Structural basis for product specificities of MLL family methyltransferases

Human mixed-lineage leukemia (MLL) family methyltransferases methylate histone H3 lysine 4 to different methylation states (me1/me2/me3) with distinct functional outputs, but the mechanism underlying the different product specificities of MLL proteins remains unclear. Here, we develop methodologies to quantitatively measure the methylation rate difference between mono-, di-, and tri-methylation steps and demonstrate that MLL proteins possess distinct product specificities in the context of the minimum MLL-RBBP5-ASH2L complex. Comparative structural analyses of MLL complexes by X-ray crystal structures, fluorine-19 nuclear magnetic resonance, and molecular dynamics simulations reveal that the dynamics of two conserved tyrosine residues at the F/Y (phenylalanine/tyrosine) switchpositions fine-tune the product specificity. The variation in the intramolecular interaction between SET-N and SET-C affects the F/Y switch dynamics, thus determining the product specificities of MLL proteins. These results indicate a modified F/Y switch rule applicable for most SET domain methyltransferases and implicate the functional divergence of MLL proteins.

Automated summary

This study develops methodologies to measure the methylation rate difference between different states of methylation and demonstrates that MLL proteins possess distinct product specificities. Structural analyses reveal that the dynamics of conserved tyrosine residues fine-tune the product specificity, and the variation in intramolecular interaction affects the dynamics, determining the product specificities of MLL proteins.