Crystal structure of archaeal tRNA(m1G37)methyltransferase aTrm5

Methylation of the N1 atom of guanosine at position 37 in tRNA, the position 3′‐adjacent to the anticodon, generates the modified nucleoside m1G37. In archaea and eukaryotes, m1G37 synthesis is catalyzed by tRNA(m1G37)methyltransferase (archaeal or eukaryotic Trm5, a/eTrm5). Here we report the crystal structure of archaeal Trm5 (aTrm5) from Methanocaldococcus jannaschii (formerly known as Methanococcus jannaschii) in complex with the methyl donor analogue at 2.2 Å resolution. The crystal structure revealed that the entire protein is composed of three structural domains, D1, D2, and D3. In the a/eTrm5 primary structures, D2 and D3 are highly conserved, while D1 is not conserved. The D3 structure is the Rossmann fold, which is the hallmark of the canonical class‐I methyltransferases. The a/eTrm5‐defining domain, D2, exhibits structural similarity to some class‐I methyltransferases. In contrast, a DALI search with the D1 structure yielded no structural homologues. In the crystal structure, D3 contacts both D1 and D2. The residues involved in the D1:D3 interactions are not conserved, while those participating in the D2:D3 interactions are well conserved. D1 and D2 do not contact each other, and the linker between them is disordered. aTrm5 fragments corresponding to the D1 and D2‐D3 regions were prepared in a soluble form. The NMR analysis of the D1 fragment revealed that D1 is well folded by itself, and it did not interact with either the D2‐D3 fragment or the tRNA. The NMR analysis of the D2‐D3 fragment revealed that it is well folded, independently of D1, and that it interacts with tRNA. Furthermore, the D2‐D3 fragment was as active as the full‐length enzyme for tRNA methylation. The positive charges on the surface of D2‐D3 may be involved in tRNA binding. Therefore, these findings suggest that the interaction between D1 and D3 is not persistent, and that the D2‐D3 region plays the major role in tRNA methylation. © 2008 Wiley‐Liss, Inc.