› 3dxy

X-ray diffraction
1.5Å resolution

Crystal structure of EcTrmB in complex with SAM

Released:
DOI: 10.2210/pdb3dxy/pdb
PDB entry 3dxy coloured by chain, front view.
PDB entry 3dxy coloured by chain, side view.
PDB entry 3dxy coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Monomeric tRNA (m(7)G46) methyltransferase from Escherichia coli presents a novel structure at the function-essential insertion.
Zhou H, Liu Q, Yang W, Gao Y, Teng M, Niu L
Proteins 76 512-5 (2009)
PMID: 19373903

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + guanine(46) in tRNA = S-adenosyl-L-homocysteine + N(7)-methylguanine(46) in tRNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141703 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (guanine-N(7)-)-methyltransferase Chain: A
Molecule details ›
Chain: A
Length: 218 amino acids
Theoretical weight: 24.83 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A8I5 (Residues: 33-239; Coverage: 87%)
Gene names: JW2927, b2960, trmB, trmI, yggH
Sequence domains: Putative methyltransferase
Structure domains: Vaccinia Virus protein VP39

Ligands and Environments


Cofactor: Ligand SAM 1 x SAM
2 bound ligands:
Ligand SO4 1 x SO4
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BSRF BEAMLINE 3W1A
Spacegroup: P21
Unit cell:
a: 46.04Å b: 46.76Å c: 58.13Å
α: 90° β: 90.4° γ: 90°
R-values:
R R work R free
0.155 0.154 0.185
Expression system: Escherichia coli

Quick links

Citations

3 review citations

7-Methylguanosine Modifications in Transfer RNA (tRNA).
Tomikawa C. (2018)
2 more

5 mentions without citation

M≡E and M=E Complexes of Iron and Cobalt that Emphasize Three-fold Symmetry (E = O, N, NR).
Saouma et al. (2011)
4 more