Histone methyltransferase which contributes to the establishment of heterochromatin by specifically methylating histone H3 to form H3K9me (PubMed:16024659, PubMed:8138176). Part of the Clr4 methyltransferase complex (ClrC). ClrC preferentially ubiquitylates H3K14 and ClrC-mediated H3 ubiquitination promotes clr4 methyltransferase activity (PubMed:31468675). Clr4 functions as a reader and writer of H3K9 methylation. It sets the H3K9me mark and afterwards this H3K9me mark is recognized by the chromodomains of clr4 and swi6/HP1, which then recruit additional clr4 leading to the methylation of neighboring nucleosomes (PubMed:11242054, PubMed:18345014, PubMed:21224386). H3K9me represents a specific tag for epigenetic transcriptional repression by recruiting swi6/HP1 to methylated histones which leads to transcriptional silencing within centromeric heterochromatin, telomeres, ribosomal DNA repeats, and the silent mating-type region (PubMed:16024659, PubMed:8138176). Clr4 methyltransferase activity promotes the assembly of a tripartite complex composed of ClrC and complexes involved in siRNA generation (PubMed:20705239). Apart from H3K9, methylates also non-histone proteins such as mlo3 (PubMed:21436456, PubMed:28143796). Interacts with mlo3 to promote the processing of centromeric and antisense RNAs (PubMed:21436456). L-lysyl(9)-[histone H3] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3] + 3 S-adenosyl-L-homocysteine N(6)-methyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-methionine = H(+) + N(6),N(6)-dimethyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-homocysteine N(6),N(6)-dimethyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-methionine = H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-homocysteine L-lysyl-[protein] + S-adenosyl-L-methionine = H(+) + N(6)-methyl-L-lysyl-[protein] + S-adenosyl-L-homocysteine N(6)-methyl-L-lysyl-[protein] + S-adenosyl-L-methionine = H(+) + N(6),N(6)-dimethyl-L-lysyl-[protein] + S-adenosyl-L-homocysteine N(6),N(6)-dimethyl-L-lysyl-[protein] + S-adenosyl-L-methionine = H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl-[protein] + S-adenosyl-L-homocysteine L-lysyl(9)-[histone H3] + S-adenosyl-L-methionine = H(+) + N(6)-methyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-homocysteine An internal loop (autoregulatory loop) inhibits the catalytic activity of the enzyme by blocking the histone H3K9 substrate-binding pocket. Autocatalytic methylation of specific lysine residues in this loop promote a conformational switch that enhances the H3K9me activity of clr4. Component of the Clr4 methyltransferase complex (ClrC) composed of at least clr4, rik1, pcu4, rbx1, raf1 and raf2. The cullin pcu4, rik1, raf1, raf2 and the ring-box protein rbx1 are components of an E3 ubiquitin ligase, whose activity is essential for heterochromatin assembly (PubMed:16024659, PubMed:16127433, PubMed:17114925, PubMed:12389037). Interacts directly with pcu4 (PubMed:16127433). Interacts with mlo3 (PubMed:21436456). The chromodomain serves to recognize and bind to H3K9me. In the pre-SET domain, Cys residues bind 3 zinc ions that are arranged in a triangular cluster; some of these Cys residues contribute to the binding of two zinc ions within the cluster. Autocatalytic methylation of specific lysine residues in an internal loop (autoregulatory loop) promote a conformational switch that enhances the H3K9me activity of clr4. Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. Suvar3-9 subfamily.