› 5emu

X-ray diffraction
1.5Å resolution

Crystal structure of deoxyribose-phosphate aldolase from Escherichia coli (K58E-Y96W mutant) after acetaldehyde treatment and heating

Released:
DOI: 10.2210/pdb5emu/pdb
PDB entry 5emu coloured by chain, front view.
PDB entry 5emu coloured by chain, side view.
PDB entry 5emu coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Mechanism-based inhibition of an aldolase at high concentrations of its natural substrate acetaldehyde: structural insights and protective strategies.
Dick M, Hartmann R, Weiergräber OH, Bisterfeld C, Classen T, Schwarten M, Neudecker P, Willbold D, Pietruszka J
OpenAccess logo Chem Sci 7 4492-4502 (2016)
PMID: 30155096

Function and Biology Details

Reaction catalysed: 
2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141373 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxyribose-phosphate aldolase Chain: A
Molecule details ›
Chain: A
Length: 265 amino acids
Theoretical weight: 28.62 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A6L0 (Residues: 1-259; Coverage: 100%)
Gene names: JW4344, b4381, deoC, dra, thyR
Sequence domains: DeoC/LacD family aldolase
Structure domains: Aldolase class I

Ligands and Environments

2 bound ligands:
Ligand 1BO 1 x 1BO
Ligand EPE 1 x EPE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: C2
Unit cell:
a: 110.78Å b: 53.3Å c: 37.86Å
α: 90° β: 98.31° γ: 90°
R-values:
R R work R free
0.152 0.15 0.175
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

2-Deoxy-D-ribose-5-phosphate aldolase (DERA): applications and modifications.
Haridas et al. (2018)
1 more

2 mentions without citation

Mechanism-based inhibition of an aldolase at high concentrations of its natural substrate acetaldehyde: structural insights and protective strategies.
Dick et al. (2016)
1 more