Abstract
BackgroundDye-decolorizing peroxidases (DyPs) represent a novel family of heme peroxidases that use H2O2 as the final electron acceptor to catalyze the oxidation of various organic compounds. A DyP from Irpex lacteus F17 (Il-DyP4, corresponding to GenBank MG209114), obtained by heterologous expression, exhibits a high catalytic efficiency for phenolic compounds and a strong decolorizing ability toward various synthetic dyes. However, the enzyme structure and the catalytic residues involved in substrate oxidation remain poorly understood.ResultsHere, we obtained a high-resolution structure (2.0 Å, PDB: 7D8M) of Il‑DyP4 with α-helices, anti-parallel β-sheets and one ferric heme cofactor sandwiched between two domains. The crystal structure of Il‑DyP4 revealed two heme access channels leading from the enzyme molecular surface to its heme region, and also showed four conserved amino acid residues forming the pocket for the conversion of hydrogen peroxide into the water molecule. In addition, we found that Trp264 and Trp380, were two important residues with different roles in Il‑DyP4, by using site-directed mutagenesis and an electron paramagnetic resonance (EPR) study. Trp264 is a noncatalytic residue that mainly is used for maintaining the normal spatial conformation of the heme region and the high-spin state of heme Fe3+ of Il‑DyP4, while Trp380 serves as the surface-exposed radical-forming residue that is closely related to the oxidation of substrates including not only bulky dyes, but also simple phenols.ConclusionsThis study is important for better understanding the catalytic properties of fungal DyPs and their structure–function relationships.
Highlights
Dye-decolorizing peroxidases (DyPs) represent a novel family of heme peroxidases that use H 2O2 as the final electron acceptor to catalyze the oxidation of various organic compounds
Dye-decolorizing peroxidases (DyPs) comprise a new family of heme peroxidases, which are commonly present in microorganisms, including fungi, bacteria and
We found two important tryptophan residues in Il‐DyP4 with completely different functions using site-directed mutagenesis and electron paramagnetic resonance (EPR) measurements
Summary
Dye-decolorizing peroxidases (DyPs) represent a novel family of heme peroxidases that use H 2O2 as the final electron acceptor to catalyze the oxidation of various organic compounds. A DyP from Irpex lacteus F17 (IlDyP4, corresponding to GenBank MG209114), obtained by heterologous expression, exhibits a high catalytic efficiency for phenolic compounds and a strong decolorizing ability toward various synthetic dyes. Dye-decolorizing peroxidases (DyPs) comprise a new family of heme peroxidases, which are commonly present in microorganisms, including fungi, bacteria and. Based on sequence homology analyses, the DyPs family can be divided into four subfamilies (class A to D) in the peroxidase database, Peroxi-Base [10,11,12]. According to the result from the structurebased sequence alignments across subfamilies, Yoshida and Sugano proposed a new classification system for the DyPs family. DyPs were reclassified into 3 classes: class P (primitive, former class B), class I (intermediate, former class A), and class V (advanced, former classes C and D) [12]
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