› 2vs1

X-ray diffraction
2.1Å resolution

The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)- methyltransferase in complex with S-adenosyl-L-homocysteine

Released:
DOI: 10.2210/pdb2vs1/pdb
PDB entry 2vs1 coloured by chain, front view.
PDB entry 2vs1 coloured by chain, side view.
PDB entry 2vs1 coloured by chain, top view.
Source organism: Pyrococcus abyssi
Primary publication:
The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-methyltransferase provides insights into its tRNA specificity.
Walbott H, Leulliot N, Grosjean H, Golinelli-Pimpaneau B
Nucleic Acids Res 36 4929-40 (2008)
PMID: 18653523

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + uracil(54) in tRNA = S-adenosyl-L-homocysteine + 5-methyluracil(54) in tRNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-194146 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (uracil(54)-C(5))-methyltransferase Chain: A
Molecule details ›
Chain: A
Length: 425 amino acids
Theoretical weight: 49.13 KDa
Source organism: Pyrococcus abyssi
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UZR7 (Residues: 1-405; Coverage: 100%)
Gene names: PAB0719, PYRAB10780
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
1 bound ligand:
Ligand PO4 1 x PO4
1 modified residue:
Ligand CSS 1 x CSS

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: C2
Unit cell:
a: 99.529Å b: 100.415Å c: 55.737Å
α: 90° β: 111.61° γ: 90°
R-values:
R R work R free
0.188 0.185 0.251
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Stereochemical mechanisms of tRNA methyltransferases.
Hou et al. (2010)
5 more