Download MendeleyStructural and biochemical analysis of the dual-specificity Trm10 enzyme fromThermococcus kodakaraensisprompts reconsideration of its catalytic mechanism.
Singh, R.K., Feller, A., Roovers, M., Van Elder, D., Wauters, L., Droogmans, L., Versees, W.(2018) RNA 24: 1080-1092
- PubMed: 29848639
- DOI: https://doi.org/10.1261/rna.064345.117
- Primary Citation of Related Structures:
6EMS, 6EMT, 6EMU, 6EMV - PubMed Abstract:
tRNA molecules get heavily modified post-transcriptionally. The N-1 methylation of purines at position 9 of eukaryal and archaeal tRNA is catalyzed by the SPOUT methyltranferase Trm10. Remarkably, while certain Trm10 orthologs are specific for either guanosine or adenosine, others show a dual specificity. Structural and functional studies have been performed on guanosine- and adenosine-specific enzymes. Here we report the structure and biochemical analysis of the dual-specificity enzyme from Thermococcus kodakaraensis ( Tk Trm10). We report the first crystal structure of a construct of this enzyme, consisting of the N-terminal domain and the catalytic SPOUT domain. Moreover, crystal structures of the SPOUT domain, either in the apo form or bound to S -adenosyl-l-methionine or S -adenosyl-l-homocysteine reveal the conformational plasticity of two active site loops upon substrate binding. Kinetic analysis shows that Tk Trm10 has a high affinity for its tRNA substrates, while the enzyme on its own has a very low methyltransferase activity. Mutation of either of two active site aspartate residues (Asp206 and Asp245) to Asn or Ala results in only modest effects on the N-1 methylation reaction, with a small shift toward a preference for m 1 G formation over m 1 A formation. Only a double D206A/D245A mutation severely impairs activity. These results are in line with the recent finding that the single active-site aspartate was dispensable for activity in the guanosine-specific Trm10 from yeast, and suggest that also dual-specificity Trm10 orthologs use a noncanonical tRNA methyltransferase mechanism without residues acting as general base catalysts.
Organizational Affiliation:
Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium.
