› 6bi4

X-ray diffraction
2.91Å resolution

2.9 Angstrom Resolution Crystal Structure of dTDP-Glucose 4,6-dehydratase (rfbB) from Bacillus anthracis str. Ames in Complex with NAD.

Released:
DOI: 10.2210/pdb6bi4/pdb
PDB entry 6bi4 coloured by chain, front view.
PDB entry 6bi4 coloured by chain, side view.
PDB entry 6bi4 coloured by chain, top view.
Source organism: Bacillus anthracis str. Ames
Primary publication:
Structure of the Bacillus anthracis dTDP-l-rhamnose biosynthetic pathway enzyme: dTDP-α-d-glucose 4,6-dehydratase, RfbB.
Gokey T, Halavaty AS, Minasov G, Anderson WF, Kuhn ML
J Struct Biol 202 175-181 (2018)
PMID: 29331609

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 analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-105708 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
dTDP-glucose 4,6-dehydratase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 346 amino acids
Theoretical weight: 39.93 KDa
Source organism: Bacillus anthracis str. Ames
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A6L7HMN5 (Residues: 2-322; Coverage: 100%)
Gene names: GBAA_1230, rfbB
Sequence domains: GDP-mannose 4,6 dehydratase
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 4 x NAD
Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
2 bound ligands:
Ligand NI 2 x NI
Ligand SO4 14 x SO4
1 modified residue:
Ligand MSE 24 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: I422
Unit cell:
a: 165.557Å b: 165.557Å c: 292.121Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.169 0.167 0.204
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Nucleotide sugar dehydratases: Structure, mechanism, substrate specificity, and application potential.
Vogel et al. (2022)
5 other articles

3 mentions without citation

Structure of the Bacillus anthracis dTDP-l-rhamnose biosynthetic pathway enzyme: dTDP-α-d-glucose 4,6-dehydratase, RfbB.
Gokey et al. (2018)
2 more