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

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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.

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Acknowledgments

We thank the staff of Protein X-ray Crystallography Research Resource (PXRR), and M. Sullivan, J. Toomey, and D. Abel in the Case Center for Synchrotron Biosciences (CSB) at the National Synchrotron Light Source for their generous support. This work was supported by the Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the U.S. Department of Energy through Grant DEAC0298CH10886 and the Laboratory Directed Research and Development Program of Brookhaven National Laboratory (11-007) to CJL; The work done by BAM was in part supported by the Biomedical Technology Centers Program of the National Institute for Biomedical Imaging and Bioengineering (P30-EB-09998) to MRC. The diffraction data were collected at X-3A, X-12C, and X-29 beamlines of National Synchrotron Light Source, USA. Use of the National Synchrotron Light Source was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-98CH10886.

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Authors and Affiliations

  1. European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 6 Rue Jules Horowitz, 38042, Grenoble Cedex 9, France

    Babu A. Manjasetty

  2. Biology Department, Brookhaven National Laboratory, 50 Bell Ave., Upton, NY, 11973, USA

    Xiao-Hong Yu & Chang-Jun Liu

  3. Australian Synchrotron, 800 Blackburn Road, Clayton, VIC, 3168, Australia

    Santosh Panjikar

  4. Division of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda, 386–8567, Japan

    Goro Taguchi

  5. Case Center for Synchrotron Biosciences, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA

    Mark R. Chance

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  1. Babu A. Manjasetty
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  2. Xiao-Hong Yu
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  3. Santosh Panjikar
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  4. Goro Taguchi
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  5. Mark R. Chance
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  6. Chang-Jun Liu
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Correspondence to Chang-Jun Liu.

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B. A. Manjasetty and X.-H. Yu contributed equally to this work.

A contribution to the Special Issue on Metabolic Plant Biology.

The coordinates and structure factors were deposited in the RCSB Protein Data Bank under accession code 2XR7.

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Manjasetty, B.A., Yu, XH., Panjikar, S. et al. Structural basis for modification of flavonol and naphthol glucoconjugates by Nicotiana tabacum malonyltransferase (NtMaT1). Planta 236, 781–793 (2012). https://doi.org/10.1007/s00425-012-1660-8

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