3OII

Crystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine

Summary for 3OII

• Entry DOI: 10.2210/pdb3oii/pdb
• Related: 3O7B 3OIJ 3OIN
• Descriptor: Essential for mitotic growth 1, S-ADENOSYL-L-HOMOCYSTEINE, GLYCEROL, ... (4 entities in total)
• Functional Keywords: emg1, scnep1, spout, ribosome biogenesis, methyltransferase, rrna processing, ribosomal protein
• Biological source: Saccharomyces cerevisiae (yeast)
• Cellular location: Nucleus, nucleolus : Q06287
• Total number of polymer chains: 2
• Total formula weight: 56847.94

Authors

Thomas, S.R.,Szyk, A.,LaRonde-LeBlanc, N. (deposition date: 2010-08-19, release date: 2010-12-01, Last modification date: 2023-09-06)

Primary citation

Thomas, S.R.,Keller, C.A.,Szyk, A.,Cannon, J.R.,Laronde-Leblanc, N.A.
Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis.
Nucleic Acids Res., 39:2445-2457, 2011

PubMed Abstract: Nucleolar Essential Protein 1 (Nep1) is required for small subunit (SSU) ribosomal RNA (rRNA) maturation and is mutated in Bowen-Conradi Syndrome. Although yeast (Saccharomyces cerevisiae) Nep1 interacts with a consensus sequence found in three regions of SSU rRNA, the molecular details of the interaction are unknown. Nep1 is a SPOUT RNA methyltransferase, and can catalyze methylation at the N1 of pseudouridine. Nep1 is also involved in assembly of Rps19, an SSU ribosomal protein. Mutations in Nep1 that result in decreased methyl donor binding do not result in lethality, suggesting that enzymatic activity may not be required for function, and RNA binding may play a more important role. To study these interactions, the crystal structures of the scNep1 dimer and its complexes with RNA were determined. The results demonstrate that Nep1 recognizes its RNA site via base-specific interactions and stabilizes a stem-loop in the bound RNA. Furthermore, the RNA structure observed contradicts the predicted structures of the Nep1-binding sites within mature rRNA, suggesting that the Nep1 changes rRNA structure upon binding. Finally, a uridine base is bound in the active site of Nep1, positioned for a methyltransfer at the C5 position, supporting its role as an N1-specific pseudouridine methyltransferase.

PubMed: 21087996
DOI: 10.1093/nar/gkq1131

Experimental method

X-RAY DIFFRACTION (1.85 Å)