› 3ay0

X-ray diffraction
3.05Å resolution

Crystal structure of Methanocaldococcus jannaschii Trm5 in complex with adenosine

Released:
DOI: 10.2210/pdb3ay0/pdb
PDB entry 3ay0 coloured by chain, front view.
PDB entry 3ay0 coloured by chain, side view.
PDB entry 3ay0 coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii
Primary publication:
Differentiating analogous tRNA methyltransferases by fragments of the methyl donor.
Lahoud G, Goto-Ito S, Yoshida K, Ito T, Yokoyama S, Hou YM
RNA 17 1236-46 (2011)
PMID: 21602303

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176595 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (guanine(37)-N1)-methyltransferase Trm5b Chains: A, B
Molecule details ›
Chains: A, B
Length: 336 amino acids
Theoretical weight: 39.07 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q58293 (Residues: 1-336; Coverage: 100%)
Gene names: MJ0883, trm5b
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand ZN 5 x ZN
Ligand ADN 2 x ADN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: P21
Unit cell:
a: 61.49Å b: 67.127Å c: 92.239Å
α: 90° β: 93.75° γ: 90°
R-values:
R R work R free
0.214 0.214 0.293
Expression system: Escherichia coli

Quick links

Citations

5 review citations

tRNA modifications regulate translation during cellular stress.
Gu et al. (2014)
4 more

2 mentions without citation

Structural insight into the methyltransfer mechanism of the bifunctional Trm5.
Wang et al. (2017)
1 more