8X4G

Crystal structure of the D117A mutant of DIMT1 from Pyrococcus horikoshii

8X4G の概要

• エントリーDOI: 10.2210/pdb8x4g/pdb
• 分子名称: Probable ribosomal RNA small subunit methyltransferase A (2 entities in total)
• 機能のキーワード: archaea, ksga/dimt1, rrna methyltransferase, sam, sah, sfg, transferase
• 由来する生物種: Pyrococcus horikoshii OT3
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 66642.22

構造登録者

Saha, S.,Kanaujia, S.P. (登録日: 2023-11-15, 公開日: 2024-08-28, 最終更新日: 2024-10-16)

主引用文献

Saha, S.,Kanaujia, S.P.
Structural and functional characterization of archaeal DIMT1 unveils distinct protein dynamics essential for efficient catalysis.
Structure, 32:1760-1775.e7, 2024

PubMed Abstract: Dimethyladenosine transferase 1 (DIMT1), an ortholog of bacterial KsgA is a conserved protein that assists in ribosome biogenesis by modifying two successive adenosine bases near the 3' end of small subunit (SSU) rRNA. Although KsgA/DIMT1 proteins have been characterized in bacteria and eukaryotes, they are yet unexplored in archaea. Also, their dynamics are not well understood. Here, we structurally and functionally characterized the apo and holo forms of archaeal DIMT1 from Pyrococcus horikoshii. Wild-type protein and mutants were analyzed to capture different transition states, including open, closed, and intermediate states. This study reports a unique inter-domain movement that is needed for substrate (RNA) positioning in the catalytic pocket, and is only observed in the presence of the cognate cofactors S-adenosyl-L-methionine (SAM) or S-adenosyl-L-homocysteine (SAH). The binding of the inhibitor sinefungine, an analog of SAM or SAH, to archaeal DIMT1 blocks the catalytic pocket and renders the enzyme inactive.

PubMed: 39146930
DOI: 10.1016/j.str.2024.07.013

実験手法

X-RAY DIFFRACTION (3.3 Å)