› 2dul

X-ray diffraction
1.9Å resolution

Crystal structure of tRNA G26 methyltransferase Trm1 in apo form from Pyrococcus horikoshii

Released:
DOI: 10.2210/pdb2dul/pdb
PDB entry 2dul coloured by chain, front view.
PDB entry 2dul coloured by chain, side view.
PDB entry 2dul coloured by chain, top view.
Source organism: Pyrococcus horikoshii
Primary publication:
Crystal structure of tRNA N2,N2-guanosine dimethyltransferase Trm1 from Pyrococcus horikoshii.
Nishimoto M, Higashijima K, Shirouzu M, Grosjean H, Bessho Y, Yokoyama S
J Mol Biol 383 871-84 (2008)
PMID: 18789948

Function and Biology Details

Reaction catalysed: 
2 S-adenosyl-L-methionine + guanine(26) in tRNA = 2 S-adenosyl-L-homocysteine + N(2)-dimethylguanine(26) in tRNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-129868 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (guanine(26)-N(2))-dimethyltransferase Chain: A
Molecule details ›
Chain: A
Length: 378 amino acids
Theoretical weight: 43.01 KDa
Source organism: Pyrococcus horikoshii
Expression system: Escherichia coli
UniProt:
  • Canonical: O59493 (Residues: 4-381; Coverage: 99%)
Gene names: PH1829, trm1
Sequence domains: N2,N2-dimethylguanosine tRNA methyltransferase
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B2
Spacegroup: C2221
Unit cell:
a: 74.909Å b: 109.662Å c: 96.676Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.195 0.227
Expression system: Escherichia coli

Quick links

Citations

5 review citations

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

1 mention without citation

Substrate tRNA recognition mechanism of a multisite-specific tRNA methyltransferase, Aquifex aeolicus Trm1, based on the X-ray crystal structure.
Awai et al. (2011)