› 3eph

X-ray diffraction
2.95Å resolution

Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism

Released:
DOI: 10.2210/pdb3eph/pdb
PDB entry 3eph coloured by chain, front view.
PDB entry 3eph coloured by chain, side view.
PDB entry 3eph coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism.
Zhou C, Huang RH
Proc Natl Acad Sci U S A 105 16142-7 (2008)
PMID: 18852462

Function and Biology Details

Reaction catalysed: 
Dimethylallyl diphosphate + adenine(37) in tRNA = diphosphate + N(6)-(3-methylbut-2-en-1-yl)-adenine(37) in tRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero tetramer
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139806 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
tRNA dimethylallyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 409 amino acids
Theoretical weight: 48.2 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P07884 (Residues: 13-421; Coverage: 96%)
Gene names: MOD5, YOR274W
Sequence domains: IPP transferase
Structure domains:
tRNA Chains: E, F
Molecule details ›
Chains: E, F
Length: 69 nucleotides
Theoretical weight: 22.22 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
Sequence domains: tRNA

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand MG 10 x MG
Ligand PPV 2 x PPV
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: C2221
Unit cell:
a: 162.463Å b: 211.596Å c: 125.518Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.197 0.236
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

11 review citations

Evolution of cytokinin biosynthesis and degradation.
Frébort et al. (2011)
10 more

9 mentions without citation

Engineering RNA-binding proteins for biology.
Chen et al. (2013)
8 more