedCrossRefGoogle Scholar
  32. Luo J, Nishiyama Y, Fuell C et al (2007) Convergent evolution in the BAHD family of acyl transferases: identification and characterization of anthocyanin acyl transferases from Arabidopsis thaliana. Plant J 50:678–695PubMedCrossRefGoogle Scholar
  33. Ma X, Koepke J, Panjikar S et al (2005) Crystal structure of vinorine synthase, the first representative of the BAHD superfamily. J Biol Chem 280:13576–13583PubMedCrossRefGoogle Scholar
  34. Markham KR, Ryan KG, Gould KS, Rickards GK (2000) Cell wall sited flavonoids in lisianthus flower petals. Phytochemistry 54:681–687PubMedCrossRefGoogle Scholar
  35. Matern U, Heller W, Himmelspach K (1983) Conformational changes of apigenin 7-O-(6-O-malonylglucoside), a vacuolar pigment from parsley, with solvent composition and proton concentration. Eur J Biochem 133:439–448PubMedCrossRefGoogle Scholar
  36. McCoy AJ, Grosse-Kunstleve RW, Adams PD et al (2007) Phaser crystallographic software. J Appl Crystallogr 40:658–674PubMedCrossRefGoogle Scholar
  37. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30:2785–2791PubMedCrossRefGoogle Scholar
  38. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53:240–255PubMedCrossRefGoogle Scholar
  39. Nakayama T, Suzuki H, Nishino T (2003) Anthocyanin acyltransferases: specificities, mechanism, phylogenetics, and applications. J Mol Catal B Enzym 23:117–132CrossRefGoogle Scholar
  40. Onwueme KC, Ferreras JA, Buglino J et al (2004) Mycobacterial polyketide-associated proteins are acyltransferases: proof of principle with Mycobacterium tuberculosis PapA5. Proc Natl Acad Sci USA 101:4608–4613PubMedCrossRefGoogle Scholar
  41. Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. In: Carter CW Jr, Sweet RM (eds) Method Enzymology: macromolecular crystallography, part A, V276. Academic Press, New York, pp 307–326Google Scholar
  42. Panjikar S, Parthasarathy V, Lamzin VS et al (2005) Auto-rickshaw: an automated crystal structure determination platform as an efficient tool for the validation of an X-ray diffraction experiment. Acta Crystallogr D Biol Crystallogr 61:449–457PubMedCrossRefGoogle Scholar
  43. Panjikar S, Parthasarathy V, Lamzin VS et al (2009) On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination. Acta Crystallogr D Biol Crystallogr 65:1089–1097PubMedCrossRefGoogle Scholar
  44. Rautengarten C et al (2012) Arabidopsis deficient in cutin ferulate encodes a transferase required for feruloylation of omega-hydroxy fatty acids in cutin polyester. Plant Physiol 158:654–665PubMedCrossRefGoogle Scholar
  45. Read RJ (1986) Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr A Found Crystallogr 42:140–149CrossRefGoogle Scholar
  46. Rossmann MG, Moras D, Olsen KW (1974) Chemical and biological evolution of nucleotide-binding protein. Nature 250:194–199PubMedCrossRefGoogle Scholar
  47. Sandermann H Jr (1994) Higher plant metabolism of xenobiotics: the “green liver” concept. Pharmacogenetics 4:225–241PubMedCrossRefGoogle Scholar
  48. Sandermann H Jr, Schmitt R, Eckey H, Bauknecht T (1991) Plant biochemistry of xenobiotics: isolation and properties of soybean O- and N-glucosyl and O- and N-malonyltransferases for chlorinated phenols and anilines. Arch Biochem Biophys 287:341–350PubMedCrossRefGoogle Scholar
  49. Schneider TR, Sheldrick GM (2002) Substructure solution with SHELXD. Acta Crystallogr D Biol Crystallogr 58:1772–1779PubMedCrossRefGoogle Scholar
  50. Sheldrick GM (2010) Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr D Biol Crystallogr 66:479–485PubMedCrossRefGoogle Scholar
  51. Sinclair JC, Sandy J, Delgoda R et al (2000) Structure of arylamine N-acetyltransferase reveals a catalytic triad. Nat Struct Biol 7:560–564PubMedCrossRefGoogle Scholar
  52. St Pierre B, De Luca V (2000) Evolution of acyltransferase genes: origin and diversification of the BAHD superfamily of acyltransferases involved in secondary metabolism. In: Romeo JT, Ibrahim R, Varin L, De Luca V (eds) Recent advances in phytochemistry. Evolution of metabolic pathways. Elsevier Science Ltd, Oxford, pp 285–315Google Scholar
  53. Strack D, Wray V (1994) The anthocyanins. In: Harborne JB (ed) The flavonoids: advances in research since 1986. Chapman & Hall, LondonGoogle Scholar
  54. Suzuki H, Nakayama T, Yonekura-Sakakibara K et al (2001) Malonyl-CoA: anthocyanin 5-O-glucoside-6″-O-malonyltransferase from scarlet sage (Salvia splendens) flowers. Enzyme purification, gene cloning, expression, and characterization. J Biol Chem 276:49013–49019PubMedCrossRefGoogle Scholar
  55. Suzuki H, Nakayama T, Yonekura-Sakakibara K et al (2002) cDNA cloning, heterologous expressions, and functional characterization of malonyl-coenzyme a:anthocyanidin 3-O-glucoside-6″-O-malonyltransferase from dahlia flowers. Plant Physiol 130:2142–2151PubMedCrossRefGoogle Scholar
  56. Suzuki H, Nakayama T, Nishino T (2003a) Proposed mechanism and functional amino acid residues of malonyl-CoA:anthocyanin 5-O-glucoside-6″-O-malonyltransferase from flowers of Salvia splendens, a member of the versatile plant acyltransferase family. Biochemistry 42:1764–1771PubMedCrossRefGoogle Scholar
  57. Suzuki H, Sawada S, Yonekura-Sakakibara K et al (2003b) Identification of a cDNA encoding malonyl-coenzyme A: anthocyanidin 3-O-glucoside 6″-O- malonyltransferase from Cineraria (Senecio cruentus) Flowers. Plant Biotechnol 20:229–234CrossRefGoogle Scholar
  58. Suzuki H, Sawada S, Watanabe K et al (2004) Identification and characterization of a novel anthocyanin malonyltransferase from scarlet sage (Salvia splendens) flowers: an enzyme that is phylogenetically separated from other anthocyanin acyltransferases. Plant J 38:994–1003PubMedCrossRefGoogle Scholar
  59. Suzuki H, Nishino T, Nakayama T (2007) cDNA cloning of a BAHD acyltransferase from soybean (Glycine max): isoflavone 7-O-glucoside-6″-O-malonyltransferase. Phytochemistry 68:2035–2042PubMedCrossRefGoogle Scholar
  60. Taguchi G, Shitchi Y, Shirasawa S et al (2005) Molecular cloning, characterization, and downregulation of an acyltransferase that catalyzes the malonylation of flavonoid and naphthol glucosides in tobacco cells. Plant J 42:481–491PubMedCrossRefGoogle Scholar
  61. Taguchi G, Ubukata T, Nozue H et al (2010) Malonylation is a key reaction in the metabolism of xenobiotic phenolic glucosides in Arabidopsis and tobacco. Plant J 63:1031–1041PubMedCrossRefGoogle Scholar
  62. Terwilliger TC (2001) Maximum-likelihood density modification using pattern recognition of structural motifs. Acta Crystallogr D Biol Crystallogr 57:1755–1762PubMedCrossRefGoogle Scholar
  63. Terwilliger TC, Berendzen J (1999) Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr 55:849–861PubMedCrossRefGoogle Scholar
  64. Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with anew scoring function, efficient optimization, and multithreading. J Comput Chem 31:455–461PubMedGoogle Scholar
  65. Tuominen LK, Johnson VE, Tsai C-J (2011) Differential phylogenetic expansions in BAHD acyltransferases across five angiosperm taxa and evidence of divergent expression among Populus paralogues. BMC Genomics 12:236PubMedCrossRefGoogle Scholar
  66. Unno H, Ichimaida F, Suzuki H et al (2007) Structural and mutational studies of anthocyanin malonyltransferases establish the features of BAHD enzyme catalysis. J Biol Chem 282:15812–15822PubMedCrossRefGoogle Scholar
  67. Upton A, Johnson N, Sandy J, Sim E (2001) Arylamine N-acetyltransferases—of mice, men and microorganisms. Trends Pharmacol Sci 22:140–146PubMedCrossRefGoogle Scholar
  68. Wink M (2010) Biochemistry of plant secondary metabolism. Wiley, New YorkGoogle Scholar
  69. Winkel-Shirley B (2002) Biosynthesis of flavonoids and effects of stress. Curr Opin Plant Biol 5:218–223PubMedCrossRefGoogle Scholar
  70. Winn MD, Isupov MN, Murshudov GN (2001) Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr D Biol Crystallogr 57:122–133PubMedCrossRefGoogle Scholar
  71. Yonekura-Sakakibara K, Tanaka Y, Fukuchi-Mizutani M et al (2000) Molecular and biochemical characterization of a novel hydroxycinnamoyl-CoA: anthocyanin 3-O-glucoside-6″-O-acyltransferase from Perilla frutescens. Plant Cell Physiol 41:495–502PubMedCrossRefGoogle Scholar
  72. Yu X-H, Chen M-H, Liu C-J (2008) Nucleocytoplasmic-localized acyltransferases catalyze the malonylation of 7-O-glycosidic (iso)flavones in Medicago truncatula. Plant J 55:382–396PubMedCrossRefGoogle Scholar
  73. Yu X-H, Gou J-Y, Liu C-J (2009) BAHD superfamily of acyl-CoA dependent acyltransferases in Populus and Arabidopsis: bioinformatics and gene expression. Plant Mol Biol 70:421–442PubMedCrossRefGoogle Scholar
  74. Zhao J, Dixon RA (2010) The ‘ins’ and ‘outs’ of flavonoid transport. Trends Plant Sci 15:72–80PubMedCrossRefGoogle Scholar
  75. Zhao J, Huhman D, Shadle G et al (2011) MATE2 mediates vacuolar sequestration of flavonoid glycosides and glycoside malonates in Medicago truncatula. Plant Cell 23:1536–1555PubMedCrossRefGoogle Scholar
  76. Zubieta C, He X-Z, Dixon RA, Noel JP (2001) Structures of two natural product methyltransferases reveal the basis for substrate specificity in plant O-methyltransferases. Nat Struct Mol Biol 8:271–279CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Babu A. Manjasetty
    • 1
  • Xiao-Hong Yu
    • 2
  • Santosh Panjikar
    • 3
  • Goro Taguchi
    • 4
  • Mark R. Chance
    • 5
  • Chang-Jun Liu
    • 2
  1. 1.European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell InteractionsUJF-EMBL-CNRSGrenoble Cedex 9France
  2. 2.Biology DepartmentBrookhaven National LaboratoryUptonUSA
  3. 3.Australian SynchrotronClaytonAustralia
  4. 4.Division of Applied Biology, Faculty of Textile Science and TechnologyShinshu UniversityUedaJapan
  5. 5.Case Center for Synchrotron Biosciences, Center for Proteomics and Bioinformatics, School of MedicineCase Western Reserve UniversityClevelandUSA

Personalised recommendations