› 3lm9

X-ray diffraction
2.45Å resolution

Crystal structure of fructokinase with ADP and Fructose bound in the active site

Released:
DOI: 10.2210/pdb3lm9/pdb
PDB entry 3lm9 coloured by chain, front view.
PDB entry 3lm9 coloured by chain, side view.
PDB entry 3lm9 coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
Structural studies of ROK fructokinase YdhR from Bacillus subtilis: insights into substrate binding and fructose specificity.
Nocek B, Stein AJ, Jedrzejczak R, Cuff ME, Li H, Volkart L, Joachimiak A
J Mol Biol 406 325-42 (2011)
PMID: 21185308

Function and Biology Details

Reaction catalysed: 
ATP + D-fructose = ADP + D-fructose 6-phosphate
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-126485 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Putative fructokinase Chain: A
Molecule details ›
Chain: A
Length: 302 amino acids
Theoretical weight: 33.08 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O05510 (Residues: 1-299; Coverage: 100%)
Gene names: BSU05860, gmuE, ydhR
Sequence domains: ROK family
Structure domains: Nucleotidyltransferase; domain 5

Ligands and Environments

4 bound ligands:
Ligand FRU 1 x FRU
Ligand SO4 1 x SO4
Ligand ADP 1 x ADP
Ligand ZN 1 x ZN
2 modified residues:
Ligand MSE 6 x MSE
Ligand MLY 2 x MLY

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P3121
Unit cell:
a: 112.333Å b: 112.333Å c: 73.958Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.159 0.157 0.196
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation.
Bräsen et al. (2014)
1 more

3 mentions without citation

Structural studies of ROK fructokinase YdhR from Bacillus subtilis: insights into substrate binding and fructose specificity.
Nocek et al. (2011)
2 more