4AU9: Crystal Structure Of A Fungal Dyp-type Peroxidase From Auricularia Auricula-judae

Citation:
Abstract
Dye-decolorizing peroxidases (DyPs) belong to the large group of heme peroxidases. They utilize hydrogen peroxide to catalyze oxidations of various organic compounds. AauDyPI from Auricularia auricula-judae (fungi) was crystallized, and its crystal structure was determined at 2.1 A resolution. The mostly helical structure also shows a beta-sheet motif typical for DyPs and Cld (chlorite dismutase)-related structures and includes the complete polypeptide chain. At the distal side of the heme molecule, a flexible aspartate residue (Asp-168) plays a key role in catalysis. It guides incoming hydrogen peroxide toward the heme iron and mediates proton rearrangement in the process of Compound I formation. Afterward, its side chain changes its conformation, now pointing toward the protein backbone. We propose an extended functionality of Asp-168, which acts like a gatekeeper by altering the width of the heme cavity access channel. Chemical modifications of potentially redox-active amino acids show that a tyrosine is involved in substrate interaction. Using spin-trapping experiments, a transient radical on the surface-exposed Tyr-337 was identified as the oxidation site for bulky substrates. A possible long-range electron transfer pathway from the surface of the enzyme to the redox cofactor (heme) is discussed.
PDB ID: 4AU9Download
MMDB ID: 106175
PDB Deposition Date: 2012/5/14
Updated in MMDB: 2012/12
Experimental Method:
x-ray diffraction
Resolution: 2.1  Å
Source Organism:
Similar Structures:
Biological Unit for 4AU9: monomeric; determined by author and by software (PISA)
Molecular Components in 4AU9
Label Count Molecule
Protein (1 molecule)
1
Dyp-type Peroxidase I
Molecule annotation
Chemicals (9 molecules)
1
1
2
4
3
3
4
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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