Catalyzes the methylthiolation of N6-threonylcarbamoyladenosine (t(6)A), leading to the formation of 2-methylthio-N6-threonylcarbamoyladenosine (ms(2)t(6)A) at position 37 in tRNAs that read codons beginning with adenine. [sulfur carrier]-SH + AH2 + N(6)-L-threonylcarbamoyladenosine(37) in tRNA + 2 S-adenosyl-L-methionine = 2-methylsulfanyl-N(6)-L-threonylcarbamoyladenosine(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. Is a tail-anchored protein that exploits the TCR40 assisted pathway for insertion into the endoplasmic reticulum. Expressed in pancreas, liver and skeletal muscle, especially in white muscle fibers. Belongs to the methylthiotransferase family. CDKAL1 subfamily.