› 1r6d

X-ray diffraction
1.35Å resolution

Crystal Structure of DesIV double mutant (dTDP-glucose 4,6-dehydratase) from Streptomyces venezuelae with NAD and DAU bound

Released:
DOI: 10.2210/pdb1r6d/pdb
PDB entry 1r6d coloured by chain, front view.
PDB entry 1r6d coloured by chain, side view.
PDB entry 1r6d coloured by chain, top view.
Source organism: Streptomyces venezuelae
Primary publication:
High resolution X-ray structure of dTDP-glucose 4,6-dehydratase from Streptomyces venezuelae.
Allard ST, Cleland WW, Holden HM
J Biol Chem 279 2211-20 (2004)
PMID: 14570895

Function and Biology Details

Reaction catalysed: 
dTDP-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195642 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
dTDP-glucose 4,6-dehydratase Chain: A
Molecule details ›
Chain: A
Length: 337 amino acids
Theoretical weight: 36.5 KDa
Source organism: Streptomyces venezuelae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9ZGH3 (Residues: 1-337; Coverage: 100%)
Gene name: desIV
Sequence domains: GDP-mannose 4,6 dehydratase
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 1 x NAD
1 bound ligand:
Ligand DAU 1 x DAU
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P21212
Unit cell:
a: 71.7Å b: 99.4Å c: 42.2Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.174 0.216
Expression system: Escherichia coli

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Citations

6 review citations

Natural-product sugar biosynthesis and enzymatic glycodiversification.
Thibodeaux et al. (2008)
5 more

4 mentions without citation

Molecular modeling of the reductase domain to elucidate the reaction mechanism of reduction of peptidyl thioester into its corresponding alcohol in non-ribosomal peptide synthetases.
Manavalan et al. (2010)
3 more