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 pathway for insertion into the endoplasmic reticulum. Expressed in pancreatic islets. Disease susceptibility is associated with variants affecting the gene represented in this entry. Belongs to the methylthiotransferase family. CDKAL1 subfamily.