› 4ypw

X-ray diffraction
2.31Å resolution

Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds

Released:
DOI: 10.2210/pdb4ypw/pdb
PDB entry 4ypw coloured by chain, front view.
PDB entry 4ypw coloured by chain, side view.
PDB entry 4ypw coloured by chain, top view.
Source organism: Haemophilus influenzae Rd KW20
Entry authors: Elkins PA, Bonnette WG, Stuckey JA

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: 254 amino acids
Theoretical weight: 28.38 KDa
Source organism: Haemophilus influenzae Rd KW20
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P43912 (Residues: 1-246; Coverage: 100%)
Gene names: HI_0202, trmD
Sequence domains: tRNA (Guanine-1)-methyltransferase
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand 4FD 1 x 4FD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: R32
Unit cell:
a: 92.892Å b: 92.892Å c: 178.097Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.197 0.192 0.248
Expression system: Escherichia coli BL21(DE3)

Quick links