› 6emu

X-ray diffraction
2.3Å resolution

Crystal Structure of dual specific Trm10 construct from Thermococcus kodakaraensis.

Released:
DOI: 10.2210/pdb6emu/pdb
PDB entry 6emu coloured by chain, front view.
PDB entry 6emu coloured by chain, side view.
PDB entry 6emu coloured by chain, top view.
Source organism: Thermococcus kodakarensis
Primary publication:
Structural and biochemical analysis of the dual-specificity Trm10 enzyme from Thermococcus kodakaraensis prompts reconsideration of its catalytic mechanism.
Singh RK, Feller A, Roovers M, Van Elder D, Wauters L, Droogmans L, Versées W
RNA 24 1080-1092 (2018)
PMID: 29848639

Function and Biology Details

Reactions catalysed: 
S-adenosyl-L-methionine + adenine(9) in tRNA = S-adenosyl-L-homocysteine + N(1)-methyladenine(9) in tRNA
S-adenosyl-L-methionine + guanine(9) in tRNA = S-adenosyl-L-homocysteine + N(1)-methylguanine(9) in tRNA
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177262 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 197 amino acids
Theoretical weight: 22.42 KDa
Source organism: Thermococcus kodakarensis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5JD38 (Residues: 97-272; Coverage: 48%)
Gene name: TK0422

Ligands and Environments


Cofactor: Ligand SAM 3 x SAM
1 bound ligand:
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 2
Spacegroup: P61
Unit cell:
a: 71.084Å b: 71.084Å c: 191.958Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.197 0.195 0.223
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Transfer RNA Modification Enzymes from Thermophiles and Their Modified Nucleosides in tRNA.
Hori et al. (2018)
4 more

1 mention without citation

Structural basis of RNA processing by human mitochondrial RNase P.
Bhatta et al. (2021)