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Structural basis for the methylation site specificity of SET7/9

Nature Structural & Molecular Biology volume 13, pages 140–146 (2006)Cite this article

Abstract

Human SET7/9 is a protein lysine methyltransferase (PKMT) that methylates histone H3, the tumor suppressor p53 and the TBP-associated factor TAF10. To elucidate the determinants of its substrate specificity, we have solved the enzyme's structure bound to a TAF10 peptide and examined its ability to methylate histone H3, TAF10 and p53 substrates bearing either mutations or covalent modifications within their respective methylation sites. Collectively, our data reveal that SET7/9 recognizes a conserved K/R-S/T/A motif preceding the lysine substrate and has a propensity to bind aspartates and asparagines on the C-terminal side of the lysine target. We then used a sequence-based approach with this motif to identify novel substrates for this PKMT. Among the putative targets is TAF7, which is methylated at Lys5 by the enzyme in vitro. These results demonstrate the predictive value of the consensus motif in identifying novel substrates for SET7/9.

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Figure 1: Structures of SET7/9 in complex with TAF10, p53 and histone H3 peptides.
Figure 2: Comparison of the SET7/9 methylation sites in histone H3, TAF10 and p53.
Figure 3: Identification of novel putative substrates of SET7/9.

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Acknowledgements

We would like to thank K. Battaile for assistance in X-ray data collection, B. Beach for her help in cloning and R. Houtz (University of Kentucky) for his gift of purified AdoMet. We wish to acknowledge R. Kwok, P. O'Brien and D. Peisach for reading the manuscript and providing useful comments. We also thank D. Bochar for his assistance with autoradiography and for reviewing the manuscript and A. Blais for his help with the program EASE. Use of the IMCA-CAT beamline 17-ID at the Advanced Photon Source was supported by the companies of the Industrial Macromolecular Crystallography Association through a contract with the Center for Advanced Radiation Sources at the University of Chicago. Use of the Advanced Photon Source was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. W-31-109-Eng-38. Use of the University of Michigan (UM) DNA Sequencing Core was supported by the US National Institutes of Health through the UM's Cancer Center Support Grant (5 P30 CA46592). This work used the UM Protein Structure Core of the Michigan Diabetes Research and Training Center funded by grant NIH5P60 DK20572 from the US National Institute of Diabetes & Digestive & Kidney Diseases. Finally, this research was supported in part by a Michigan Diabetes and Research Training Center Pilot Grant (F007819) to R.C.T.

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  1. Glenn Hauk

    Present address: Novartis Institutes for BioMedical Research, Inc., 250 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA

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  1. Department of Biological Chemistry, University of Michigan, 1301 Catherine Road, Ann Arbor, 48109-0606, Michigan, USA

    Jean-François Couture, Evys Collazo, Glenn Hauk & Raymond C Trievel

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Correspondence to Raymond C Trievel.

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Couture, JF., Collazo, E., Hauk, G. et al. Structural basis for the methylation site specificity of SET7/9. Nat Struct Mol Biol 13, 140–146 (2006). https://doi.org/10.1038/nsmb1045

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