› 2d3q

X-ray diffraction
2.8Å resolution

Crystal Structure of a Decolorizing Peroxidase (DyP) That Catalyses the Biological Oxidation of Anthraquinone Derivatives

Released:
DOI: 10.2210/pdb2d3q/pdb
PDB entry 2d3q coloured by chain, front view.
PDB entry 2d3q coloured by chain, side view.
PDB entry 2d3q coloured by chain, top view.
Source organism: Bjerkandera adusta
Primary publication:
The catalytic mechanism of dye-decolorizing peroxidase DyP may require the swinging movement of an aspartic acid residue.
Yoshida T, Tsuge H, Konno H, Hisabori T, Sugano Y
FEBS J 278 2387-94 (2011)
PMID: 21569205

Function and Biology Details

Reaction catalysed: 
Reactive Blue 5 + 2 H(2)O(2) = phthalate + 2,2'-disulfonyl azobenzene + 3-((4-amino-6-chloro-1,3,5-triazin-2-yl)amino)benzenesulfonate + 2 H(2)O
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-186817 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DyP Chains: A, B
Molecule details ›
Chains: A, B
Length: 442 amino acids
Theoretical weight: 47.5 KDa
Source organism: Bjerkandera adusta
Expression system: Aspergillus oryzae
UniProt:
  • Canonical: Q8WZK8 (Residues: 57-498; Coverage: 93%)
Gene name: dyp
Sequence domains:

Ligands and Environments


Cofactor: Ligand HEM 2 x HEM
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-18B
Spacegroup: P6522
Unit cell:
a: 136.212Å b: 136.212Å c: 363.596Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.265 0.234 0.267
Expression system: Aspergillus oryzae

Quick links

Citations

5 review citations

DyP-type peroxidases: a promising and versatile class of enzymes.
Colpa et al. (2014)
4 more

13 mentions without citation

Substrate, product, and cofactor: The extraordinarily flexible relationship between the CDE superfamily and heme.
Celis et al. (2015)
12 more