› 5e72

X-ray diffraction
1.74Å resolution

Crystal structure of the archaeal tRNA m2G/m22G10 methyltransferase (aTrm11) in complex with S-adenosyl-L-methionine (SAM) from Thermococcus kodakarensis

Released:
DOI: 10.2210/pdb5e72/pdb
PDB entry 5e72 coloured by chain, front view.
PDB entry 5e72 coloured by chain, side view.
PDB entry 5e72 coloured by chain, top view.
Source organism: Thermococcus kodakarensis KOD1
Primary publication:
Structural and functional analyses of the archaeal tRNA m2G/m22G10 methyltransferase aTrm11 provide mechanistic insights into site specificity of a tRNA methyltransferase that contains common RNA-binding modules.
Hirata A, Nishiyama S, Tamura T, Yamauchi A, Hori H
Nucleic Acids Res 44 6377-90 (2016)
PMID: 27325738

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177306 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
THUMP domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 346 amino acids
Theoretical weight: 39.3 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5JID5 (Residues: 1-331; Coverage: 100%)
Gene name: TK0981
Sequence domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P212121
Unit cell:
a: 47.602Å b: 53.688Å c: 134.787Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.187 0.223
Expression system: Escherichia coli

Quick links

Citations

8 review citations

Trm112, a Protein Activator of Methyltransferases Modifying Actors of the Eukaryotic Translational Apparatus.
Bourgeois et al. (2017)
7 more

2 mentions without citation

Structural and functional analyses of the archaeal tRNA m2G/m22G10 methyltransferase aTrm11 provide mechanistic insights into site specificity of a tRNA methyltransferase that contains common RNA-binding modules.
Hirata et al. (2016)
1 more