› 3vdm

X-ray diffraction
1.98Å resolution

Crystal Structure of VldE, the pseudo-glycosyltransferase which catalyzes non-glycosidic C-N coupling in Validamycin A biosynthesis

Released:
DOI: 10.2210/pdb3vdm/pdb
PDB entry 3vdm coloured by chain, front view.
PDB entry 3vdm coloured by chain, side view.
PDB entry 3vdm coloured by chain, top view.
Source organism: Streptomyces hygroscopicus subsp. limoneus
Entry authors: Cavalier MC, Yim Y-S, Asamizu S, Neau D, Mahmud T, Lee Y-H

Function and Biology Details

Reaction catalysed: 
GDP-valienol + validamine 7-phosphate = validoxylamine A 7'-phosphate + GDP
Biochemical function:
Biological process:
Cellular component:
Sequence domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-172444 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Validamine 7-phosphate valienyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 497 amino acids
Theoretical weight: 55.01 KDa
Source organism: Streptomyces hygroscopicus subsp. limoneus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15JG1 (Residues: 1-497; Coverage: 100%)
Gene names: SHL15_8006, vldE
Sequence domains: Glycosyltransferase family 20
Structure domains: Glycogen Phosphorylase B;

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P2
Unit cell:
a: 85.237Å b: 48.562Å c: 123.049Å
α: 90° β: 91.88° γ: 90°
R-values:
R R work R free
0.189 0.188 0.222
Expression system: Escherichia coli

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