Separate molecules of West Nile virus methyltransferase can independently catalyze the N7 and 2′-O methylations of viral RNA cap

West Nile virus methyltransferase catalyzes N7 and 2′-O methylations of the viral RNA cap (GpppA-RNA → m⁷GpppAm-RNA). The two methylation events are independent, as evidenced by efficient N7 methylation of GpppA-RNA → m⁷GpppA-RNA and GpppAm-RNA → m⁷GpppAm-RNA, and by the 2′-O methylation of GpppA-RNA → GpppAm-RNA and m⁷GpppA-RNA → m⁷GpppAm-RNA. However, the 2′-O methylation activity prefers substrate m⁷GpppA-RNA to GpppA-RNA, thereby determining the dominant methylation pathway as GpppA-RNA → m⁷GpppA-RNA → m⁷GpppAm-RNA. Mutant enzymes with different methylation defects can trans complement one another in vitro. Furthermore, sequential treatment of GpppA-RNA with distinct methyltransferase mutants generates fully methylated m⁷GpppAm-RNA, demonstrating that separate molecules of the enzyme can independently catalyze the two cap methylations in vitro.