› 4yvk

X-ray diffraction
3Å resolution

Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA variant (G36C)

Released:
DOI: 10.2210/pdb4yvk/pdb
PDB entry 4yvk coloured by chain, front view.
PDB entry 4yvk coloured by chain, side view.
PDB entry 4yvk coloured by chain, top view.
Source organisms:
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:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155155 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
tRNA (guanine-N(1)-)-methyltransferase Chains: A, B
Molecule details ›
Chains: A, B
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:
tRNA Chain: C
Molecule details ›
Chain: C
Length: 74 nucleotides
Theoretical weight: 23.82 KDa
Source organism: Thermotoga maritima MSB8
Expression system: Not provided
Sequence domains: tRNA

Ligands and Environments


Cofactor: Ligand SFG 2 x SFG
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: P41212
Unit cell:
a: 87.45Å b: 87.45Å c: 228.72Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.218 0.283
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

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

1 mention without citation

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