› 3mm2

X-ray diffraction
1.45Å resolution

Dye-decolorizing peroxidase (DyP) in complex with cyanide

Released:
DOI: 10.2210/pdb3mm2/pdb
PDB entry 3mm2 coloured by chain, front view.
PDB entry 3mm2 coloured by chain, side view.
PDB entry 3mm2 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 analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-186817 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DyP Chain: A
Molecule details ›
Chain: A
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 1 x HEM
2 bound ligands:
Ligand NAG 1 x NAG
Ligand CYN 1 x CYN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: P21
Unit cell:
a: 46.958Å b: 95.915Å c: 50.322Å
α: 90° β: 103.8° γ: 90°
R-values:
R R work R free
0.178 0.177 0.192
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

3 mentions without citation

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