Protein-lysine methyltransferase that selectively trimethylates the flavoprotein ETFB in mitochondria. Thereby, may negatively regulate the function of ETFB in electron transfer from Acyl-CoA dehydrogenases. Interacts with HSPD1; this protein may possibly be a methylation substrate. Concentrated in cytoplasmic granular foci. Belongs to the methyltransferase superfamily. ETFBKMT family.