Mutation Analysis of the Violaxanthin de-epoxidase identifies substrate binding sites and residues involved in catalysis

Plants are able to deal with variable environmental conditions: when exposed to strong illumination, they safely dissipate excess energy as heat and increase their capacity for scavenging reacting oxygen species. Both these protection mechanisms involve activation of the xanthophyll cycle, in which the carotenoid violaxanthin is converted to zeaxanthin by Violaxanthin De-Epoxidase (VDE), using ascorbate as the source of reducing power. In this work, following determination of the three-dimensional structure of the VDE catalytic domain, we identified the putative binding sites for violaxanthin and ascorbate by in silico docking. Amino acid residues lying in close contact with the two substrates were analysed for their involvement in the catalytic mechanism. Experimental results supported the proposed substrate binding sites and point to two residues, D177 and Y198, which are suggested to participate in the catalytic mechanism, based on complete loss of activity in mutant proteins. The role of other residues and the mechanistic similarity to aspartic proteases and epoxide hydrolases are discussed.