Structural characterization of B. subtilis m(1)A(22) tRNA methyltransferase TrmK: insights into tRNA recognition

1-Methyladenosine (m(1)A) is a modified nucleoside found at positions 9, 14, 22 and 58 of tRNAs, which arises from the transfer of a methyl group onto the N1-atom of adenosine. The yqfN gene of Bacillus subtilis encodes the methyltransferase TrmK ((Bs)TrmK) responsible for the formation of m(1)A(22) in tRNA. Here, we show that (Bs)TrmK displays a broad substrate specificity, and methylates seven out of eight tRNA isoacceptor families of B. subtilis bearing an A(22). In addition to a non-Watson–Crick base-pair between the target A(22) and a purine at position 13, the formation of m(1)A(22) by (Bs)TrmK requires a full-length tRNA with intact tRNA elbow and anticodon stem. We solved the crystal structure of (Bs)TrmK showing an N-terminal catalytic domain harbouring the typical Rossmann-like fold of Class-I methyltransferases and a C-terminal coiled-coil domain. We used NMR chemical shift mapping to drive the docking of (Bs)tRNA(Ser) to (Bs)TrmK in complex with its methyl-donor cofactor S-adenosyl-L-methionine (SAM). In this model, validated by methyltransferase activity assays on (Bs)TrmK mutants, both domains of (Bs)TrmK participate in tRNA binding. (Bs)TrmK recognises tRNA with very few structural changes in both partner, the non-Watson–Crick R(13)–A(22) base-pair positioning the A(22) N1-atom close to the SAM methyl group.