Liuqing Li1,2, Tao Wang1,2, Taohua Chen1,2, Wenhan Huang1,2, Yinliang Zhang1,2, Rong Jia3,4, Chao He5,6. 1. School of Life Science, Economic and Technology Development Zone, Anhui University, 111 jiulong Road, Hefei, Anhui, PR China, 230601. 2. Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China. 3. School of Life Science, Economic and Technology Development Zone, Anhui University, 111 jiulong Road, Hefei, Anhui, PR China, 230601. ahdxjiarong@126.com. 4. Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China. ahdxjiarong@126.com. 5. School of Life Science, Economic and Technology Development Zone, Anhui University, 111 jiulong Road, Hefei, Anhui, PR China, 230601. chaohe@ahu.edu.cn. 6. Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, Anhui Province, China. chaohe@ahu.edu.cn.
Abstract
BACKGROUND: Dye-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. RESULTS: Here, 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. CONCLUSIONS: This study is important for better understanding the catalytic properties of fungal DyPs and their structure-function relationships.
BACKGROUND: Dye-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. RESULTS: Here, 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. CONCLUSIONS: This study is important for better understanding the catalytic properties of fungal DyPs and their structure-function relationships.
Authors: Amanda K Chaplin; Tadeo Moreno Chicano; Bethany V Hampshire; Michael T Wilson; Michael A Hough; Dimitri A Svistunenko; Jonathan A R Worrall Journal: Chemistry Date: 2019-04-04 Impact factor: 5.236
Authors: Rommel Santiago Granja-Travez; Gabriela Felix Persinoti; Fabio M Squina; Timothy D H Bugg Journal: Appl Microbiol Biotechnol Date: 2020-02-22 Impact factor: 4.813
Authors: Chloe Zubieta; Rosanne Joseph; S Sri Krishna; Daniel McMullan; Mili Kapoor; Herbert L Axelrod; Mitchell D Miller; Polat Abdubek; Claire Acosta; Tamara Astakhova; Dennis Carlton; Hsiu-Ju Chiu; Thomas Clayton; Marc C Deller; Lian Duan; Ylva Elias; Marc-André Elsliger; Julie Feuerhelm; Slawomir K Grzechnik; Joanna Hale; Gye Won Han; Lukasz Jaroszewski; Kevin K Jin; Heath E Klock; Mark W Knuth; Piotr Kozbial; Abhinav Kumar; David Marciano; Andrew T Morse; Kevin D Murphy; Edward Nigoghossian; Linda Okach; Silvya Oommachen; Ron Reyes; Christopher L Rife; Paul Schimmel; Christina V Trout; Henry van den Bedem; Dana Weekes; Aprilfawn White; Qingping Xu; Keith O Hodgson; John Wooley; Ashley M Deacon; Adam Godzik; Scott A Lesley; Ian A Wilson Journal: Proteins Date: 2007-11-01
Authors: Chloe Zubieta; S Sri Krishna; Mili Kapoor; Piotr Kozbial; Daniel McMullan; Herbert L Axelrod; Mitchell D Miller; Polat Abdubek; Eileen Ambing; Tamara Astakhova; Dennis Carlton; Hsiu-Ju Chiu; Thomas Clayton; Marc C Deller; Lian Duan; Marc-André Elsliger; Julie Feuerhelm; Slawomir K Grzechnik; Joanna Hale; Eric Hampton; Gye Won Han; Lukasz Jaroszewski; Kevin K Jin; Heath E Klock; Mark W Knuth; Abhinav Kumar; David Marciano; Andrew T Morse; Edward Nigoghossian; Linda Okach; Silvya Oommachen; Ron Reyes; Christopher L Rife; Paul Schimmel; Henry van den Bedem; Dana Weekes; Aprilfawn White; Qingping Xu; Keith O Hodgson; John Wooley; Ashley M Deacon; Adam Godzik; Scott A Lesley; Ian A Wilson Journal: Proteins Date: 2007-11-01