› 2zzm

X-ray diffraction
2.65Å resolution

The complex structure of aTrm5 and tRNALeu

Released:
DOI: 10.2210/pdb2zzm/pdb
PDB entry 2zzm coloured by chain, front view.
PDB entry 2zzm coloured by chain, side view.
PDB entry 2zzm coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii
Primary publication:
Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation.
Goto-Ito S, Ito T, Kuratani M, Bessho Y, Yokoyama S
Nat Struct Mol Biol 16 1109-15 (2009)
PMID: 19749755

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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176596 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
tRNA (guanine(37)-N1)-methyltransferase Trm5b Chain: A
Molecule details ›
Chain: A
Length: 336 amino acids
Theoretical weight: 39.12 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:
RNA (84-MER) Chain: B
Molecule details ›
Chain: B
Length: 88 nucleotides
Theoretical weight: 28.33 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Not provided
Sequence domains: tRNA

Ligands and Environments


Cofactor: Ligand SAM 1 x SAM
1 bound ligand:
Ligand MG 5 x MG
1 modified residue:
Ligand MLZ 4 x MLZ

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21212
Unit cell:
a: 78.399Å b: 138.39Å c: 61.654Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.215 0.289
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

15 review citations

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

20 mentions without citation

Wybutosine biosynthesis: structural and mechanistic overview.
Perche-Letuvée et al. (2014)
19 more