› 6djt

X-ray diffraction
1.64Å resolution

Structure of TYW1 with a lysine-pyruvate adduct bound

Released:
DOI: 10.2210/pdb6djt/pdb
PDB entry 6djt coloured by chain, front view.
PDB entry 6djt coloured by chain, side view.
PDB entry 6djt coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii
Primary publication:
Biochemical and Structural Characterization of a Schiff Base in the Radical-Mediated Biosynthesis of 4-Demethylwyosine by TYW1.
Grell TAJ, Young AP, Drennan CL, Bandarian V
J Am Chem Soc 140 6842-6852 (2018)
PMID: 29792696

Function and Biology Details

Reaction catalysed: 
N(1)-methylguanine(37) in tRNA(Phe) + pyruvate + S-adenosyl-L-methionine = 4-demethylwyosine(37) in tRNA(Phe) + L-methionine + 5'-deoxyadenosine + CO(2) + H(2)O
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176461 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase Chain: A
Molecule details ›
Chain: A
Length: 331 amino acids
Theoretical weight: 39.01 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q57705 (Residues: 1-311; Coverage: 100%)
Gene names: MJ0257, taw1
Sequence domains:
Structure domains: Aldolase class I

Ligands and Environments

4 bound ligands:
Ligand SF4 1 x SF4
Ligand GOL 8 x GOL
Ligand PEG 2 x PEG
Ligand FS0 1 x FS0
1 modified residue:
Ligand KPI 1 x KPI

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 58.26Å b: 80.109Å c: 86.456Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.168 0.195
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Iron in Translation: From the Beginning to the End.
Romero et al. (2021)
2 more

1 mention without citation

Biochemical Pathways Leading to the Formation of Wyosine Derivatives in tRNA of Archaea.
Urbonavičius et al. (2020)