3MB5

Crystal structure of P. abyssi tRNA m1A58 methyltransferase in complex with S-adenosyl-L-methionine

Summary for 3MB5

• Entry DOI: 10.2210/pdb3mb5/pdb
• Related: 3LGA 3LHD
• Descriptor: SAM-dependent methyltransferase, S-ADENOSYLMETHIONINE, SULFATE ION, ... (6 entities in total)
• Functional Keywords: rna methyltransferase, m1a, trmi, intermolecular contacts, region-specificity, tetramer, disulfide bond, hyperthermostability, methyltransferase, transferase
• Biological source: Pyrococcus abyssi
• Total number of polymer chains: 1
• Total formula weight: 30377.07

Authors

Guelorget, A.,Golinelli-Pimpaneau, B. (deposition date: 2010-03-25, release date: 2010-05-12, Last modification date: 2023-09-06)

Primary citation

Guelorget, A.,Roovers, M.,Guerineau, V.,Barbey, C.,Li, X.,Golinelli-Pimpaneau, B.
Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase.
Nucleic Acids Res., 38:6206-6218, 2010

PubMed Abstract: The S-adenosyl-L-methionine dependent methylation of adenine 58 in the T-loop of tRNAs is essential for cell growth in yeast or for adaptation to high temperatures in thermophilic organisms. In contrast to bacterial and eukaryotic tRNA m(1)A58 methyltransferases that are site-specific, the homologous archaeal enzyme from Pyrococcus abyssi catalyzes the formation of m(1)A also at the adjacent position 57, m(1)A57 being a precursor of 1-methylinosine. We report here the crystal structure of P. abyssi tRNA m(1)A57/58 methyltransferase ((Pab)TrmI), in complex with S-adenosyl-L-methionine or S-adenosyl-L-homocysteine in three different space groups. The fold of the monomer and the tetrameric architecture are similar to those of the bacterial enzymes. However, the inter-monomer contacts exhibit unique features. In particular, four disulfide bonds contribute to the hyperthermostability of the archaeal enzyme since their mutation lowers the melting temperature by 16.5°C. His78 in conserved motif X, which is present only in TrmIs from the Thermococcocales order, lies near the active site and displays two alternative conformations. Mutagenesis indicates His78 is important for catalytic efficiency of (Pab)TrmI. When A59 is absent in tRNA(Asp), only A57 is modified. Identification of the methylated positions in tRNAAsp by mass spectrometry confirms that (Pab)TrmI methylates the first adenine of an AA sequence.

PubMed: 20483913
DOI: 10.1093/nar/gkq381

Experimental method

X-RAY DIFFRACTION (1.6 Å)