› 1kc3

X-ray diffraction
2.7Å resolution

Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH and dTDP-L-rhamnose

Released:
DOI: 10.2210/pdb1kc3/pdb
PDB entry 1kc3 coloured by chain, front view.
PDB entry 1kc3 coloured by chain, side view.
PDB entry 1kc3 coloured by chain, top view.
Source organism: Salmonella enterica subsp. enterica serovar Typhimurium
Primary publication:
Variation on a theme of SDR. dTDP-6-deoxy-L- lyxo-4-hexulose reductase (RmlD) shows a new Mg2+-dependent dimerization mode.
Blankenfeldt W, Kerr ID, Giraud MF, McMiken HJ, Leonard G, Whitfield C, Messner P, Graninger M, Naismith JH
Structure 10 773-86 (2002)
PMID: 12057193

Function and Biology Details

Reaction catalysed: 
dTDP-beta-L-rhamnose + NADP(+) = dTDP-4-dehydro-beta-L-rhamnose + NADPH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-150735 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
dTDP-4-dehydrorhamnose reductase Chain: A
Molecule details ›
Chain: A
Length: 299 amino acids
Theoretical weight: 32.59 KDa
Source organism: Salmonella enterica subsp. enterica serovar Typhimurium
Expression system: Escherichia coli
UniProt:
  • Canonical: P26392 (Residues: 1-299; Coverage: 100%)
Gene names: STM2096, rfbD, rmlD
Sequence domains: RmlD substrate binding domain
Structure domains:

Ligands and Environments


Cofactor: Ligand NDP 1 x NDP
2 bound ligands:
Ligand MG 1 x MG
Ligand TRH 1 x TRH
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P21212
Unit cell:
a: 47.98Å b: 72.261Å c: 82.682Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.191 0.289
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Bacterial glycobiology: rhamnose-containing cell wall polysaccharides in Gram-positive bacteria.
Mistou et al. (2016)
3 more

6 mentions without citation

The structural biology of enzymes involved in natural product glycosylation.
Singh et al. (2012)
5 more