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Mechanism of multiple lysine methylation by the SET domain enzyme Rubisco LSMT

Abstract

SET domain protein methyltransferases catalyze the transfer of methyl groups from the cofactor S-adenosylmethionine (AdoMet) to specific lysine residues of protein substrates, such as the N-terminal tails of histones H3 and H4 and the large subunit of the Rubisco holoenzyme complex. The crystal structures of pea Rubisco large subunit methyltransferase (LSMT) in ternary complexes with either lysine or ε-N-methyllysine (MeLys) and the product S-adenosylhomocysteine (AdoHcy) were determined to resolutions of 2.65 and 2.55 Å, respectively. The ζ-methyl group of MeLys is bound to the enzyme via carbon–oxygen hydrogen bonds that play a key role in catalysis. The methyl donor and acceptor are aligned in a linear geometry for SN2 nucleophilic transfer of the methyl group during catalysis. Differences in hydrogen bonding between the MeLys ε-amino group and Rubisco LSMT and SET7/9 explain why Rubisco LSMT generates multiply methylated Lys, wheras SET7/9 generates only MeLys.

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Figure 1: Lys and MeLys are alternative substrates for Rubisco LSMT.
Figure 2: Binding of Lys in the lysine-binding pocket of LSMT.
Figure 3: Binding of MeLys in the lysine-binding pocket of LSMT.
Figure 4: Stereochemical mechanism of methyl group transfer.
Figure 5: Comparison of hydrogen bonding in the active sites of LSMT and SET7/9.
Figure 6: Space filling comparison of the lysine-binding sites of LSMT and SET7/9.
Figure 7: Substrate specificity of LSMT.

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Acknowledgements

We would like to thank S. Gamblin for SET7/9–AdoHcy–histone H3 ternary complex coordinates, and D. Engelman and G. Felsenfeld for insightful discussions. Research by R.L.H. and E.M.F. was supported by the DOE, Division of Energy Biosciences.

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Correspondence to James H Hurley.

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Trievel, R., Flynn, E., Houtz, R. et al. Mechanism of multiple lysine methylation by the SET domain enzyme Rubisco LSMT. Nat Struct Mol Biol 10, 545–552 (2003). https://doi.org/10.1038/nsb946

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