Structure–function analyses and molecular modeling of caffeic acid‐ O ‐methyltransferase and caffeoyl‐ C o A ‐ 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 ( CC o AOMT ), 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 (3 D ) structure, and substrate binding. The isoelectric points of all the COMT and CC o AOMT sequences analyzed were found to vary in the p H range of 5 to 6. Molecular weight analyses suggested CC o AOMT to be smaller monomeric proteins (27–29 kDa) as compared with those of COMT s (39–40 kDa), which were dimeric. On the basis of phylogenetic analysis, COMT and CC o AOMT 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 CC o AOMT sequences of alfalfa ( Medicago sativa ) revealed that both were quite different at the 3 D 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 CC o AOMT being more efficient.