Catalyzes the methylthiolation of N6-(dimethylallyl)adenosine (i(6)A), leading to the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine. [sulfur carrier]-SH + AH2 + N(6)-dimethylallyladenosine(37) in tRNA + 2 S-adenosyl-L-methionine = 2-methylsulfanyl-N(6)-dimethylallyladenosine(37) in tRNA + 5'-deoxyadenosine + [sulfur carrier]-H + A + 2 H(+) + L-methionine + S-adenosyl-L-homocysteine Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Monomer. Insertion mutant accumulates lower amounts of moenomycin and is impaired in morphogenesis as compared to the parental strain. Mutant shows reduced level of thiomethylation at position 37 in the anticodon of tRNA. Belongs to the methylthiotransferase family. MiaB subfamily.