The Arabidopsis Histone Methyltransferase SUVR4 Binds Ubiquitin via a Domain with a Four-Helix Bundle Structure.

In eukaryotes, different chromatin states facilitate or repress gene expression and restrict the activity of transposable elements. Post-translational modifications (PTMs) of amino acid residues on the N-terminal tails of histones are suggested to define such states. The histone lysine methyltransferase (HKMTase) SUVAR3-9 RELATED4 (SUVR4) of Arabidopsis thaliana functions as a ...
repressor of transposon activity. Binding of ubiquitin by the WIYLD domain facilitates the addition of two methyl groups to monomethylated lysine 9 of histone H3. By using NMR spectroscopy we identified SUVR4 WIYLD (S4WIYLD) as a domain with a four-helix bundle structure, in contrast to three-helix bundles of other ubiquitin binding domains. NMR titration analyses, showed that residues of helix α1 (Q38, L39, D40) and helix α4, (N68, T70, A71, V73, D74, I76, S78, E82) of S4WYILD, and residues between the first and second -strand (T9, G10), and on -strands three (R42, G47, K48, Q49) and four (H68, R72, L73), undergo significant chemical shift changes when the two proteins interact. A model of the complex, generated using HADDOCK, suggests that the N-terminal and C-terminal parts of S4WIYLD constitute a surface that interacts with charged residues close to the hydrophobic patch of ubiquitin. The WIYLD domains of the closely related SUVR1 and SUVR2 Arabidopsis proteins also bind ubiquitin, indicating that this is a general feature of this domain. Whether SUVR proteins act both as readers of monoubiquitinated H2B and writers of histone PTMs is discussed.
Date: Mar. 13, 2014
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