› 4yvh

X-ray diffraction
1.6Å resolution

Crystal Structure of H. influenzae TrmD in complex with sinefungin

Released:
DOI: 10.2210/pdb4yvh/pdb
PDB entry 4yvh coloured by chain, front view.
PDB entry 4yvh coloured by chain, side view.
PDB entry 4yvh coloured by chain, top view.
Source organism: Haemophilus influenzae Rd KW20
Primary publication:
Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
Ito T, Masuda I, Yoshida K, Goto-Ito S, Sekine S, Suh SW, Hou YM, Yokoyama S
Proc Natl Acad Sci U S A 112 E4197-205 (2015)
PMID: 26183229

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

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155154 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (guanine-N(1)-)-methyltransferase Chain: A
Molecule details ›
Chain: A
Length: 266 amino acids
Theoretical weight: 29.75 KDa
Source organism: Haemophilus influenzae Rd KW20
Expression system: Escherichia coli
UniProt:
  • Canonical: P43912 (Residues: 1-246; Coverage: 100%)
Gene names: HI_0202, trmD
Sequence domains: tRNA (Guanine-1)-methyltransferase
Structure domains:

Ligands and Environments


Cofactor: Ligand SFG 1 x SFG
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: R32
Unit cell:
a: 93.766Å b: 93.766Å c: 177.907Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.188 0.186 0.219
Expression system: Escherichia coli

Quick links

Citations

9 review citations

m1A Post-Transcriptional Modification in tRNAs.
Oerum et al. (2017)
8 more

2 mentions without citation

Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
Ito et al. (2015)
1 more