Indole prenyltransferases AnaPT, CdpC3PT, and CdpNPT are known to catalyze the formation of prenylated pyrroloindoline diketopiperazines from tryptophan-containing cyclic dipeptides in one-step reactions. In this study, we investigated the different stereoselectivities of these enzymes toward all the stereoisomers of cyclo-Trp-Ala and cyclo-Trp-Pro. The stereoselectivities of AnaPT and CdpC3PT mainly depend on the configuration of the tryptophanyl moiety in the substrates, and they usually introduce the prenyl moiety from the opposite sides. CdpNPT showed lower stereoselectivity, and the structure of the second amino acid moiety in the substrates is important for the stereospecificity in its enzyme catalysis. Moreover, we determined the crystal structure of AnaPT in complex with thiolodiphosphate and compared it with the known structures of CdpNPT. Our results clearly revealed the presence of an indole binding mode that has so far not been characterized.
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