6EMT

Crystal Structure of dual specific Trm10 construct from Thermococcus kodakaraensis.

6EMT の概要

• エントリーDOI: 10.2210/pdb6emt/pdb
• 分子名称: tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase, ACETATE ION, GLYCEROL, ... (5 entities in total)
• 機能のキーワード: trm10, dual specificity enzymes, spout, mtases, rna binding protein
• 由来する生物種: Thermococcus kodakarensis (Pyrococcus kodakaraensis)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 23201.28

構造登録者

Singh, R.K.,Versees, W. (登録日: 2017-10-03, 公開日: 2018-06-13, 最終更新日: 2024-01-17)

主引用文献

Singh, R.K.,Feller, A.,Roovers, M.,Van Elder, D.,Wauters, L.,Droogmans, L.,Versees, W.
Structural and biochemical analysis of the dual-specificity Trm10 enzyme fromThermococcus kodakaraensisprompts reconsideration of its catalytic mechanism.
RNA, 24:1080-1092, 2018

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 (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 -adenosyl-l-methionine or -adenosyl-l-homocysteine reveal the conformational plasticity of two active site loops upon substrate binding. Kinetic analysis shows that 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 mG formation over mA 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.

PubMed: 29848639
DOI: 10.1261/rna.064345.117

実験手法

X-RAY DIFFRACTION (1.794 Å)