Structural Basis of Setd6-Mediated Regulation of the Nf-Kb Network Via Methyl-Lysine Signaling

Article (PDF Available)inNucleic Acids Research 39(15):6380-9 · April 2011with40 Reads
DOI: 10.1093/nar/gkr256 · Source: PubMed
SET domain containing 6 (SETD6) monomethylates the RelA subunit of nuclear factor kappa B (NF-κB). The ankyrin repeats of G9a-like protein (GLP) recognizes RelA monomethylated at Lys310. Adjacent to Lys310 is Ser311, a known phosphorylation site of RelA. Ser311 phosphorylation inhibits Lys310 methylation by SETD6 as well as binding of Lys310me1 by GLP. The structure of SETD6 in complex with RelA peptide containing the methylation site, in the presence of S-adenosyl-l-methionine, reveals a V-like protein structure and suggests a model for NF-κB binding to SETD6. In addition, structural modeling of the GLP ankyrin repeats bound to Lys310me1 peptide provides insight into the molecular basis for inhibition of Lys310me1 binding by Ser311 phosphorylation. Together, these findings provide a structural explanation for a key cellular signaling pathway centered on RelA Lys310 methylation, which is generated by SETD6 and recognized by GLP, and incorporate a methylation–phosphorylation switch of adjacent lysine and serine residues. Finally, SETD6 is structurally similar to the Rubisco large subunit methyltransferase. Given the restriction of Rubisco to plant species, this particular appearance of the protein lysine methyltransferase has been evolutionarily well conserved.
    • "Anergic CD8+ T lymphocytes lack phosphorylation of S311, as well as acetylation of K310 indicating S311 as an important regulator of NF-κB activity in T cells [80]. In dendritic cells, PKCζ phosphorylation of p65 at S311 prevents the binding of histone methyltransferase G9a-like protein (GLP) to relieve the repression of p65 target genes [81,82]. IL-1β induced phosphorylation of p65 at S316 leads to increased transactivation and cell growth [83]. "
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    • "All ternary structures of SET domain methyltransferases in complex with cofactor and substrate have the substrate peptide lying in a narrow groove formed by the I-SET domain on one side, and the post-SET domain on the opposite side. This peptide binding groove is responsible for substrate sequence specificity and positions the substrate lysine side chain into a conserved channel that goes deep into the core of the SET domain and meets the cofactor at the conserved active site as described above (Figure 2) ([38,43,44,47,48,49,50,51,52] and PDB code 4AU7). The width of the peptide-binding groove is critical for catalysis, and the distance separating the two edges is between 7.2 and 7.8 Å across all available structures of active SET domain constructs (see materials and methods section for details). "
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