Methylthiotransferase that catalyzes the conversion of N6-(dimethylallyl)adenosine (i(6)A) to 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 (adjacent to the 3'-end of the anticodon) of four mitochondrial DNA-encoded tRNAs (Ser(UCN), Phe, Tyr and Trp) (By similarity). Essential for efficient and highly accurate protein translation by the ribosome (By similarity). Specifically inhibits CDK5 activation by CDK5R1 (By similarity). Essential for efficient mitochondrial protein synthesis and respiratory chain (By similarity). [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. Interacts with CDK5R1 (p35 form) (PubMed:10721722). CDK5RAP1, CDK5RAP2 and CDK5RAP3 show competitive binding to CDK5R1 (By similarity). Forms a complex with CDK5R1 and CDK5 (By similarity). Expressed in brain. Belongs to the methylthiotransferase family. MiaB subfamily.