Structurefunction analyses and molecular modeling of caffeic acid-O-methyltransferase and caffeoyl-CoA-O-methyltransferase: Revisiting the basis of alternate methylation pathways during monolignol biosynthesis

Ten protein sequences, each of caffeic acid-O-methyltransferase (COMT) and caffeoyl-coenzyme A-O-methyltransferase (CCoAOMT), catalyzing methylation of precursors of monolignol from selected dicots and monocots have been analyzed and compared on the basis of their amino acid sequence, motifs/domains, three-dimensional (3D) structure, and substrate binding. The isoelectric points of all the COMT and CCoAOMT sequences analyzed were found to vary in the pH range of 5 to 6. Molecular weight analyses suggested CCoAOMT to be smaller monomeric proteins (2729 kDa) as compared with those of COMTs (3940 kDa), which were dimeric. On the basis of phylogenetic analysis, COMT and CCoAOMT were clustered into two major groups, each of which could be further divided into two subgroups of monocots and dicots. Modeling and superimposition of COMT and CCoAOMT sequences of alfalfa (Medicago sativa) revealed that both were quite different at the 3D levels, although they had similarity in the core region. Molecular docking of 16 putative substrates (intermediates of monolignol biosynthesis pathway) revealed that both enzymes interact with all 16 substrates in a similar manner, with thiol esters being the most potent and binding of these putative substrates to CCoAOMT being more efficient.