› 3wku

X-ray diffraction
2.7Å resolution

Crystal structure of the anaerobic DesB-gallate complex

Released:
DOI: 10.2210/pdb3wku/pdb
PDB entry 3wku coloured by chain, front view.
PDB entry 3wku coloured by chain, side view.
PDB entry 3wku coloured by chain, top view.
Source organism: Sphingobium sp. SYK-6
Primary publication:
Molecular mechanism of strict substrate specificity of an extradiol dioxygenase, DesB, derived from Sphingobium sp. SYK-6.
Sugimoto K, Senda M, Kasai D, Fukuda M, Masai E, Senda T
OpenAccess logo PLoS One 9 e92249 (2014)
PMID: 24657997

Function and Biology Details

Reaction catalysed: 
Linoleate + O(2) = (9S,10E,12Z)-9-hydroperoxy-10,12-octadecadienoate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-124246 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Gallate dioxygenase Chains: A, B
Molecule details ›
Chains: A, B
Length: 418 amino acids
Theoretical weight: 46.95 KDa
Source organism: Sphingobium sp. SYK-6
Expression system: Escherichia coli
UniProt:
  • Canonical: G2IKE5 (Residues: 1-418; Coverage: 100%)
Gene names: SLG_03330, desB
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand FE 2 x FE
Ligand GDE 1 x GDE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P21
Unit cell:
a: 57.435Å b: 60.765Å c: 117.986Å
α: 90° β: 98.58° γ: 90°
R-values:
R R work R free
0.237 0.233 0.314
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Opportunities and challenges in biological lignin valorization.
Beckham et al. (2016)
1 more

2 mentions without citation

Molecular mechanism of strict substrate specificity of an extradiol dioxygenase, DesB, derived from Sphingobium sp. SYK-6.
Sugimoto et al. (2014)
1 more