› 2v3k

X-ray diffraction
2Å resolution

The yeast ribosome synthesis factor Emg1 alpha beta knot fold methyltransferase

Released:
DOI: 10.2210/pdb2v3k/pdb
PDB entry 2v3k coloured by chain, front view.
PDB entry 2v3k coloured by chain, side view.
PDB entry 2v3k coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
The yeast ribosome synthesis factor Emg1 is a novel member of the superfamily of alpha/beta knot fold methyltransferases.
Leulliot N, Bohnsack MT, Graille M, Tollervey D, Van Tilbeurgh H
OpenAccess logo Nucleic Acids Res 36 629-39 (2008)
PMID: 18063569

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + pseudouridine(1191) in yeast 18S rRNA = S-adenosyl-L-homocysteine + N(1)-methylpseudouridine(1191) in yeast 18S rRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170324 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribosomal RNA small subunit methyltransferase NEP1 Chain: A
Molecule details ›
Chain: A
Length: 258 amino acids
Theoretical weight: 29.05 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q06287 (Residues: 1-252; Coverage: 100%)
Gene names: EMG1, L9470.5, NEP1, YLR186W
Sequence domains: EMG1/NEP1 methyltransferase
Structure domains: Alpha/beta knot

Ligands and Environments


Cofactor: Ligand SAM 1 x SAM
1 bound ligand:
Ligand SO4 2 x SO4
1 modified residue:
Ligand MSE 6 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P212121
Unit cell:
a: 42.044Å b: 78.719Å c: 89.575Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.197 0.247
Expression system: Escherichia coli

Quick links

Citations

8 review citations

The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA.
Watkins et al. (2012)
7 more

5 mentions without citation

Mutation of a gene essential for ribosome biogenesis, EMG1, causes Bowen-Conradi syndrome.
Armistead et al. (2009)
4 more