› 1oc2

X-ray diffraction
1.5Å resolution

The structure of NADH in the dTDP-D-glucose dehydratase (RmlB) enzyme

Released:
DOI: 10.2210/pdb1oc2/pdb
PDB entry 1oc2 coloured by chain, front view.
PDB entry 1oc2 coloured by chain, side view.
PDB entry 1oc2 coloured by chain, top view.
Source organism: Streptococcus suis
Primary publication:
The structure of NADH in the enzyme dTDP-d-glucose dehydratase (RmlB).
Beis K, Allard ST, Hegeman AD, Murshudov G, Philp D, Naismith JH
J Am Chem Soc 125 11872-8 (2003)
PMID: 14505409

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-184523 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
dTDP-glucose 4,6-dehydratase Chains: A, B
Molecule details ›
Chains: A, B
Length: 348 amino acids
Theoretical weight: 38.98 KDa
Source organism: Streptococcus suis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8GIP9 (Residues: 1-348; Coverage: 100%)
Gene names: CWI26_07360, EI219_02305, ERS132356_00723, ERS132370_01395, ERS132374_01253, ERS132410_01682, ERS132414_00580, ERS132421_00412, ERS132431_00441, ERS132440_01438, ERS132444_01827, ERS132457_01850, ERS132461_00211, ERS132462_01604, ERS132531_00495, ERS132536_02274, ERS156295_00908, FAJ39_02870, FH692_06610, HU146_09535, NOL11_01020, NOL13_08695, rfbB, rmlB
Sequence domains: GDP-mannose 4,6 dehydratase
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 2 x NAD
2 bound ligands:
Ligand TDX 2 x TDX
Ligand SO4 3 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P212121
Unit cell:
a: 61.41Å b: 94.829Å c: 183.543Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.173 0.17 0.2
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

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

3 mentions without citation

Transporter and Lysosomal Mediated (Multi)drug Resistance to Tyrosine Kinase Inhibitors and Potential Strategies to Overcome Resistance.
de Klerk et al. (2018)
2 more