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Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins

Nature Structural & Molecular Biology volume 18, pages 1414–1420 (2011)Cite this article

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Abstract

Arginine dimethylation plays critical roles in the assembly of ribonucleoprotein complexes in pre-mRNA splicing and piRNA pathways. We report solution structures of SMN and SPF30 Tudor domains bound to symmetric and asymmetric dimethylated arginine (DMA) that is inherent in the RNP complexes. An aromatic cage in the Tudor domain mediates dimethylarginine recognition by electrostatic stabilization through cation-π interactions. Distinct from extended Tudor domains, dimethylarginine binding by the SMN and SPF30 Tudor domains is independent of proximal residues in the ligand. Yet, enhanced micromolar affinities are obtained by external cooperativity when multiple methylation marks are presented in arginine- and glycine-rich peptide ligands. A hydrogen bond network in the SMN Tudor domain, including Glu134 and a tyrosine hydroxyl of the aromatic cage, enhances cation-π interactions and is impaired by a mutation causing an E134K substitution associated with spinal muscular atrophy. Our structural analysis enables the design of an optimized binding pocket and the prediction of DMA binding properties of Tudor domains.

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Figure 1: Tudor binding to methylated arginines.
Figure 2: Recognition of sDMA and aDMA by SMN and SPF30 Tudor domains.
Figure 3: Implications of sDMA recognition in snRNP and piRNP assembly pathways.

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Acknowledgements

The authors are grateful to G. Demiraslan (Helmholtz Zentrum München) for protein production. We thank I. Poser and T. Hyman (Max Planck Institute of Molecular Cell Biology and Genetics) for the gift of the SMN-GFP stable cell line, J. Brennecke for helpful discussion and the Bavarian NMR Centre for NMR time. K.T. acknowledges support by the Alexander von Humboldt foundation; T.M. acknowledges support by a European Molecular Biology Organization Long Term Fellowship and a Schrödinger Fellowship from the Austrian Science Fund. This work was supported by the Deutsche Forschungsgemeinschaft (M.S. and K.M.N.).

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Authors and Affiliations

  1. Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany

    Konstantinos Tripsianes, Tobias Madl & Michael Sattler

  2. Department Chemie, Munich Center for Integrated Protein Science at the Chair of Biomolecular NMR, Technische Universität München, Garching, Germany

    Konstantinos Tripsianes, Tobias Madl & Michael Sattler

  3. Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

    Martin Machyna & Karla M Neugebauer

  4. Dipartimento di Tecnologie Alimentari e Microbiologiche, Università di Milano, Milano, Italy

    Dimitrios Fessas

  5. Department of Biochemistry, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany

    Clemens Englbrecht & Utz Fischer

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  1. Konstantinos Tripsianes
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Contributions

K.T. carried out molecular biology experiments, protein purification, NMR analysis and structure calculations. T.M. did quantum chemical calculations and contributed to NMR experiments. D.F. analyzed the ITC experiments. K.M.N. and U.F. designed, and M.M. and C.E. conducted, immunoprecipitation experiments. K.T. and M.S. conceived and designed the project and wrote the paper. All authors discussed the results and commented on the manuscript.

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Correspondence to Michael Sattler.

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Tripsianes, K., Madl, T., Machyna, M. et al. Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins. Nat Struct Mol Biol 18, 1414–1420 (2011). https://doi.org/10.1038/nsmb.2185

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