9JGD

Crystal structure of Nep1 in complex with 5'-methylthioadenosine from Pyrococcus horikoshii OT3

9JGD の概要

• エントリーDOI: 10.2210/pdb9jgd/pdb
• 分子名称: Ribosomal RNA small subunit methyltransferase Nep1, CHLORIDE ION, 5'-DEOXY-5'-METHYLTHIOADENOSINE, ... (7 entities in total)
• 機能のキーワード: conserved arginine residues, globular loop extension, inter-subunit interactions, nep1, n1-pseudouridine methyltransferase, trefoil knot, transferase
• 由来する生物種: Pyrococcus horikoshii OT3
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 27564.52

構造登録者

Saha, S.,Kanaujia, S.P. (登録日: 2024-09-06, 公開日: 2025-03-12, 最終更新日: 2025-05-21)

主引用文献

Saha, S.,Kanaujia, S.P.
Structural analysis of the ribosome assembly factor Nep1, an N1-specific pseudouridine methyltransferase, reveals mechanistic insights.
Febs J., 292:2338-2358, 2025

PubMed Abstract: Nucleolar essential protein 1 (Nep1; also known as ribosomal RNA small subunit methyltransferase Nep1) is a crucial factor in forming small ribosomal subunits in eukaryotes and archaea. Nep1 possesses an S-adenosyl-L-methionine (SAM)-dependent SpoU-TrmD (SPOUT) ribosomal RNA (rRNA) methyltransferase (MTase) fold and catalyzes pseudouridine (Ψ) methylation at specific sites of the small subunit (SSU) rRNA. Mutations in Nep1 proteins result in a severe developmental disorder in humans and reduced growth in yeast, suggesting its role in ribosome biogenesis. In this study, the crystal structures of Nep1 from the archaebacterium Pyrococcus horikoshii (PhNep1), both in its apo and holo (adenosine or 5-methylthioadenosine bound) forms have been reported. The structural analysis of PhNep1 revealed an α/β fold featuring a deep trefoil knot akin to the SPOUT domain, with two novel extensions-a globular loop and a β-α-β extension. Moreover, the cofactor-binding site of PhNep1 exhibits a preformed pocket, topologically similar to that of other SPOUT-class MTases. Further, structural analysis of PhNep1 revealed that it forms a homodimer coordinated by inter-subunit hydrogen bonds and hydrophobic interactions. Moreover, the results of this study indicate that PhNep1 can specifically methylate consensus RNAs, having a pseudouridine (ψ) located at position 926 of helix 35 (h35) of 16S rRNA in P. horikoshii. The stability of the Nep1-RNA complex seems to be primarily assisted by the conserved arginine residues located at the dimeric interface.

PubMed: 39918246
DOI: 10.1111/febs.70005

実験手法

X-RAY DIFFRACTION (2.2 Å)