› 2yy8

X-ray diffraction
2.48Å resolution

Crystal structure of archaeal tRNA-methylase for position 56 (aTrm56) from Pyrococcus horikoshii, complexed with S-adenosyl-L-methionine

Released:
DOI: 10.2210/pdb2yy8/pdb
PDB entry 2yy8 coloured by chain, front view.
PDB entry 2yy8 coloured by chain, side view.
PDB entry 2yy8 coloured by chain, top view.
Source organism: Pyrococcus horikoshii
Primary publication:
Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O-methylcytidine at position 56 of tRNA.
Kuratani M, Bessho Y, Nishimoto M, Grosjean H, Yokoyama S
J Mol Biol 375 1064-75 (2008)
PMID: 18068186

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + cytidine(56) in tRNA = S-adenosyl-L-homocysteine + 2'-O-methylcytidine(56) 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-129686 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (cytidine(56)-2'-O)-methyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 201 amino acids
Theoretical weight: 22.86 KDa
Source organism: Pyrococcus horikoshii
Expression system: Escherichia coli
UniProt:
  • Canonical: O58214 (Residues: 1-195; Coverage: 96%)
Gene name: PH0461
Sequence domains: tRNA ribose 2'-O-methyltransferase, aTrm56
Structure domains: Alpha/beta knot

Ligands and Environments


Cofactor: Ligand SAM 1 x SAM
1 bound ligand:
Ligand MTA 1 x MTA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P32
Unit cell:
a: 56.151Å b: 56.151Å c: 121.844Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.216 0.216 0.268
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Methylated nucleosides in tRNA and tRNA methyltransferases.
Hori H. (2014)
3 more

1 mention without citation

Tied up in knots: Untangling substrate recognition by the SPOUT methyltransferases.
Strassler et al. (2022)