7WM6

Crystal structure of SAH-bound TrmM from Mycoplasma capricolum

Summary for 7WM6

• Entry DOI: 10.2210/pdb7wm6/pdb
• Descriptor: Methyltransferase, S-ADENOSYL-L-HOMOCYSTEINE, SULFATE ION, ... (4 entities in total)
• Functional Keywords: trna, m6a, methyltransferase, transferase
• Biological source: Mycoplasma capricolum subsp. capricolum
• Total number of polymer chains: 4
• Total formula weight: 116474.50

Authors

Jeong, H.,Kim, J. (deposition date: 2022-01-14, release date: 2022-06-29, Last modification date: 2023-11-29)

Primary citation

Jeong, H.,Lee, Y.,Kim, J.
Structural and functional characterization of TrmM in m 6 A modification of bacterial tRNA.
Protein Sci., 31:e4319-e4319, 2022

PubMed Abstract: N -methyladenosine (m A), widely distributed in both coding and noncoding RNAs, regulates the epigenetic signals and RNA metabolism in eukaryotes. Although this posttranscriptional modification is frequently observed in messenger and ribosomal RNA, it is relatively rare in transfer RNA. In Escherichia coli, TrmM encoded by yfiC is the tRNA-specific N methyltransferase, which modifies the A37 residue of tRNA (cmo UAC) using S-adenosyl-l-methionine as a methyl donor. However, the structure-function relationship of this enzyme is not completely understood. In this report, we determined two x-ray crystal structures of Mycoplasma capricolum TrmM with and without S-adenosyl-l-homocysteine, which is a reaction product. We also demonstrated the cellular and in vitro activities of this enzyme in the m A modification of tRNA and the requirement of a divalent metal ion for its function, which is unprecedented in other RNA N methyltransferases, including the E. coli TrmM. Our results reveal that the dimeric form of M. capricolum TrmM is important for efficient tRNA binding and catalysis, thereby offering insights into the distinct substrate specificity of the monomeric E. coli homolog.

PubMed: 35481631
DOI: 10.1002/pro.4319

Experimental method

X-RAY DIFFRACTION (2.54 Å)