› 1kew

X-ray diffraction
1.8Å resolution

The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium with thymidine diphosphate bound

Released:
DOI: 10.2210/pdb1kew/pdb
PDB entry 1kew coloured by chain, front view.
PDB entry 1kew coloured by chain, side view.
PDB entry 1kew coloured by chain, top view.
Source organism: Salmonella enterica subsp. enterica serovar Typhimurium
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-150734 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
dTDP-glucose 4,6-dehydratase Chains: A, B
Molecule details ›
Chains: A, B
Length: 361 amino acids
Theoretical weight: 40.77 KDa
Source organism: Salmonella enterica subsp. enterica serovar Typhimurium
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P26391 (Residues: 1-361; Coverage: 100%)
Gene names: STM2097, rfbB
Sequence domains: GDP-mannose 4,6 dehydratase
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 2 x NAD
2 bound ligands:
Ligand TYD 2 x TYD
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SRS BEAMLINE PX14.2
Spacegroup: P61
Unit cell:
a: 169.897Å b: 169.897Å c: 92.834Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.205 0.205 0.221
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

8 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)
7 more

1 mention 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)