› 1kep

X-ray diffraction
1.8Å resolution

The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-xylose bound

Released:
DOI: 10.2210/pdb1kep/pdb
PDB entry 1kep coloured by chain, front view.
PDB entry 1kep coloured by chain, side view.
PDB entry 1kep coloured by chain, top view.
Source organism: Streptococcus suis
Primary publication:
Toward a structural understanding of the dehydratase mechanism.
Allard ST, Beis K, Giraud MF, Hegeman AD, Gross JW, Wilmouth RC, Whitfield C, Graninger M, Messner P, Allen AG, Maskell DJ, Naismith JH
Structure 10 81-92 (2002)
PMID: 11796113

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 SO4 3 x SO4
Ligand TDX 2 x TDX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SRS BEAMLINE PX9.6
Spacegroup: P212121
Unit cell:
a: 62.449Å b: 97.182Å c: 185.471Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.148 0.145 0.172
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 review citations

Medium- and short-chain dehydrogenase/reductase gene and protein families : the SDR superfamily: functional and structural diversity within a family of metabolic and regulatory enzymes.
Kavanagh et al. (2008)
6 more

6 mentions without citation

Rhamnose-Containing Compounds: Biosynthesis and Applications.
Li et al. (2022)
5 more