Structural characterization of B. subtilis m1A22 tRNA methyltransferase TrmK: insights into tRNA recognition

• Published in: Nucleic acids research 2019-05, Vol.47 (9), p.4736-4750
• Main Authors: Dégut, Clément, Roovers, Martine, Barraud, Pierre, Brachet, Franck, Feller, André, Larue, Valéry, Al Refaii, Abdalla, Caillet, Joël, Droogmans, Louis, Tisné, Carine
• Format: Article
• Language: English
• Subjects: Anticodon - chemistry; Anticodon - genetics; Bacillus subtilis - chemistry; Bacillus subtilis - enzymology; Biochemistry, Molecular Biology; Catalytic Domain - genetics; Crystallography, X-Ray; Life Sciences; Methylation; Nucleic Acid Enzymes; Protein Conformation; RNA Recognition Motif Proteins - chemistry; RNA Recognition Motif Proteins - genetics; RNA, Transfer - chemistry; RNA, Transfer - genetics; S-Adenosylmethionine - chemistry; Structural Biology; Substrate Specificity; tRNA Methyltransferases - chemistry; tRNA Methyltransferases - genetics
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkz230

Abstract 1-Methyladenosine (m1A) 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 (BsTrmK) responsible for the formation of m1A22 in tRNA. Here, we show that BsTrmK displays a broad substrate specificity, and methylates seven out of eight tRNA isoacceptor families of B. subtilis bearing an A22. In addition to a non-Watson-Crick base-pair between the target A22 and a purine at position 13, the formation of m1A22 by BsTrmK requires a full-length tRNA with intact tRNA elbow and anticodon stem. We solved the crystal structure of BsTrmK 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 BstRNASer to BsTrmK in complex with its methyl-donor cofactor S-adenosyl-L-methionine (SAM). In this model, validated by methyltransferase activity assays on BsTrmK mutants, both domains of BsTrmK participate in tRNA binding. BsTrmK recognises tRNA with very few structural changes in both partner, the non-Watson-Crick R13-A22 base-pair positioning the A22 N1-atom close to the SAM methyl group.