› 3ai9

X-ray diffraction
1.55Å resolution

Crystal structure of DUF358 protein reveals a putative SPOUT-class rRNA methyltransferase

Released:
DOI: 10.2210/pdb3ai9/pdb
PDB entry 3ai9 coloured by chain, front view.
PDB entry 3ai9 coloured by chain, side view.
PDB entry 3ai9 coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii
Primary publication:
Crystal structure of Mj1640/DUF358 protein reveals a putative SPOUT-class RNA methyltransferase.
Chen HY, Yuan YA
J Mol Cell Biol 2 366-74 (2010)
PMID: 21098051

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + pseudouridine(54) in tRNA = S-adenosyl-L-homocysteine + N(1)-methylpseudouridine(54) in tRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176769 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (pseudouridine(54)-N(1))-methyltransferase Chain: X
Molecule details ›
Chain: X
Length: 211 amino acids
Theoretical weight: 24.65 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q59034 (Residues: 1-205; Coverage: 100%)
Gene names: MJ1640, trmY
Sequence domains: Putative SAM-dependent RNA methyltransferase
Structure domains: Alpha/beta knot

Ligands and Environments

2 bound ligands:
Ligand SAM 1 x SAM
Ligand MG 2 x MG
1 modified residue:
Ligand MSE 6 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: C2
Unit cell:
a: 84.288Å b: 48.133Å c: 62.362Å
α: 90° β: 126.09° γ: 90°
R-values:
R R work R free
0.192 0.19 0.237
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Methylated nucleosides in tRNA and tRNA methyltransferases.
Hori H. (2014)
3 more