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Although the crystal structure of Vibrio harveyi luciferase has been elucidated, the binding sites for the flavin mononucleotide and fatty aldehyde substrates are still unknown. The determined location of the phosphate‐binding site close to Arg 107 on the α subunit of luciferase is supported here by point mutagenesis. This information, together with previous structure‐activity data for the length of the linker connecting the phosphate group to the isoalloxazine ring represent important characteristics of the luciferase‐bound conformation of the flavin mononucleotide. A model of the luciferase–flavin complex is developed here using flexible docking supplemented by these structural constraints. The location of the phosphate moiety was used as the anchor in a flexible docking procedure performed by conformation search by using the Monte Carlo minimization approach. The resulting databases of energy‐ranked feasible …