› 2yvl

X-ray diffraction
2.2Å resolution

Crystal structure of tRNA (m1A58) methyltransferase TrmI from Aquifex aeolicus

Released:
DOI: 10.2210/pdb2yvl/pdb
PDB entry 2yvl coloured by chain, front view.
PDB entry 2yvl coloured by chain, side view.
PDB entry 2yvl coloured by chain, top view.
Source organism: Aquifex aeolicus VF5
Primary publication:
Crystal structure of tRNA m(1)A58 methyltransferase TrmI from Aquifex aeolicus in complex with S-adenosyl-L-methionine.
Kuratani M, Yanagisawa T, Ishii R, Matsuno M, Si SY, Katsura K, Ushikoshi-Nakayama R, Shibata R, Shirouzu M, Bessho Y, Yokoyama S
J Struct Funct Genomics 15 173-80 (2014)
PMID: 24894648

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + adenine(58) in tRNA = S-adenosyl-L-homocysteine + N(1)-methyladenine(58) in tRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-214687 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (adenine(58)-N(1))-methyltransferase TrmI Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 248 amino acids
Theoretical weight: 28.7 KDa
Source organism: Aquifex aeolicus VF5
Expression system: Escherichia coli
UniProt:
  • Canonical: O66653 (Residues: 1-248; Coverage: 100%)
Gene name: aq_311
Sequence domains: tRNA methyltransferase complex GCD14 subunit
Structure domains:

Ligands and Environments


Cofactor: Ligand SAM 4 x SAM
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 69.826Å b: 97.237Å c: 212.687Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.194 0.23
Expression system: Escherichia coli

Quick links

Citations

3 review citations

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

4 mentions without citation

Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase.
Guelorget et al. (2010)
3 more