› 3a26

X-ray diffraction
2.5Å resolution

Crystal structure of P. horikoshii TYW2 in complex with MeSAdo

Released:
DOI: 10.2210/pdb3a26/pdb
PDB entry 3a26 coloured by chain, front view.
PDB entry 3a26 coloured by chain, side view.
PDB entry 3a26 coloured by chain, top view.
Source organism: Pyrococcus horikoshii
Primary publication:
Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2.
Umitsu M, Nishimasu H, Noma A, Suzuki T, Ishitani R, Nureki O
Proc Natl Acad Sci U S A 106 15616-21 (2009)
PMID: 19717466

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + 4-demethylwyosine(37) in tRNA(Phe) = S-methyl-5'-thioadenosine + 7-((3S)-3-amino-3-carboxypropyl)-4-demethylwyosine(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-129735 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase Chain: A
Molecule details ›
Chain: A
Length: 301 amino acids
Theoretical weight: 34.77 KDa
Source organism: Pyrococcus horikoshii
Expression system: Escherichia coli
UniProt:
  • Canonical: O58523 (Residues: 1-278; Coverage: 100%)
Gene names: PH0793, taw2
Sequence domains: Met-10+ like-protein
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand MTA 1 x MTA
Ligand PG4 1 x PG4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: R3
Unit cell:
a: 132.571Å b: 132.571Å c: 96.669Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.215 0.213 0.247
Expression system: Escherichia coli

Quick links

Citations

16 review citations

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

3 mentions without citation

Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2.
Umitsu et al. (2009)
2 more