› 3mb5

X-ray diffraction
1.6Å resolution

Crystal structure of P. abyssi tRNA m1A58 methyltransferase in complex with S-adenosyl-L-methionine

Released:
DOI: 10.2210/pdb3mb5/pdb
PDB entry 3mb5 coloured by chain, front view.
PDB entry 3mb5 coloured by chain, side view.
PDB entry 3mb5 coloured by chain, top view.
Source organism: Pyrococcus abyssi
Primary publication:
Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase.
Guelorget A, Roovers M, Guérineau V, Barbey C, Li X, Golinelli-Pimpaneau B
Nucleic Acids Res 38 6206-18 (2010)
PMID: 20483913

Function and Biology Details

Reaction catalysed: 
2 S-adenosyl-L-methionine + adenine(57)/adenine(58) in tRNA = 2 S-adenosyl-L-homocysteine + N(1)-methyladenine(57)/N(1)-methyladenine(58) in tRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-194163 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI Chain: A
Molecule details ›
Chain: A
Length: 255 amino acids
Theoretical weight: 29.16 KDa
Source organism: Pyrococcus abyssi
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9V1J7 (Residues: 1-253; Coverage: 100%)
Gene names: PAB0283, PYRAB04300, pimT-like, trmI
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand SAM 1 x SAM
3 bound ligands:
Ligand SO4 4 x SO4
Ligand EDO 6 x EDO
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: I222
Unit cell:
a: 86.55Å b: 89.26Å c: 110.32Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.184 0.199
Expression system: Escherichia coli

Quick links

Citations

6 review citations

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

5 mentions without citation

Dynamics of RNA modification by a multi-site-specific tRNA methyltransferase.
Hamdane et al. (2014)
4 more