› 2zwa

X-ray diffraction
1.7Å resolution

Crystal structure of tRNA wybutosine synthesizing enzyme TYW4

Released:
DOI: 10.2210/pdb2zwa/pdb
PDB entry 2zwa coloured by chain, front view.
PDB entry 2zwa coloured by chain, side view.
PDB entry 2zwa coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4.
Suzuki Y, Noma A, Suzuki T, Ishitani R, Nureki O
Nucleic Acids Res 37 2910-25 (2009)
PMID: 19287006

Function and Biology Details

Reactions catalysed: 
S-adenosyl-L-methionine + 7-((3S)-3-amino-3-carboxypropyl)wyosine(37) in tRNA(Phe) = S-adenosyl-L-homocysteine + 7-((3S)-3-amino-3-(methoxycarbonyl)propyl)wyosine(37) in tRNA(Phe)
S-adenosyl-L-methionine + 7-((3S)-3-amino-3-(methoxycarbonyl)propyl)wyosine(37) in tRNA(Phe) + CO(2) = S-adenosyl-L-homocysteine + wybutosine(37) in tRNA(Phe)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170625 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA wybutosine-synthesizing protein 4 Chains: A, B
Molecule details ›
Chains: A, B
Length: 695 amino acids
Theoretical weight: 79.05 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q08282 (Residues: 1-695; Coverage: 100%)
Gene names: PPM2, TYW4, YOL141W
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand SAH 2 x SAH
2 bound ligands:
Ligand CIT 2 x CIT
Ligand EDO 6 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 76.578Å b: 89.444Å c: 236.286Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.17 0.211
Expression system: Escherichia coli

Quick links

Citations

12 review citations

tRNA biology charges to the front.
Phizicky et al. (2010)
11 more

4 mentions without citation

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