› 2yx0

X-ray diffraction
2.21Å resolution

Crystal structure of P. horikoshii TYW1

Released:
DOI: 10.2210/pdb2yx0/pdb
PDB entry 2yx0 coloured by chain, front view.
PDB entry 2yx0 coloured by chain, side view.
PDB entry 2yx0 coloured by chain, top view.
Source organism: Pyrococcus horikoshii
Primary publication:
Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis.
Goto-Ito S, Ishii R, Ito T, Shibata R, Fusatomi E, Sekine SI, Bessho Y, Yokoyama S
Acta Crystallogr D Biol Crystallogr 63 1059-68 (2007)
PMID: 17881823

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-129857 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase Chain: A
Molecule details ›
Chain: A
Length: 342 amino acids
Theoretical weight: 39.9 KDa
Source organism: Pyrococcus horikoshii
Expression system: Escherichia coli
UniProt:
  • Canonical: O59412 (Residues: 1-342; Coverage: 100%)
Gene names: PH1705, taw1
Sequence domains:
Structure domains: Aldolase class I

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A, PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P212121
Unit cell:
a: 41.92Å b: 60.85Å c: 153.81Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.194 0.242
Expression system: Escherichia coli

Quick links

Citations

18 review citations

Transfer RNA modifications: nature's combinatorial chemistry playground.
Jackman et al. (2013)
17 more

7 mentions without citation

Radical S-adenosylmethionine enzymes.
Broderick et al. (2014)
6 more