2YX1

Crystal structure of M.jannaschii tRNA m1G37 methyltransferase

Summary for 2YX1

• Entry DOI: 10.2210/pdb2yx1/pdb
• Descriptor: Hypothetical protein MJ0883, ZINC ION, SINEFUNGIN, ... (4 entities in total)
• Functional Keywords: methyl transferase, trna modification enzyme, transferase
• Biological source: Methanocaldococcus jannaschii
• Cellular location: Cytoplasm (Potential): Q58293
• Total number of polymer chains: 2
• Total formula weight: 79935.92

Authors

Goto-Ito, S.,Ito, T.,Ishii, R.,Bessho, Y.,Yokoyama, S. (deposition date: 2007-04-23, release date: 2008-04-22, Last modification date: 2024-10-30)

Primary citation

Goto-Ito, S.,Ito, T.,Ishii, R.,Muto, Y.,Bessho, Y.,Yokoyama, S.
Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5.
Proteins, 72:1274-1289, 2008

PubMed Abstract: Methylation of the N1 atom of guanosine at position 37 in tRNA, the position 3'-adjacent to the anticodon, generates the modified nucleoside m(1)G37. In archaea and eukaryotes, m(1)G37 synthesis is catalyzed by tRNA(m(1)G37)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 A 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.

PubMed: 18384044
DOI: 10.1002/prot.22019

Experimental method

X-RAY DIFFRACTION (2.2 Å)