Methyltransferase involved in the biosynthesis of the benzylisoquinoline alkaloid noscapine (PubMed:22535422, PubMed:29723437, PubMed:27378283, PubMed:29610307). Catalyzes the conversion of (S)-scoulerine to (S)-tetrahydrocolumbamine (PubMed:22535422). (S)-scoulerine + S-adenosyl-L-methionine = (S)-tetrahydrocolumbamine + H(+) + S-adenosyl-L-homocysteine Alkaloid biosynthesis. Homodimer (PubMed:29723437). Forms heterodimer with SOMT2 (PubMed:29723437, PubMed:27378283). The heterodimer SOMT2-SOMT3 possesses 3-O-acetyl-4'-O-demethylpapaveroxine 4'-O-methyltransferase activity, where SOMT2 is the catalytic subunit (PubMed:29723437, PubMed:27378283). Highly expressed in capsules (PubMed:22653730). Expressed is stems (PubMed:22653730, PubMed:22535422). Expressed at low levels in roots (PubMed:22535422). Belongs to the class I-like SAM-binding methyltransferase superfamily. Cation-independent O-methyltransferase family. COMT subfamily.