9JGD

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

Summary for 9JGD

• Entry DOI: 10.2210/pdb9jgd/pdb
• Descriptor: Ribosomal RNA small subunit methyltransferase Nep1, CHLORIDE ION, 5'-DEOXY-5'-METHYLTHIOADENOSINE, ... (7 entities in total)
• Functional Keywords: conserved arginine residues, globular loop extension, inter-subunit interactions, nep1, n1-pseudouridine methyltransferase, trefoil knot, transferase
• Biological source: Pyrococcus horikoshii OT3
• Total number of polymer chains: 1
• Total formula weight: 27564.52

Authors

Saha, S.,Kanaujia, S.P. (deposition date: 2024-09-06, release date: 2025-03-12, Last modification date: 2025-05-21)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.2 Å)