› 2yx1

X-ray diffraction
2.2Å resolution

Crystal structure of M.jannaschii tRNA m1G37 methyltransferase

Released:
DOI: 10.2210/pdb2yx1/pdb
PDB entry 2yx1 coloured by chain, front view.
PDB entry 2yx1 coloured by chain, side view.
PDB entry 2yx1 coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii
Primary publication:
Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5.
Goto-Ito S, Ito T, Ishii R, Muto Y, Bessho Y, Yokoyama S
Proteins 72 1274-89 (2008)
PMID: 18384044

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + guanine(37) in tRNA = S-adenosyl-L-homocysteine + N(1)-methylguanine(37) in tRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-176595 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (guanine(37)-N1)-methyltransferase Trm5b Chains: A, B
Molecule details ›
Chains: A, B
Length: 336 amino acids
Theoretical weight: 39.26 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q58293 (Residues: 1-336; Coverage: 100%)
Gene names: MJ0883, trm5b
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand SFG 2 x SFG
1 bound ligand:
Ligand ZN 10 x ZN
1 modified residue:
Ligand MSE 8 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P21
Unit cell:
a: 62Å b: 69.79Å c: 87.15Å
α: 90° β: 96.07° γ: 90°
R-values:
R R work R free
0.224 0.224 0.276
Expression system: Escherichia coli

Quick links

Citations

10 review citations

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

13 mentions without citation

Wybutosine biosynthesis: structural and mechanistic overview.
Perche-Letuvée et al. (2014)
12 more