C-methylation programming of non-reducing polyketide synthases: based on AlphaFold 2 and molecular docking

Abstract:

[Objective] To explore the reasons for differences in the C-methylation programming of non-reducing polyketide synthases (NR-Pkss). [Methods] We used bioinformatics tools and AlphaFold 2 to compare the domain sequences and structures of the NR-Pkss involved in the synthesis of Monascus pigment and citrinin in Monascus ruber M7, i.e., Mr-PksPT and Mr-PksCT. Furthermore, we employed molecular docking to compare the binding of C-methyltransferase domains (CMeTs) with other domains and the intermediates of the two NR-Pkss. [Results] The large differences of the overall structure and the high similarity of domain sequence and structure between the two NR-Pkss suggested that the differences of C-methylation programming between NR-Pkss may be resulted from domain interactions. The CMeT of Mr-PksCT was more likely to bind to the acyl carrier protein (ACP) carrying the substrate than that of Mr-PksPT, making the intermediate more easily catalyzed by CMeT. Moreover, CMeT had lower binding free energy to methyl receptor substrate than the β-ketosynthase domain (KS). [Conclusion] The CMeTs of NR-Pkss can affect the C-methylation of the products by competing with KS. The findings provide a new idea for the study of C-methylation programming of Pkss.