Lysine Methyl Transferase, Homo Sapiens
Introduction
Histone Methylation
Histone proteins aid in the packing of DNA for the purpose of compacting the genome in the nucleus of the cell and regulating physical accessibility of genes for transcription. The protein itself is an octamer made of heterodimer core proteins H2a, H2b, H3, and H4, with H1 and H5 acting as linker proteins. About 145-157 base pairs wind around a histone core protein. (1) Modifications to histone core proteins can affect the accessibility of genes in the genome and their ability to be transcribed. Some of these modifications include methylation/demethylation, acetylation/deacetylation, and ubiquitination/deubiquitination. (2)
Specifically, histone methylation is associated with gene activation. (3) Many domain families fall under the Histone methylase family, one of these enzymes being the SET7 domain family, which can target H3, H4, or H2a; each of these methylation sites can have different effects on gene expression within the genome. Typically, methylation of some of these sites are always present on both active and inactive genes, extra methylations required for activity. (4) Some tumor related genes such as p53 are site specifically methylated to promote biological function (5), whereas hypomethylation of CpG is linked to tumor genesis. (2) A particular enzyme in the SET7 domain family is lysine methyltransferase, which acts on the histone by adding a methyl group to Lys4 on H3; the addition results in promotion of gene unwinding and gene transcription. (4,3)
The Substrate
The SAM Cofactor
KMT Structure
Composition
The secondary structure is composed of 10% and 37% . The helical composition includes 3 , with two residing in the SET domain and one in the C-terminal domain. The alpha helices in the SET domain are two turns while the C-terminal helix is by far the largest with 4 turns. There are also 2 in the SET domain which are each one turn. There are 21 total beta strands which reside in the N-terminal domain and the SET domain. The beta strands are primarily anti-parallel and multiple antiparallel strands are connected by and beta turns.
The C-Terminal Domain
The of lysine methyltransferase is essential for the catalytic activity of the enzyme. Hydrophobic packing of the C-terminal segment (residues 345-366) forms the lysine access channel. Residues 337-349 create a that stabilizes the orientation of two tyrosine residues Tyr 335 and Tyr337 that form the lysine access channel. The hydrophobic packing of the C-terminal against beta sheet 19 (specifically residue 299) orient the SAM cofactor so the methyl donating group is oriented toward the lysine access channel. donating group is oriented toward the lysine access channel.
The SET 7/9 Domain
The Active Site
Inhibitors
Sinefungin is a potent methyltransferase inhibitor. It is a structural analog of S-adenosylmethionine that is more stable due to the ability to create two additional hydrogen bonds to its amine group in the active site. It has been used experimentally to inhibit the SET 7/9 protein on peritoneal fibrosis in mice and in human peritoneal mesothelial cells. Tamura et al. (2018) found that sinefungin suppressed the cell accumulation and thickening in methylglyoxal peritoneal fibrosis.
