PDBsum entry 3oin

Ribosomal protein

PDB id: 3oin

Contents

Protein chains

217 a.a. *

DNA/RNA

Ligands

GOL ×2

SAH

Metals

_CL

_MG

Waters ×241

* Residue conservation analysis

PDB id:

3oin

Name:

Ribosomal protein

Title:

Crystal structure of saccharomyces cerevisiae nep1/emg1 bound to s- adenosylhomocysteine and 1 molecule of cognate RNA

Structure:

Ribosomal RNA small subunit methyltransferase nep1. Chain: a, b. Synonym: 18s rrna (pseudouridine(1189)-n1)-methyltransferase,18s rrna psi1189 methyltransferase,essential for mitotic growth protein 1, nucleolar essential protein 1. Engineered: yes. 5'-r( Gp Gp Gp Cp Up Up Cp Ap Ap Cp Gp Cp Cp C)-3'. Chain: c. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: emg1, nep1, ylr186w, l9470.5. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Synthetic: yes. Other_details: cognate RNA synthesized to mimic natural RNA substrate

Resolution:

1.90Å R-factor: 0.194 R-free: 0.230

Authors:

S.R.Thomas,N.Laronde-Leblanc

Key ref:

S.R.Thomas et al. (2011). Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis. Nucleic Acids Res, 39, 2445-2457. PubMed id: 21087996

Date:

19-Aug-10 Release date: 01-Dec-10

Protein chains

Q06287  (NEP1_YEAST) -  Ribosomal RNA small subunit methyltransferase NEP1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 252 a.a.

Struc: 217 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chain

G-G-G-C-U-U-C-A-A-C-G-C-C-C 14 bases

Enzyme reactions

• Enzyme class: E.C.2.1.1.260 - rRNA small subunit pseudouridine methyltransferase Nep1.
• Reaction: pseudouridine₁₁₉₁ in yeast 18S rRNA + S-adenosyl-L-methionine = N₁- methylpseudouridine₁₁₉₁ in yeast 18S rRNA + S-adenosyl-L-homocysteine + H⁺

pseudouridine(1191) in yeast 18S rRNA + S-adenosyl-L-methionine = N(1)- methylpseudouridine(1191) in yeast 18S rRNA + S-adenosyl-L-homocysteine + H(+) (Bound ligand (Het Group name = SAH) matches with 96.15% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

Nucleic Acids Res 39:2445-2457 (2011)

PubMed id: 21087996

Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis.

S.R.Thomas, C.A.Keller, A.Szyk, J.R.Cannon, N.A.Laronde-Leblanc.

ABSTRACT

No abstract given.